odin-1.8.5/0000755000175000017500000000000011735135552007466 500000000000000odin-1.8.5/NEWS0000644000175000017500000000000011322062355010063 00000000000000odin-1.8.5/TODO0000644000175000017500000000061611322062355010071 00000000000000Free memory after simulating large/long sequences Single state machine for methods -> better reporting of messages Check for occurences of SeqVecIter inside loops and unroll if necessary setfreq/setneg for padded ADC on IDEA Add flow compensation to SeqGradEcho Improve homepage: highlight features of ODIN: - List publications which used ODIN Cache simulation steps (operations) for speedup odin-1.8.5/docs/0000755000175000017500000000000011735135552010416 500000000000000odin-1.8.5/docs/homepage/0000755000175000017500000000000011735135552012203 500000000000000odin-1.8.5/docs/homepage/favicon.png0000644000175000017500000000055011322062337014246 00000000000000PNG  IHDR szz/IDATXW 0 QhG\0#;vD@'!FA@$$6BAYxƙinC`b4-8G>X."jHY)N~KB/3H^ePvjϸNPa(є \Yo𸪳Yn=JRrGk3ZgkyOn5 ӛ . "C HK:X=8߈Z ;!ZyIkE\V +Z+ {t{VWsZGg+r_ ٲIENDB`odin-1.8.5/docs/homepage/documentation.wml0000644000175000017500000000076611322062337015516 00000000000000#include "head.wml"

A short tutorial which describes sequence programming with ODIN:

  • odintut.pdf

    • A publication about ODIN (Journal of Magnetic Resonance 170:67-78, 2004) is available for download as PDF:

  • odin.pdf

    • Another publication (Journal of Magnetic Resonance 180:29-38, 2006) which explains the simulation algorithm used within ODIN:

  • magsi.pdf

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    Hello World
    Welcome to the ODIN homepage! ODIN is a C++ software framework to develop and simulate magnetic resonance sequences. It is

  • State-of-the-Art: Contemporary magnetic resonance imaging techniques are available, for example sequence modules for echo-planar imaging and spiral-imaging, parallel imaging with GRAPPA reconstruction, two-dimensional pulses and field-map-based distortion corrections.

  • Easy-to-Use: All common steps, from compiling your sequence to plotting or simulating it, can be performed within a graphical user interface.

  • Hardware Independent: ODIN runs on a variety of operating systems and scanners. Once you develop a sequence, it can be executed/simulated on very different hardware, ranging from a real-time sequence controller to your personal workstation.

  • Truly Object-Oriented: Written in C++ with an object-oriented design, ODIN is very modular, flexible and requires very little code to write: The sequences that come with ODIN are easy to understand and modify.

  • Open Source: ODIN is a free software framework. It contains well-established techniques in magnetic resonance which were documented in scientific publications. It can be used and modified without restrictions.



    • Some Highlights of ODIN

  • Plotting of the sequence timecourse in a graphical user interface.

  • Simulating the spin-physics of the sequence (Bloch-Torrey equations) using a virtual phantom to generate a virtual MR signal. System imperfections (eddy currents, B1 inhomogeneity, noise) can be switched on/off at will during the simulation.

  • Visualization of the k-space trajectory, b-values, eddy currents, etc.

  • Highly-customizable, multi-threaded image reconstruction framework.




    • ODIN Components

    Odin [Screenshot] [Screenshot]
    The control center for developing, testing, visualizing and simulating NMR sequences. It is a front-end to the ODIN libraries, allowing interactive editing, recompiling and dynamic linking of sequence modules.


    Pulsar [Screenshot]
    A graphical user interface for the generation and simulation of RF pulses is provided by the Pulsar program. Parameters of the pulse can be edited interactively and the corresponding excitation profile is displayed simultaneously. A modular approach is used for maximum flexibility: The pulse shape, k-space trajectory and filter function of the pulse are generated by independent functions. They can be combined in many ways, e.g. a box-shaped pulse can be generated using any of the spiral trajectories and any of the filter functions. The functions of the pulse are implemented using a plug-in mechanism (abstract C++ base classes where the functions are implemented in the derived classes). Thus new pulse shapes, trajectories and filter functions can be added easily by defining new function classes.


    MiView [Screenshot]
    A command line driven data viewer that supports the following formats: #include "formats.wml"
    Display properties (contrast, brightness) can be adjusted. The value of regions and single points can be retrieved and scan-line profiles can be generated interactively.



    Geoedit [Screenshot]
    A lightweight geometry editor that exports the selected geometry parameters to the ODIN sequence development framework.



    Many Useful Command-Line Utilities


    The main functionality of ODIN can be found in a couple of libraries:

    tjutils
    This library contains various helper classes and functions that are not specific to MR.

    odinpara
    Library to handle MR parameters, such as system properties, scan geometry, sequence parameters. Input/output of parameters is achieved via JCAMP-DX file format.

    odinseq
    This library contains the interface for sequence programming. It also contains the hardware specific driver routines.

    odindata
    The Blitz++ library is used for handling multidimensional arrays in ODIN. In addition, many MR-specific routines (FFT, phase correction) were added and placed in this library.

    #include "tail.wml" odin-1.8.5/docs/homepage/tail.wml0000644000175000017500000000336511456021426013576 00000000000000

    Contact
    If you have any questions, bug-reports or improvements, if you need professional support with ODIN, or if you know how to make a better web page than this, please do not hesitate to contact me (Thies Jochimsen). or post your request on the mailing list.

    Licensing
    ODIN is published under the terms of the GNU General Public License.

    Disclaimer
    ODIN is a framework for research purposes only. It is not certified for clinical use. Hence, it cannot replace approved solutions from commercial manufacturers.

    Get ODIN at SourceForge.net. Fast, secure and Free Open Source software downloads

    Last update: $(DATE)

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    Supported Spectrometers / Scanners:

  • Bruker MEDSPEC with Paravision 3
  • Siemens NUMARIS4 (VA15 - VA35, VB12 - VB17)
  • GE Signa/Epic (Code Generator)

    • Drivers (plugins) for these platforms are not included in the ODIN distribution, but are available upon request to research sites.

    Tested Operating Systems / Compilers:

  • Debian GNU/Linux 3.0 - 5.0
  • Red Hat Enterprise Linux 3/4
  • Windows NT4/XP/Vista (Using MinGW)
  • MacOS X 10.4 (Tiger), 10.5 (Leopard)
  • VxWorks

    • (ODIN uses the autoconf, automake and libtool. Thus, it should compile on any recent UNIX/Linux operating system.)

    Supported Image/Data Formats: #include "formats.wml"

    #include "tail.wml" odin-1.8.5/docs/homepage/head.wml0000644000175000017500000000572611456021426013551 00000000000000 ODIN - Object Oriented Development Interface for NMR


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    Screenshots:







    More
    		odin-1.8.5/docs/homepage/download.wml0000644000175000017500000000421511455553535014461 00000000000000#include "head.wml"

    Live CD
    Try ODIN without installation! This Live CD based on Knoppix contains a recent version of ODIN. Just download the ISO image, write it to CD, and boot from it.


    Source Code
    Please take a look at the INSTALL file for instructions on how to compile ODIN for your platform.

    Latest release (ChangeLog):

  • odin-$(VERSION).tar.gz

    • Previous releases and additional stuff:

  • All files

    • Latest source code:
    Checking out the latest source code using Subversion is possible with the command 

    svn checkout https://od1n.svn.sourceforge.net/svnroot/od1n/trunk/odin
    Use the command 
    ./bootstrap
    in the checkout to generate the configure script.


    Windows Binaries
    The Windows distribution of ODIN contains everything that is necessary to compile/run sequences (3rd party libraries, MinGW compiler), just install the following package:

  • odin-$(VERSION).exe


    • Debian/Ubuntu packages
    An official debian package is available here. ODIN is part of NeuroDebian. As a nice feature, NeuroDebian provides virtual machines to run ODIN without a Debian/Ubuntu installation.


    Virtual Samples
    The archive contains more virtual samples which can be used to simulate ODIN sequences.

  • samples.tar.gz


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\usepackage{index} %\usepackage{doublespace} \usepackage{eurosym} \usepackage{xspace} \usepackage{ulem} \usepackage{moreverb} % more space on page %\addtolength{\voffset}{-1.5cm} \addtolength{\textheight}{3.0cm} \addtolength{\hoffset}{-1.0cm} \addtolength{\textwidth}{2.0cm} % More compact headings \usepackage[compact]{titlesec} % Lamport's page style: \pagestyle{fancy} \addtolength{\headwidth}{\marginparsep} \addtolength{\headwidth}{\marginparwidth} %\renewcommand{\chaptermark}[1]{\markboth{#1}{}} \renewcommand{\sectionmark}[1]{\markright{\thesection\ #1}} \fancyhf{} \fancyhead[LE,RO]{\bfseries\thepage} \fancyhead[LO]{\bfseries\rightmark} \fancyhead[RE]{\bfseries\leftmark} \fancypagestyle{plain}{ \fancyhead{} \renewcommand{\headrulewidth}{0pt} } % Arial font, either one of these lines works \renewcommand{\rmdefault}{phv}\renewcommand{\sfdefault}{phv} %\usepackage{helvet} \renewcommand{\familydefault}{\sfdefault} \newcommand{\refsec}[1]{section \ref{#1}} \newcommand{\reffig}[1]{Fig. \ref{#1}} % keywords \newcommand{\keyword}[1]{\emph{#1}\index[ind]{#1}} \newcommand{\srckeyword}[1]{\keyword{\tt#1\normalfont}} % Notations, Math symbols \newcommand{\symb}[2]{\index[not]{#1: #2}} % definitions of abbreviations \newcommand{\abbrev}[2]{#1 (#2)\symb{#2}{#1}} % definitions of abbreviations \newcommand{\keywordabbrev}[2]{\emph{#1} (#2)\index[ind]{#1}\symb{#2}{#1}} % figure and table caption \newcommand{\tjcaption}[3]{\caption[#1]{\label{#2} \small #3 \normalsize \\$\quad$\\ }} \newcommand{\TE}{T\!E} \newcommand{\TR}{T\!R} \newcommand{\kspace}{$k$-space~} \newcommand{\grad}{\ensuremath{^{\circ}}} \input{lineno} \makeindex \newindex{not}{ndx}{nnd}{List of Abbreviations} \newindex{ind}{idx}{ind}{Index} %\shortindexingon %\proofmodetrue \begin{document} \normalem %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \author{Thies H. Jochimsen} \title{Short Tutorial for ODIN, the Object-oriented Development Interface for NMR} \maketitle %\Huge %This is work in progress! %\normalsize \tableofcontents \newpage %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %\section{Using ODIN} %\subsection{Graphical User Interface} %\subsection{Command-Line Interface} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Sequence Programming} \subsection{Introduction} % In this step-by-step tutorial, we will discover how to program a \abbrev{magnetic resonance}{MR} sequence with ODIN. % As a representative example, a \abbrev{fast spin-echo}{FSE} sequence (also termed turbo spin echo or RARE sequence) will be implemented in this tutorial to introduce ODIN's sequence programming interface and to highlight the benefits of using a truly object-oriented approach for sequence development. % To fully appreciate this tutorial, you should be familiar with the concepts of \abbrev{object-oriented programming}{OOP} (data encapsulation, inheritance, polymorphism), and in particular, with OOP programming in C++. % Before going into detail, here is the full source code of the FSE sequence: \listinginput{1}{sequence_listing.cpp} %listing with line numbers from moreverb package This code can be compiled by saving it to a file with extension .cpp and open it in the ODIN user interface by File$\rightarrow$Open. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \subsection{The MR sequence is a C++ class} % Because each MR sequence is an entity with local data (sequence parameters, sequence objects) and functions to operate on this data (initialization, execution, simulation), it is obvious to bundle this structure in a C++ class. % This is exactly how sequences are implemented in ODIN: You create a class that is derived from the base class of all sequences, \srckeyword{SeqMethod}. This is done in \LINENOclass. % Please note that instead of using the term sequence, the term \keyword{method} is often used instead within ODIN to emphasize that the sequence as whole is addressed instead of single sequence objects. Three remarks: First, the \verb|#include| statement in \LINENOinclude integrates all headers necessary for sequence programming. % Second, the macro \srckeyword{METHOD\_CLASS} must be used as the class label for every sequence.\footnote{It will be replaced by a unique string each time the sequence is compiled within the ODIN user interface so that each time it is linked into the process space, a unique symbol is available.} % Third, the macro \srckeyword{ODINMETHOD\_ENTRY\_POINT} in \LINENOentrypoint expands to some extra code required by ODIN and must be at the end of each sequence file. Next, we need a public constructor that accepts a string as a single argument and passes this string to \verb|SeqMethod| as done in \LINENOconstructor. % This constructor is necessary to be able to create an instance of the class while giving it a unique label which is used throughout the ODIN framework to refer to this sequence. % The wicked \srckeyword{STD\_string} is equivalent to \verb|std::string| for internal reasons.\footnote{Some ancient systems have none or a broken C++ standard library and no namespaces. Thus, the macros starting with \tt{}STD\_\normalfont~ are used instead of \tt{}std::\normalfont~ so that ODIN can replace them by its own implementations, if necessary.} Finally, to complete our skeleton of the sequence, we must implement a bunch of virtual functions as shown in \LINENOvirtual. % The purpose of these functions is: \begin{tabular}{l l} & \\ \srckeyword{method\_pars\_init} & Initialize sequence parameters \\ \srckeyword{method\_seq\_init} & Initialize sequence objects and create sequence layout \\ \srckeyword{method\_rels} & (Re)calculate sequence timings \\ \srckeyword{method\_pars\_set} & Final preparations before executing the sequence \\ & \\ \end{tabular} \noindent The ODIN framework will call these functions during initialization/preparation of the sequence. In order to realize our custom sequence, we have to implement these functions. Hence, in the remainder of this tutorial, we will fill these functions with the appropriate code to program our FSE sequence. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \subsection{Sequence Parameters and Their Initialization} % In the following, the term \keyword{sequence parameters} refers to properties that modify the layout, and hence, the resolution, timing, etc.~of the sequence. Examples are the \abbrev{echo time}{$\TE$}, the \abbrev{repetition time}{$\TR$} and the \abbrev{field of view}{FOV}. % A number of pre-defined sequence parameters are available within the sequence class. They can be accessed via the following pointers and contain the specified class of parameters: \begin{tabular}{l l l} & & \\ Pointer label: & Pointing to type: & Description: \\ \srckeyword{commonPars} & \srckeyword{SeqPars} & Common MR parameters (e.g. $\TE$, $\TR$) \\ \srckeyword{geometryInfo} & \srckeyword{Geometry} & Geometry parameters (e.g. FOV) \\ \srckeyword{systemInfo} & \srckeyword{System} & System settings (e.g. field strength) \\ & & \\ \end{tabular} \noindent Single parameters of these \keyword{parameter blocks} can be retrieved and modified with appropriate \verb|get_| and \verb|set_| methods, as we will see later. % We will also refer to these global objects as \keyword{proxies} because the hide platform specific stuff behind a common interface. % Please refer to the online manual for a list of available member functions. If you write a custom sequence, you probably want to be able to define and use an extra set of parameters. % As it turns out, this is pretty easy in ODIN, all you have to do is to declare the parameter as a (private) member of your method class and tell ODIN that this is a new sequence parameter. % For example, we will need an extra parameter, \verb|Shots|, in our FSE sequence for the number of excitations for each image. % Thus, we first add the parameter as a member to our class (\LINENOshotsdecl). % \srckeyword{JDXint} is the type of our new parameter and makes \verb|Shots| behave exactly like a built-in \verb|int|.\footnote{There are many other types emulating built-in types, such as \tt{}JDXfloat\normalfont~ and \tt{}JDXdouble\normalfont. Composite types are also available, such as \tt{}JDXstring\normalfont, \tt{}JDXcomplex\normalfont~ and arrays. Please refer to the online manual for a complete list.} % Next, we can assign a default value to the parameter in \verb|method_pars_init| (\LINENOshotsdefault). % To register the parameter so that it is recognized by ODIN, for example to display it in the \abbrev{graphical user interface}{GUI}, we must call the function \srckeyword{append\_parameter} in \verb|method_pars_init| of our sequence (\LINENOshotsappend). % After compiling the method, you will see a field with the new parameter on the right-hand side of the ODIN GUI. % As we will see later, the parameter can be used exactly like a regular \verb|int| in our method code. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \subsection{Designing the Sequence} % In this section, we will create all the sequence objects required for our FSE sequence. The term \keyword{sequence objects} refers to all basic elements of an MR sequence, such as RF pulses, gradient pulses and periods of data acquisitions. % In ODIN, these sequence objects are data members of the sequence class. % In addition, we will see how these sequence objects are combined into sequence containers and used together with sequence loops to form the whole sequence. \subsubsection{RF Pulses} % As the FSE sequence is basically a \abbrev{Carr-Purcell-Meiboom-Gill}{CPMG} sequence, we will need an excitation pulse and a refocusing pulse. % The excitation pulse \verb|exc| is declared in \LINENOexcdecl. It is of type \srckeyword{SeqPulsar} because it uses the same functions as the Pulsar program to calculate pulses. % The pulse is initialized in \LINENOexcinit by using the constructor of the specialized pulse class \srckeyword{SeqPulsarSinc}\footnote{ The following goes on behind the scenes: First, a temporary (unnamed) object of type \tt{}SeqPulsarSinc\normalfont~ is created with the given parameters. Next, the assignment operator of \tt{}SeqPulsar\normalfont~ is called. Because \tt{}SeqPulsarSinc\normalfont~ is derived from \tt{}SeqPulsar\normalfont, all data members of \tt{}SeqPulsar\normalfont~ of the temporary object are copied over to \tt{}exc\normalfont, thereby initializing \tt{}exc\normalfont.}. Several parameters are passed to the constructor: The first assigns a label to the object created. It is convenient to use the same label as that used in source code. The label will be used to refer to the sequence object, for example when plotting the sequence. Next, the constructor expects the slice thickness which is simply taken from the global geometry proxy pointed to by \verb|geometryInfo|. The third parameter is set to \verb|true|, to automatically add a rephasing gradient to the excitation pulse. Finally, we specify the pulse duration (4th parameter) and the flip angle (5th parameter). In an FSE sequence, it is usually a good idea to use the same pulse shape for excitation and refocusing, except for the flip angle. % Thus, for the refocusing pulse \verb|refoc| (declared in \LINENOrefocdecl) we make use of the assignment operator of \verb|SeqPulsar| to create a copy of \verb|exc| and change only those properties which differ (\LINENOrefocinit): % First, the label is changed to \verb|refoc|. Then, the rephasing gradient pulse is removed because it is not necessary for a refocusing pulse. Next, the phase is set to 90\grad (CPMG condition) and the flip angle is changed. Finally, the pulse type is set to \srckeyword{refocusing}\footnote{ This has no direct effect on the sequence time course, but makes calculation gradient moments (e.g. \kspace analysis) possible in the plotting GUI.}. \subsubsection{Gradient Pulses} % For phase encoding, i.e scanning of lines in \kspace, two gradient pulses with variable strength are required to create a linear phase prior to data acquisition and to rewind this phase after acquisition. % We could use the class \srckeyword{SeqGradVector} to achieve this, but then we would have to calculate the gradient strengths ourselves to cover a certain FOV for a certain resolution. Since we are lazy, and ODIN provides a convenient class \srckeyword{SeqGradPhaseEnc} to achieve just that, we will use it to declare both objects (\LINENOpedecl). % The initialization of the first phase encoding gradient \verb|pe1| in \LINENOpeinit requires some explanation: % After specifying the label, resolution (matrix size) and FOV, the channel of the gradient pulse is set to \verb|phaseDirection|\footnote{ This is one of the three possible channels \srckeyword{readDirection}, \srckeyword{phaseDirection} and \srckeyword{sliceDirection} which correspond to the three orthogonal directions in the logical patient coordinate system, which usually differs from the coordinate system spanned by the three gradient coils if the imaging plane is tilted. }. % Next, the maximum gradient strength is set to 1/4 of that possible with the available gradient hardware. The duration of the gradient pulse will then be calculated to achieve the desired phase encoding. % The argument \srckeyword{centerOutEncoding} specifies that instead of linear encoding (scanning \kspace from one edge to the other in sequential order), the central lines are acquired first and then moving outwards from the center. % Finally, the last two arguments are used to separate the phase encoding lines into \verb|Shots| interleaves by using \srckeyword{interleavedSegmented} as the \keyword{reordering scheme}. We will see later how iterate through the phase encoding interleaves and shots by sequence loops. % In \LINENOpecopy, the phase rewinder \verb|pe2| is initialized by making it a copy of \verb|pe1| and inverting its polarity. To suppress free-induction signal of the refocusing pulses, a pair of spoiler gradients is required around each refocusing pulse. % This fairly simple constant gradient pulse of type \srckeyword{SeqGradConstPulse} is declared in \LINENOspoilerdecl and initialized in \LINENOspoilerinit with 1/2 of the maximum gradient strength and 1 ms duration. \subsubsection{Data Acquisition} To sample one line in \kspace between two refocusing pulses in our FSE sequence, an acquisition period has to be created together with a simultaneous read gradient. % We could create this composite object ourselves by using a simple acquisition of type \srckeyword{SeqAcq} and a trapezoidal gradient \srckeyword{SeqGradTrapez}, but again, ODIN provides a convenient composite class to achieve this, namely \srckeyword{SeqAcqRead} which is an acquisition together with a gradient pulse of the same duration. % The object \verb|read| of this type is declared in \LINENOreaddecl and initialized in \LINENOreadinit. % As usual, the first argument to the constructor of \verb|SeqAcqRead| is the object's label. Then, the sweep width (sampling frequency) is specified together with the matrix size in read direction (number of sampling points) and the desired FOV. The desired gradient channel for the gradient is the \verb|readDirection|. This is a good place to explain the concept of \keyword{Interface base classes}, sometimes called \keyword{interface classes}: % An Interface base class is a class which provides a set of (mostly virtual) member function. This class cannot be instantiated, i.e. no object of this class can be created, but it serves as a base class to concrete implementations of this set of member functions (the interface). % For example the class \verb|SeqAcqRead| implements two interfaces, namely \srckeyword{SeqAcqInterface}, which is the base class for all acquisition classes, and \srckeyword{SeqGradInterface}, which is the base class for all classes with one or more gradient pulses. % In this way, all acquisition (or gradient) objects share a common interface. For instance, the member function \srckeyword{get\_acquisition\_start} is reimplemented in each acquisition class to return the duration from the start of the sequence object to the beginning of the actual acquisition (this is necessary for proper timing calculations, see below). % The implementation of this function can be very different, depending on the concrete acquisition class used: % \verb|SeqAcq| will return the duration to trigger the digitizer, and \verb|SeqAcqRead| will also consider the duration of the gradient ramp of the read gradient. % However, the programming interface is the same in both cases which makes it easy to remember the member functions and, more importantly, allows \keyword{polymorphism}: If different acquisition types should be supported within one sequence, member functions can be called via a pointer (or reference) to type \verb|SeqAcqInterface| instead of several \verb|if|-statements. In order to start sampling at one edge of \kspace in read direction, we also need a pre-dephasing gradient pulse. % Again, we could create this ourselves using a \verb|SeqGradConstPulse| object, but there is a more convenient class \srckeyword{SeqAcqDeph} which can be employed. It is declared in \LINENOdephdecl. After the obligatory label as the first argument to the constructor (\LINENOdephinit), a reference to an object derived from \verb|SeqAcqInterface| is expected for which the dephaser will be created. % As we have seen above, the object \verb|read| is derived from \verb|SeqAcqInterface| and can therefore be used as the second argument so that a suitable pre-dephaser will be created. % The last argument \verb|spinEcho| specifies that the pre-dephaser will have the same polarity as the read gradient which is suitable for spin-echo (and, therefore, CPMG) acquisition. \subsubsection{Sequence Containers and Delays} % Having initialized all our basic sequence elements, we now start to group them together to build the whole MR sequence. % For this purpose, \keyword{sequence containers} of type \srckeyword{SeqObjList} are used: For example, we will group the objects within one refocusing interval together in \LINENOechopartinit and assign this composite object to \verb|echopart| (declared in \LINENOechopartdecl) so that we can loop over this part of the sequence later. % As you can see, sequence objects are concatenated by using the + operator. However, just concatenating objects is not enough for our FSE sequence, we must also fulfill CPMG timing constraints. % Therefore, the \keyword{sequence delay} \verb|echodelay| of type \srckeyword{SeqDelay} (declared in \LINENOechodelaydecl and initialized in \LINENOechodelayinit\footnote{Although setting the label is not crucial, it helps debugging as this label shows up in all visualizations of the sequence.}) is used to insert certain waiting periods into the sequence. % We will calculate the duration of this delay later together with the duration of other delay objects. % For now, we just create the basic layout of the sequence. It is also convenient to group the preparation phase into the object \verb|prep| (\LINENOprepdecl) as shown in \LINENOprepinit. % Here, the delay \verb|prepdelay| (\LINENOprepdelaydecl, \LINENOprepdelayinit) will be used to achieve CPMG timing. % Again, we use the + operator to concatenate sequence objects. But since \verb|spoiler| and \verb|deph| are on different gradient channels, they can be played out simultaneously. This is exactly what the / operator does: It makes sequence objects simultaneous, if possible. Otherwise, it will generate an error message. \subsubsection{Sequence Loops} % Next, we will build the sequence part of one shot, that is, the preparation part \verb|prep| followed by a loop over \verb|echopart| (the sequence part of one echo). % In ODIN, loops are possible with the class \srckeyword{SeqObjLoop}, which is, like \verb|SeqObjList|, a container to hold other sequence objects in sequential order. In the following, this contents will be called the \keyword{kernel} of the loop. % In addition, \verb|SeqObjLoop| allows looping over the kernel to repeat its execution. % At each iteration, properties of so-called \keyword{sequence vectors} can be changed. These sequence vectors are all classes derived from \srckeyword{SeqVector}. % Thereby, a loop can be employed as follows: % First, a loop object is declared in \LINENOecholoopdecl. Then, to iterate over a kernel \verb|kern| while iterating properties of \verb|vec1|, \verb|vec2|, ..., the basic syntax is\footnote{This syntax becomes possible by overloading the ( ) and [ ] operator of \tt{}SeqObjLoop\normalfont.} \begin{verbatim} echoloop ( kern ) [vec1][vec2]... \end{verbatim} % In our sequence, this syntax is used in \LINENOoneshotinit to iterate over \verb|echopart| while iterating the values of \verb|pe1| and \verb|pe2|. Here iterating simply means to change the strength of the phase encoding gradient so that different lines in \kspace are scanned at each echo, according to the encoding and reordering scheme specified above. But we are not done yet because we have only build the sequence for one shot. % Thus, we need another loop \verb|shotloop| (\LINENOshotloopdecl) to iterate over the different shots. % At each of these iterations, \verb|pe1| and \verb|pe2| have to be aware that the next interleave of phase encoding steps has to be used. % For this purpose, each sequence vector has a \keyword{reordering vector}. Whenever a certain reordering scheme is used (as done above by the constructor of \verb|SeqGradPhaseEnc| or by the function \srckeyword{set\_reorder\_scheme}), the reordering vector is used to iterate over the set of modified arrangements of the values of the vector, for example over the interleaves, if \verb|interleavedSegmented| is used as the reordering scheme. % The reordering vector, just like every other vector, can be attached to a loop to iterate over it. % It can be retrieved from its parent vector by the function \srckeyword{get\_reorder\_vector}. % This is done in \LINENOsetsequence: The reordering vectors of \verb|pe1| and \verb|pe2| are attached to the loop \verb|shotloop| while repeating \verb|oneshot|. % A padding delay \verb|relaxdelay| (\LINENOrelaxdelaydecl, \LINENOrelaxdelayinit) is also added which we use later to adjust the correct $\TR$. Within the same line, the function \srckeyword{set\_sequence} of the base class \verb|SeqMethod| is used to specify the whole sequence, i.e. to tell the ODIN framework what to use when plotting/executing/simulating our sequence. % Using this function is usually the last step in \verb|method_seq_init|. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \subsection{(Re)Calculating Sequence Timings} In the previous section, we have created the basic layout of the sequence, but ignored the timing constraints of our FSE sequence. % This will be done now, namely in the member function \verb|method_rels| of our method class\footnote{Using a separate member function for timing calculations, which are usually fast compared to all the initialization stuff in \tt{}method\_seq\_init\normalfont, has the advantage that, if only timing settings of the sequence change, \tt{}method\_rels\normalfont~ is the only function to be called. }. % First, we will calculate the minimum $\TE$ possible which is equivalent to the CPMG refocusing interval. % This either limited by the minimum duration possible with our preparation (\LINENOminTEprep), or by the refocusing interval (\LINENOminTEecho). % Here, the functions \srckeyword{get\_duration} and \srckeyword{get\_magnetic\_center} return the duration of the corresponding sequence object\footnote{ The container \tt{}echopart\normalfont~ is a sequence object itself whereby \tt{}get\_duration\normalfont~ returns the total duration of the concattenated objects it contains.} and the time point of the center of the pulse relative to its beginning, respectively. % Next, we calculate the maximum of both in \LINENOminTE and set the global $\TE$ (in \verb|commonars|) to this value (\LINENOsetTE). Here, the second argument \srckeyword{noedit} indicates that the parameter cannot be edited by the user, it will be indicated as such in the GUI. % Finally, we adjust the duration of the padding delays to match the calculated $\TE$ in \LINENOprepdelayset and \LINENOechodelayset using the \srckeyword{set\_duration} function. A similar technique is used to set the minimum $\TR$ possible and adjust the corresponding padding delay (\LINENOsetTR). %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \subsection{Image Reconstruction} The sequence is now complete and could be executed on the scanner, but image reconstruction would fail because ODIN does not know where to put each line, which was acquired with the \verb|read| object, in \kspace. We have to inform ODIN explicitely that the vector object \verb|pe1| was responsible for phase encoding. This is done in \LINENOrecoline. The first argument of \srckeyword{set\_reco\_vector} is of type \srckeyword{recoDim} which is an enum used to specify so-called \keyword{reconstruction dimensions}. These can be, for instance: % \begin{itemize} \item Phase encoding step (\srckeyword{line}) \item Slice index (\srckeyword{slice}) \item Echo number (\srckeyword{echo}) \item User-defined index (\srckeyword{userdef}) \end{itemize} % The second argument is a vector object which was responsible to iterate through this dimension. % For example, if we would add multi-slice excitation, we would add a frequency list to \verb|exc| (using \srckeyword{set\_freqlist}) and then use \verb|exc| as the slice vector. After execution of the sequence, the complex data of the acquired NMR signal is stored on disk in the so-called \abbrev{scan directory}{scandir} in the order it was acquired. This is achieved by using the native mechanisms (e.g. on Bruker and GE) or by a custom reconstruction routine which does nothing but dumping the raw data to the hard drive (e.g. on Siemens). % However, just storing the raw data would not be enough to reconstruct an image. Extra information like the one above (location of each acquisition in \kspace) is required. Therefore, an extra file \srckeyword{recoInfo}, which contains this information in human-readable ASCII format, is stored together with the raw data in the scandir. % The file is a serialized version of the class \srckeyword{RecoPars}, which means that on object of this type can read/write the file and queried subsequently for its values. Finally, the program \srckeyword{odinreco}, which is part of ODIN will retrieve all information from \verb|recoInfo| and generate image data. It is executed in the scandir on the command line with \begin{verbatim} odinreco \end{verbatim} to create the reconstructed image data. Please refer to the online manual for further documentation how to fine tune the reconstruction. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %\subsection{Sequence Internals} %In this section, the internal layout of the example sequence will be described, %i.e. how the sequence objects used are composed of other more basic sequence objects. %\subsubsection{Excitation pulse} % %We will start with the excitation pulse \verb|exc|: It is of type \srckeyword{SeqPulsarSinc} %which is derived from \srckeyword{SeqPulsar} (class for representing arbitrary RF pulses). %In the constructor of \srckeyword{SeqPulsarSinc}, various pulse parameters (shape, filter, ...) %of \srckeyword{SeqPulsar} are set so that a sinc-shaped pulse is generated. %The class \srckeyword{SeqPulsar} has two base classes: \srckeyword{SeqPulsNdim} %and \srckeyword{OdinPulse}. The latter contains the logic to calculate %RF and gradient waveforms for frequency and/or spatially selective pulses. %It has a number of \verb|set|/\verb|get| functions to set pulse specific %parameters. % %Since \srckeyword{OdinPulse} is a bass class of \srckeyword{SeqPulsar}, these %\verb|set|/\verb|get| functions are all available in \srckeyword{SeqPulsar} %to specify all details of a pulse in the method. % %However, \srckeyword{OdinPulse} does not know how to insert itself into the sequence. %Therefore, the second base class \srckeyword{SeqPulsNdim} contains sub-objects %to play out the calculated RF and gradient shapes in the sequence: % %In essence, it contains an atomic RF object \srckeyword{SeqPuls} and three %atomic \srckeyword{SeqGradWave} to play out the gradient waveform(s). %The class \srckeyword{SeqPuls} will talk to the actual scanner hardware via %the driver plugin for RF (the member \verb|pulsdriver|). % %This member is a wrapper which has a pointer-like syntax. %With this 'pointer', a driver interface \srckeyword{SeqPulsDriver} is accessible. %The actual object behind this interface is the an implementation of \srckeyword{SeqPulsDriver} %of the current platform. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \newpage \addcontentsline{toc}{section}{\numberline{}Index} \printindex[ind] \newpage \addcontentsline{toc}{section}{\numberline{}List of Abbreviations} \printindex[not] \end{document} odin-1.8.5/docs/tutorials/Makefile.am0000644000175000017500000000217611322062337014416 00000000000000EXTRA_DIST = main.tex if ONLY_LIBS else sequence_listing.cpp: sequence.cpp cat sequence.cpp | sed s/\\/\\/.*// > sequence_listing.cpp lineno.tex: main.tex lineno.awk sequence_listing.cpp cat sequence.cpp | awk -f ./lineno.awk > lineno.tex main.ndx: main.tex lineno.tex sequence_listing.cpp latex main.tex && latex main.tex && latex main.tex main.ind: main.idx makeindex main.idx main.nnd: main.ndx makeindex main.ndx mv main.ilg 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"odindialog_tree.h" #include "odincomp.h" TreeDialog::TreeDialog(QWidget *parent, const char* caption, const svector& column_labels) : GuiDialog(parent,caption,false) { grid=new GuiGridLayout(GuiDialog::get_widget(), 1, 1); root=new GuiListView(GuiDialog::get_widget(), column_labels, 400, 400, 0, true); grid->add_widget( root->get_widget(), 0, 0 ); } TreeDialog::~TreeDialog() { delete root; delete grid; } void TreeDialog::display_node(const SeqClass* thisnode, const SeqClass* parentnode, int treelevel, const svector& columntext) { Log odinlog("TreeDialog","display_node"); GuiListItem* item=0; if(lastitemmap.size()) { // sub-node GuiListItem* parentitem=nodemap[parentnode]; GuiListItem* lastitem=lastitemmap[parentitem]; ODINLOG(odinlog,normalDebug) << "columntext=" << columntext.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "parentnode/parentitem/lastitem=" << (void*)parentnode << "/" << parentitem << "/" << lastitem << STD_endl; item=new GuiListItem(parentitem, lastitem, columntext); ODINLOG(odinlog,normalDebug) << "item=" << item << STD_endl; lastitemmap[parentitem]=item; } else { // top-level node item=new GuiListItem(root,columntext); ODINLOG(odinlog,normalDebug) << "(root)item=" << item << STD_endl; } lastitemmap[item]=0; // insert dummy element at beginning nodemap[thisnode]=item; } odin-1.8.5/odin/odindialog_pulsar.cpp0000644000175000017500000000421211322062346014531 00000000000000#include "odindialog_pulsar.h" #include "odincomp.h" #include PulsarDialog::PulsarDialog(const STD_list& pulses, const STD_string& pulsarcmd, STD_list& subprocs, const STD_string& tmpdir, const STD_string& systemInfoFile, QWidget *parent) : GuiDialog(parent,"Pulsar Pulses",false), pulsar_cmd(pulsarcmd), procs(subprocs), tmp_dir(tmpdir), systemInfo_file(systemInfoFile) { grid=new GuiGridLayout(GuiDialog::get_widget(), 2, 1); svector collabel; collabel.resize(3); collabel[0]="Pulse (Click to view in Pulsar)"; collabel[1]="Duration["+STD_string(ODIN_TIME_UNIT)+"]"; collabel[2]="Properties"; pulsar_list=new GuiListView (GuiDialog::get_widget(), collabel, 200, 300, this); grid->add_widget( pulsar_list->get_widget(), 0, 0 ); for(STD_list::const_iterator it=pulses.begin(); it!=pulses.end(); ++it) { collabel[0]=(*it)->get_label(); collabel[1]=ftos((*it)->get_Tp()); collabel[2]=(*it)->get_properties(); GuiListItem* pulse_item=new GuiListItem(pulsar_list, collabel); pulse_map[pulse_item]=(*it); } pb_done = new GuiButton( GuiDialog::get_widget(), this, SLOT(emitDone()), "Done" ); grid->add_widget( pb_done->get_widget(), 1, 0, GuiGridLayout::Center ); // connect( pb_done->get_widget(), SIGNAL(clicked()), this,SLOT(emitDone()) ); GuiDialog::show(); } void PulsarDialog::clicked(GuiListItem* item) { Log odinlog("PulsarDialog","clicked"); ODINLOG(odinlog,normalDebug) << "item=" << item << STD_endl; if(item) { STD_string plsfile(tmp_dir+"pulsar.pls"); pulse_map[item]->write(plsfile); STD_string cmdstring("\""+pulsar_cmd+"\" -noedit -s \""+systemInfo_file+"\" \""+plsfile+"\""); ODINLOG(odinlog,normalDebug) << "cmdstring=" << cmdstring << STD_endl; Process proc; proc.start(cmdstring); procs.push_back(proc); } } void PulsarDialog::emitDone() { GuiDialog::done(); } PulsarDialog::~PulsarDialog() { for(STD_map::const_iterator it=pulse_map.begin(); it!=pulse_map.end(); ++it) { delete it->first; } delete pulsar_list; delete pb_done; delete grid; } odin-1.8.5/odin/odindialog_debug.cpp0000644000175000017500000000413411322062346014314 00000000000000#include #include // for connecting signals #include "odindialog_debug.h" DebugDialog::DebugDialog(QWidget *parent) : GuiDialog(parent, "Debugging/Tracing Options",false) { #ifdef ODIN_DEBUG int mapsize=LogBase::global->components.size(); grid = new GuiGridLayout( GuiDialog::get_widget(), mapsize+1, 2 ); STD_map::const_iterator it; svector debuglevels; debuglevels.resize(numof_log_priorities); for(int i=0; icomponents.begin();it!=LogBase::global->components.end();++it) { QLabel* ql=new QLabel(GuiDialog::get_widget()); ql->setText(it->first.c_str()); grid->add_widget( ql, row, 0, GuiGridLayout::Center ); GuiComboBox* cb = new GuiComboBox( GuiDialog::get_widget(), debuglevels ); log_component_fptr fp=it->second; cb->set_current_item(fp(ignoreArgument)); grid->add_widget( cb->get_widget(), row, 1, GuiGridLayout::Center ); connect( cb->get_widget(), SIGNAL(activated(int)),this, SLOT(levelChanged(int)) ); debugenums.push_back(cb); row++; } pb_done = new GuiButton( GuiDialog::get_widget(), this, SLOT(emitDone()), "Done" ); grid->add_widget( pb_done->get_widget(), mapsize, 1, GuiGridLayout::Center ); // connect( pb_done->get_widget(), SIGNAL(clicked()), this,SLOT(emitDone()) ); GuiDialog::show(); #endif } DebugDialog::~DebugDialog() { #ifdef ODIN_DEBUG for(STD_list::const_iterator dbgit=debugenums.begin();dbgit!=debugenums.end();++dbgit) delete (*dbgit); delete pb_done; delete grid; #endif } void DebugDialog::levelChanged(int) { #ifdef ODIN_DEBUG STD_map::const_iterator it=LogBase::global->components.begin(); for(STD_list::const_iterator dbgit=debugenums.begin();dbgit!=debugenums.end();++dbgit) { LogBase::set_log_level(it->first.c_str(),logPriority((*dbgit)->get_current_item())); ++it; } #endif } void DebugDialog::emitDone() { #ifdef ODIN_DEBUG GuiDialog::done(); emit finished(); #endif } odin-1.8.5/odin/odindialog_pulsar.h0000644000175000017500000000361111322062346014200 00000000000000/*************************************************************************** odindialog_pulsar.h - description ------------------- begin : Mon Oct 10 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_PULSAR_H #define ODINDIALOG_PULSAR_H #include #include #include class SeqPulsar; // forward declaration class PulsarDialog : public QObject, public GuiDialog, public GuiListViewCallback { Q_OBJECT public: PulsarDialog(const STD_list& pulses, const STD_string& pulsarcmd, STD_list& subprocs, const STD_string& tmpdir, const STD_string& systemInfoFile, QWidget *parent); ~PulsarDialog(); private slots: void emitDone(); private: // overloading virtual function of GuiListViewCallback void clicked(GuiListItem* item); GuiGridLayout* grid; GuiListView* pulsar_list; GuiButton* pb_done; STD_map pulse_map; STD_string pulsar_cmd; STD_list& procs; STD_string tmp_dir; STD_string systemInfo_file; }; #endif odin-1.8.5/odin/odindebugger.cpp0000644000175000017500000000164311322062346013475 00000000000000#include "odindebugger.h" #include "odincomp.h" #include "odinconf.h" #ifdef HAVE_UNISTD_H #include #endif /////////////////////////////////////////////////////////////////////////////// bool OdinDebugger::attach() { Log odinlog("OdinDebugger","attach"); int mypid=-1; #ifdef HAVE_UNISTD_H mypid=getpid(); #endif if(mypid<=0) return false; #ifdef HAVE_GDB_XTERM STD_string batfile("c"); // continue cmd for gdb STD_string batfname(OdinConf::get_tmpdir()+SEPARATOR_STR+"gdb.bat."+itos(mypid)); ::write(batfile,batfname); STD_string cmd("xterm -geometry 80x10+0+0 -e 'gdb -x "+batfname+" odin "+itos(mypid)+"'"); ODINLOG(odinlog,normalDebug) << "Running command " << cmd << STD_endl; return debugger_proc.start(cmd); #else ODINLOG(odinlog,errorLog) << "gdb or xterm is missing" << STD_endl; return false; #endif } bool OdinDebugger::detach(){ return debugger_proc.kill(); } odin-1.8.5/odin/odindebugger.h0000644000175000017500000000242111322062346013135 00000000000000/*************************************************************************** logger.h - description ------------------- begin : Fri Nov 11 21:30:11 CEST 2003 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef OdinDebugger_H #define OdinDebugger_H #include ///////////////////////////////////////////// class OdinDebugger { public: OdinDebugger() {} bool attach(); bool detach(); private: Process debugger_proc; }; #endif odin-1.8.5/odin/odincomp.h0000644000175000017500000000223611322062346012313 00000000000000/*************************************************************************** odincomp.h - description ------------------- begin : Sun Oct 3 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINCOMP_H #define ODINCOMP_H // for debugging ODIN component class OdinComp { public: static const char* get_compName(); }; #endif odin-1.8.5/odin/odinconf.h0000644000175000017500000000570011455553540012311 00000000000000/*************************************************************************** odinconf.h - description ------------------- begin : Fri Nov 11 21:30:11 CEST 2003 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef OdinConf_H #define OdinConf_H #include #include #include #include /////////////////////////////////////////////////////////////////// #define DEFAULT_METH_ROOT "odin-methods" /////////////////////////////////////////////////////////////////// class QWidget; // forward declaration /////////////////////////////////////////////////////////////////// struct OdinConf : public JcampDxBlock { OdinConf(const STD_string& label="unnamedOdinConf", bool ignore_environment = false); JDXfileName sourcecode; JDXfileName editor; JDXfileName browser; JDXfileName methroot; JDXfileName smpfile; JDXfileName protfile; JDXfileName compiler; // Set once on startup, do not include in file JDXfileName linker; // Set once on startup, do not include in file JDXstring compiler_flags; JDXstring extra_includes; JDXstring extra_libs; JDXstringArr selectedMethods; JDXbool attachDebugger; bool init(QWidget* parent); svector get_method_compile_chain() const; // helper functions static STD_string get_binprefix(); static STD_string get_homedir(); static STD_string get_seqexamplesdir(); static STD_string get_samplesdir(); static STD_string get_coilsdir(); static STD_string get_confdir(); static STD_string get_tmpdir(); static STD_string get_manual_location(); bool display_html(const STD_string& location, STD_list& subprocs); bool open_ascfile(const STD_string& filename, STD_list& subprocs); static STD_string get_installdir(); #ifndef USING_WIN32 static bool start_proc(const STD_string& program, const STD_string& filename, STD_list& subprocs); #endif private: static STD_string get_registryvalue(const STD_string& keyname, const STD_string& valuename); static STD_string get_datadir(); static bool ignore_env; // for clean start in IDEA }; #endif odin-1.8.5/odin/odindialog_idea.cpp0000644000175000017500000012276211322062346014140 00000000000000#include "odindialog_idea.h" #include "odincomp.h" #include "odindialog_process.h" #include #include //////////////////////////////////////////////////////////////////////////////////////// // Helper functions bool select_alternative(JDXfileName& result, const STD_list& alternatives, QWidget *parent=0) { Log odinlog("","select_alternative"); if(parent && alternatives.size()>1) { // Ask with dialog if parent is provided JDXenum alts; alts.set_label("Alternatives"); for(STD_list::const_iterator it=alternatives.begin(); it!=alternatives.end(); ++it) alts.add_item(*it); JcampDxBlock block("Select Alternative"); block.append(alts); new JDXwidgetDialog(block,1,parent,true); result=alts.operator STD_string(); } else { for(STD_list::const_iterator it=alternatives.begin(); it!=alternatives.end(); ++it) { result=*it; bool exists=result.exists(); ODINLOG(odinlog,normalDebug) << "exists(" << result << ")=" << exists << STD_endl; if(exists) return true; result=""; } } return false; } void select_idea_include_dirs(STD_string& result, const STD_list& possible_dirs, const IdeaOpts& opts) { JDXfileName testdir; testdir.set_dir(true); STD_string ideadir_slash=opts.get_ideadir_slash(); for(STD_list::const_iterator it=possible_dirs.begin(); it!=possible_dirs.end(); ++it) { testdir=ideadir_slash+SEPARATOR_STR+(*it); if(testdir.exists()) { result+=" -I"+ideadir_slash+"/"+(*it); // use forward slashes for includes } } } svector match_in_dir(const STD_string& dir, const STD_string& match) { svector result; svector dirs=browse_dir(dir, true,true); for(unsigned int i=0; i odinlog("IdeaOpts","set_defaults"); STD_list possible_arch; possible_arch.push_back(conf.get_installdir()+SEPARATOR_STR+"src"+SEPARATOR_STR+PACKAGE+"-"+VERSION+".tar.gz"); select_alternative(arch,possible_arch); STD_list possible_ideadirs; JDXfileName midearoot("C:/MIDEA"); midearoot.set_dir(true); if(midearoot.exists()) { // VB* svector mideadirs=match_in_dir("C:/MIDEA", "n4_"); for(unsigned int i=0; i possible_seqdirs; possible_seqdirs.push_back(ideadir+SEPARATOR_STR+"n4/pkg/MrServers/MrImaging/seq"); possible_seqdirs.push_back(ideadir+SEPARATOR_STR+"n4/comp/Application/seq"); select_alternative(seqdir,possible_seqdirs); odin2idea_label="odin"; STD_list possible_icedirs; possible_icedirs.push_back(ideadir+SEPARATOR_STR+"n4/pkg/MrServers/MrIcePrograms"); // pre VB15 possible_icedirs.push_back(ideadir+SEPARATOR_STR+"n4/pkg/MrServers/MrVista/Ice/IceIdeaFunctors"); // VB15 possible_icedirs.push_back(seqdir); // fallback select_alternative(icedir,possible_icedirs); vxworks_heap_size=3; debug_vxworks_host=false; JDXfileName ccpentium(ideadir+"/n4_fsp/tornado/i86/host/x86-win32/bin/ccpentium.exe"); if(ccpentium.exists()) vxworks_cpu.set_actual("PENTIUM"); else vxworks_cpu.set_actual("PPC750"); make_jobs=numof_cores(); make_clean=true; } ///////////////////////////////////////////////////////////////////////////// STD_string IdeaOpts::get_vxworks_postfix() const { STD_string result; if(tolowerstr(vxworks_cpu).find("pentium")!=STD_string::npos) result="pentium"; else result="ppc"; return result; } STD_string IdeaOpts::get_vxworks_ext() const { STD_string result; if(tolowerstr(vxworks_cpu).find("pentium")!=STD_string::npos) result="i86"; else result="ppc"; return result; } STD_string IdeaOpts::get_vxworks_Makefile() const { STD_string result; if(tolowerstr(vxworks_cpu).find("pentium")!=STD_string::npos) result="MakI86.txt"; else result="MakPpc3.txt"; return result; } ///////////////////////////////////////////////////////////////////////////// IdeaDialog::IdeaDialog(QWidget *parent, IdeaOpts& opts, const OdinConf& conf) : GuiDialog(parent,"Compile ODIN for IDEA",true), opts_cache(opts), conf_cache(conf) { Log odinlog("IdeaDialog","IdeaDialog"); grid=new GuiGridLayout(GuiDialog::get_widget(), 2, 3); optswidget=new JDXwidget(opts,2,GuiDialog::get_widget()); connect(optswidget,SIGNAL(valueChanged()),this,SLOT(update())); grid->add_widget( optswidget, 0, 0, GuiGridLayout::Default, 1, 3 ); pb_cancel = new GuiButton( GuiDialog::get_widget(), this, SLOT(cancel()), "Cancel" ); grid->add_widget( pb_cancel->get_widget(), 1, 0, GuiGridLayout::Center ); pb_defaults = new GuiButton( GuiDialog::get_widget(), this, SLOT(defaults()), "Defaults" ); grid->add_widget( pb_defaults->get_widget(), 1, 1, GuiGridLayout::Center ); pb_compile = new GuiButton( GuiDialog::get_widget(), this, SLOT(compile()), "Compile" ); grid->add_widget( pb_compile->get_widget(), 1, 2, GuiGridLayout::Center ); update(); // initialize on startup GuiDialog::show(); } void IdeaDialog::cancel() { GuiDialog::cancel(); } void IdeaDialog::defaults() { opts_cache.set_defaults(conf_cache, GuiDialog::get_widget()); update(); // update other parameters optswidget->updateWidget(); emit changed(); } void IdeaDialog::compile() { emit changed(); do_compile(); GuiDialog::done(); } void IdeaDialog::error_msg(const STD_string& msg) { message_question(msg.c_str(), "Error Compiling ODIN for IDEA", GuiDialog::get_widget(), false, true); } int IdeaDialog::find_in_alternatives(const STD_string& findstr, const STD_list& alternatives) { JDXfileName fname; if(!select_alternative(fname, alternatives)) { error_msg("Cannot find file containing "+findstr); return -1; } else { STD_string str; if(load (str, fname)<0) { error_msg("Cannot load file "+fname); return -1; } else { if(str.find(findstr)!=STD_string::npos) { return 1; } } } return 0; } STD_string IdeaDialog::hosttarget(bool debug, const STD_string& build_includes, const STD_string& global_conf, const STD_string& mprefix, const STD_string& make_install) const { STD_string flags; STD_string target; if(debug) {flags=opts_cache.hostd_flags; target="hostd";} else {flags=opts_cache.host_flags; target="host";} STD_string win_cxx_mgwpath=mgwpath(opts_cache.win_cxx); STD_string confstr; confstr+=" LD="+mgwpath(opts_cache.msvcdir)+"/VC98/Bin/link.exe"; confstr+=" CXX="+win_cxx_mgwpath; confstr+=" CXXFLAGS=\""+flags+" "+build_includes+"\""; confstr+=" CC="+win_cxx_mgwpath; confstr+=" CFLAGS=\""+flags+"\""; confstr+=" ../../${ARCHNAME}/configure "+global_conf; confstr+=" --prefix="+opts_cache.get_odindir_slash()+"/"+target; if(debug) confstr+=" --enable-debug"; else confstr+=" ${DEBUGOPT}"; confstr+=" --with-extra-odinseq-include-path=-I"+opts_cache.get_ideadir_slash()+"/SWF_extern/SDK/include"; // Since VB15 code compiles only with the SDK provided by IDEA, and ODIN compiles only with VC++ SDK, we need a separate include path for odinseq where IDEA code is included STD_string result; result+="configure-"+target+":\n"; result+=mprefix+"cd "+target+"/build && "+confstr+"\n"; result+=mprefix+"cat "+target+"/build/libtool | sed s/\\\\.libs/libs/g > "+target+"/build/libtool.tmp\n"; // dot in .libs confuses lib.exe in MinGW result+=mprefix+"mv "+target+"/build/libtool.tmp "+target+"/build/libtool\n\n"; result+="build-"+target+":\n"; result+=mprefix+"cd "+target+"/build && "+make_install+"\n\n"; result+="build-"+target+"-clean: build-"+target+"\n"; result+=mprefix+"rm -rf "+target+"/build\n\n"; return result; } STD_string IdeaDialog::errcodes_src(const STD_string& msgfile) { STD_string str=dos2unix(msgfile); STD_string blockbegin("MessageId:"); STD_string blockend("#define"); STD_string result; STD_string txt; do { txt=extract(str, blockbegin, blockend); if(txt!="") { STD_string errcode=shrink(extract(txt, "", "*/")); STD_string msg=extract(txt, "MessageText:", ""); msg=replaceStr(msg, "/*", ""); msg=replaceStr(msg, "*/", ""); msg=justificate(msg,0,false,1000); msg=replaceStr(msg, "\n", ""); result+="if(code=="+errcode+") return \""+msg+"\";\n"; str=rmblock(str, blockbegin, blockend, true, true, false); } } while(txt!=""); return result; } void IdeaDialog::do_compile() { Log odinlog("IdeaDialog","do_compile"); JDXfileName msys_bin(conf_cache.get_installdir()+SEPARATOR_STR+"msys"+SEPARATOR_STR+"bin"); JDXfileName make(msys_bin+"/make.exe"); if(!make.exists()) { error_msg("Cannot find make program "+make); return; } if(createdir(opts_cache.odindir.c_str())) { error_msg("Cannot create target directory "+opts_cache.odindir); return; } if(copyfile(opts_cache.arch.c_str(), (opts_cache.odindir+SEPARATOR_STR+opts_cache.arch.get_basename()).c_str())) { error_msg("Cannot copy "+opts_cache.arch+" to target directory "+opts_cache.odindir); return; } // Parse IDEA error codes JDXfileName msgfile; STD_list msgfile_alternatives; msgfile_alternatives.push_back(opts_cache.ideadir+"/n4/x86/delivery/include/Measurement/Sequence/libRT/libRTmsg.h"); // pre VA25 msgfile_alternatives.push_back(opts_cache.ideadir+"/n4/x86/delivery/include/MrServers/MrMeasSrv/SeqIF/libRT/libRTmsg.h"); // VA25 and later if(!select_alternative(msgfile, msgfile_alternatives)) { error_msg("Cannot find file for IDEA error codes"); return; } STD_string msgfilestr; if(load(msgfilestr,msgfile)<0) { error_msg("Cannot load file for IDEA error codes"); return; } STD_string msgsrc=errcodes_src(msgfilestr); STD_string msgsrc_fname="idea_errcodes.cpp"; if(write(msgsrc,opts_cache.odindir+SEPARATOR_STR+msgsrc_fname)<0) { error_msg("Cannot write file for IDEA error codes"); return; } STD_string makestr="\""+mgwpath(make)+"\""; STD_string make_install=makestr+" install"; if(opts_cache.make_jobs>1) { make_install="MAKEFLAGS=\"-j "+itos(opts_cache.make_jobs)+"\" "+makestr+" -e install"; } STD_string makefile; JDXfileName shell=msys_bin+SEPARATOR_STR+"sh.exe"; if(!shell.exists()) { error_msg("Cannot find shell "+shell); return; } makefile+="SHELL = \""+mgwpath(shell)+"\"\n\n"; makefile+="SETPATH = PATH=\""+mgwpath(msys_bin)+"\":$$PATH;\n\n"; STD_string mprefix="\t${SETPATH} "; makefile+="SUBDIRS = vxworks host hostd\n\n"; makefile+="ARCHNAME = "+replaceStr(opts_cache.arch.get_basename(),".tar.gz","")+"\n\n"; makefile+="ODIN2IDEA_LABEL = "+opts_cache.odin2idea_label+"\n"; makefile+="ODIN2IDEADIR_MGWPATH = "+mgwpath(opts_cache.seqdir)+"/${ODIN2IDEA_LABEL}\n"; makefile+="ODIN2IDEADIR_SLASH = "+replaceStr(opts_cache.seqdir,"\\","/")+"/${ODIN2IDEA_LABEL}\n\n"; makefile+="ICEODINDIR = \""+mgwpath(opts_cache.icedir)+"/IceOdin\"\n\n"; makefile+="DEBUGOPT = "; if(!opts_cache.debug_vxworks_host) makefile+="# "; // just comment out if release is enabled makefile+="--enable-debug\n\n"; STD_string global_conf="--enable-only-idea-plugin --enable-ideasupport --disable-cmdline --disable-threads --disable-unit-test --enable-static --disable-shared"; STD_string odindir_slash=opts_cache.get_odindir_slash(); // use forward slashes for includes STD_string build_includes="-I"+odindir_slash+"/${ARCHNAME}"; makefile+="all: build\n\n"; // default: recompile odin makefile+="unpack:\n"; makefile+=mprefix+"tar -xvzf ${ARCHNAME}.tar.gz\n"; makefile+=mprefix+"cp "+msgsrc_fname+" ${ARCHNAME}/platforms/IDEA_n4/odinseq_idea/\n"; makefile+=mprefix+"mkdir -p /tmp\n"; // hacking configure: // 1) default file extension for C++ source code since .cc somehow fails with autoconf 2.59 ... // 2) replace limits.h (which fails on VB15) by stdlib.h as header for GCC sanity check makefile+=mprefix+"cat ${ARCHNAME}/configure | sed s/ac_ext=cc/ac_ext=cpp/ | sed s/limits.h/stdlib.h/g> ${ARCHNAME}/configure.tmp\n"; makefile+=mprefix+"mv ${ARCHNAME}/configure.tmp ${ARCHNAME}/configure\n"; STD_string mpcu_postfix=opts_cache.get_vxworks_postfix(); STD_string vxworks_cxx=opts_cache.vxworks_dir+"/bin/cc"+opts_cache.get_vxworks_postfix()+".exe"; STD_string gcc=mgwpath(conf_cache.get_installdir()+"/bin/g++"); makefile+=mprefix+"mkdir -p bin\n"; STD_string vxworks_path_slash=replaceStr(opts_cache.vxworks_path,"\\","/"); // create *wrapper.exe STD_map tools; tools["ld"]=tools["ar"]=tools["ranlib"]=tools["cpp"]=tools["nm"]=""; // add entries, nm is just for debugging purpose for(STD_map::iterator it=tools.begin(); it!=tools.end(); ++it) { STD_string tool=it->first; makefile+=mprefix+"echo \"tool=\\\""+replaceStr(opts_cache.vxworks_dir+"/bin/"+tool+mpcu_postfix+".exe","\\","/")+"\\\";\" > ${ARCHNAME}/replacements/toolwrapper_config.h\n"; if(opts_cache.vxworks_path!="") makefile+=mprefix+"echo \"toolpath=\\\""+vxworks_path_slash+"\\\";\" >> ${ARCHNAME}/replacements/toolwrapper_config.h\n"; makefile+=mprefix+gcc+" ${ARCHNAME}/replacements/toolwrapper.cpp -o bin/"+tool+"wrapper.exe\n"; it->second=mgwpath(opts_cache.odindir)+"/bin/"+tool+"wrapper.exe"; } // create cxxwrapper.exe makefile+=mprefix+"echo \"cxx=\\\""+replaceStr(vxworks_cxx,"\\","/")+"\\\";\" > ${ARCHNAME}/replacements/cxxwrapper_config.h\n"; if(opts_cache.vxworks_path!="") makefile+=mprefix+"echo \"cxxpath=\\\""+vxworks_path_slash+"\\\";\" >> ${ARCHNAME}/replacements/cxxwrapper_config.h\n"; makefile+=mprefix+gcc+" ${ARCHNAME}/replacements/cxxwrapper.cpp -o bin/cxxwrapper.exe\n"; tools["cxx"]=mgwpath(opts_cache.odindir)+"/bin/cxxwrapper.exe"; // create build dirs makefile+=mprefix+"for dir in ${SUBDIRS}; do mkdir -p $$dir/build; done\n\n"; STD_string vxworks_cxxflags=opts_cache.vxworks_flags+" "+opts_cache.vxworks_opts+" "+build_includes; STD_string vxworks_cppflags=opts_cache.vxworks_flags; // only defines // configure/build vxworks STD_string confstr; confstr+=" LD="+tools["ld"]; confstr+=" AR="+tools["ar"]; confstr+=" RANLIB="+tools["ranlib"]; confstr+=" CXX="+tools["cxx"]; confstr+=" CXXFLAGS=\""+vxworks_cxxflags+"\""; confstr+=" CXXCPP=\""+tools["cpp"]+" "+vxworks_cppflags+"\""; confstr+=" CC="+tools["cxx"]; confstr+=" CFLAGS=\""+vxworks_cxxflags+"\""; confstr+=" CPP=\""+tools["cpp"]+" "+vxworks_cppflags+"\""; confstr+=" ../../${ARCHNAME}/configure --host="+mpcu_postfix+"-wrs-vxworks "+global_conf; confstr+=" --enable-custom-heap="+itos(opts_cache.vxworks_heap_size)+" --disable-filehandling"; confstr+=" ${DEBUGOPT} --prefix="+odindir_slash+"/vxworks"; makefile+="configure-vxworks:\n"; makefile+=mprefix+"cd vxworks/build && "+confstr+"\n\n"; makefile+="build-vxworks:\n"; makefile+=mprefix+"cd vxworks/build && "+make_install+"\n\n"; makefile+="build-vxworks-clean: build-vxworks\n"; makefile+=mprefix+"rm -rf vxworks/build\n\n"; // configure/build host(d) makefile+=hosttarget(true, build_includes, global_conf, mprefix, make_install); makefile+=hosttarget(false, build_includes, global_conf, mprefix, make_install); // targets for all makefile+="debug:\n"; makefile+=mprefix+"echo $$PATH\n"; makefile+=mprefix+"echo $$SHELL\n\n"; makefile+="clean:\n"; makefile+=mprefix+"rm -rf ${SUBDIRS} ${ARCHNAME} bin build_complete_tag\n\n"; makefile+="configure: configure-vxworks configure-hostd configure-host\n\n"; makefile+="build: build-vxworks build-hostd build-host\n"; makefile+=mprefix+"touch build_complete_tag\n\n"; makefile+="build-clean: build-vxworks-clean build-hostd-clean build-host-clean\n"; makefile+=mprefix+"touch build_complete_tag\n\n"; makefile+="rebuild: unpack configure build\n\n"; makefile+="rebuild-clean: clean unpack configure build-clean\n\n"; // Set up IDEA sequence makefile+="ideaseq:\n"; makefile+=mprefix+"mkdir -p ${ODIN2IDEADIR_MGWPATH}\n"; makefile+=mprefix+"echo \"\\\""+replaceStr(conf_cache.get_installdir(),"\\","/")+"/bin/odin.exe\\\" -m \\\"${ODIN2IDEADIR_SLASH}\\\"\" > ${ODIN2IDEADIR_MGWPATH}/odin.bat\n"; // copying files makefile+=mprefix+"cp ${ARCHNAME}/platforms/IDEA_n4/odin2idea.cpp ${ODIN2IDEADIR_MGWPATH}\n"; makefile+=mprefix+"cp ${ARCHNAME}/platforms/IDEA_n4/tjdx4idea.h ${ODIN2IDEADIR_MGWPATH}\n"; makefile+=mprefix+"cat ${ARCHNAME}/platforms/IDEA_n4/makefile.trs | sed s/ODIN2IDEA_TAG/${ODIN2IDEA_LABEL}/ > ${ODIN2IDEADIR_MGWPATH}/makefile.trs\n"; // find location of IDEA libs JDXfileName idea_libdir; svector n4_delis=match_in_dir(opts_cache.ideadir, "n4_deli_"); if(n4_delis.size()) { idea_libdir=n4_delis[0]+"/x86/delivery/lib"; // VA 25 } else { idea_libdir=opts_cache.ideadir+"/n4_prod/x86/prod/lib"; // default (e.g. VA15) } // Create libs_host(d).txt which contains all libs found in the directory where IDEA libs are stored makefile+=mprefix+"rm -f ${ODIN2IDEADIR_MGWPATH}/libs_host.txt ${ODIN2IDEADIR_MGWPATH}/libs_hostd.txt\n"; makefile+=mprefix+"for file in "+mgwpath(idea_libdir)+"/*d.lib; do \\\n"; makefile+="\t bname=`basename $$file d.lib`; \\\n"; makefile+="\t if test -f "+mgwpath(idea_libdir)+"/$${bname}.lib; then \\\n"; makefile+="\t echo \"LDLIBS += \"$${bname}.lib >> ${ODIN2IDEADIR_MGWPATH}/libs_host.txt; \\\n"; makefile+="\t echo \"LDDLLS += \"$${bname}.dll >> ${ODIN2IDEADIR_MGWPATH}/libs_host.txt; \\\n"; makefile+="\t echo \"LDLIBS += \"$${bname}d.lib >> ${ODIN2IDEADIR_MGWPATH}/libs_hostd.txt; \\\n"; makefile+="\t echo \"LDDLLS += \"$${bname}d.dll >> ${ODIN2IDEADIR_MGWPATH}/libs_hostd.txt; \\\n"; makefile+="\t fi; \\\n"; makefile+="\tdone\n"; // find location of IDEA includes STD_list possible_includepaths; // pre VA25 possible_includepaths.push_back("n4/comp"); possible_includepaths.push_back("n4/comp/STLport"); possible_includepaths.push_back("n4_extsw/x86/extsw/MedCom/versant/5_2_2/NT/h"); possible_includepaths.push_back("n4/comp/Measurement/Sequence"); possible_includepaths.push_back("n4/comp/Measurement/Sequence/libSBB"); possible_includepaths.push_back("n4/comp/Measurement/PerAns/PerProxies"); possible_includepaths.push_back("n4/comp/Measurement/MeasPatient"); possible_includepaths.push_back("n4/comp/Application/seq"); possible_includepaths.push_back("n4/comp/ExamUI/ExamDb/Protocol/UILink/StdProtRes"); possible_includepaths.push_back("n4/comp/Common/STL"); // VA25 and later possible_includepaths.push_back("n4/pkg"); possible_includepaths.push_back("n4/pkg/STLport"); possible_includepaths.push_back("n4_extsw/x86/extsw/MedCom/versant/vds605/h"); possible_includepaths.push_back("n4/pkg/MrServers/MrMeasSrv/SeqIF"); possible_includepaths.push_back("n4/pkg/MrServers/MrMeasSrv/MeasPatient"); possible_includepaths.push_back("n4/pkg/MrServers/MrImaging/libSBB"); possible_includepaths.push_back("n4/pkg/MrServers/MrPerAns/PerProxies"); possible_includepaths.push_back("n4/pkg/MrServers/MrImaging/seq"); possible_includepaths.push_back("n4/pkg/MrServers/MrProtSrv/MrProtocol/UILink/StdProtRes"); possible_includepaths.push_back("n4/pkg/MrCommon/MrCFramework/STL"); JDXfileName testdir; testdir.set_dir(true); STD_string idea_includes; for(STD_list::const_iterator it=possible_includepaths.begin(); it!=possible_includepaths.end(); ++it) { testdir=opts_cache.ideadir+SEPARATOR_STR+(*it); if(testdir.exists()) { idea_includes+=" "+opts_cache.get_ideadir_slash()+"/"+(*it); } } makefile+=mprefix+"rm -f ${ODIN2IDEADIR_MGWPATH}/idea_includes.txt\n"; makefile+=mprefix+"for include in "+idea_includes+"; do \\\n"; makefile+="\t echo \"CPPFLAGS_LOCAL += -I$${include}\" >> ${ODIN2IDEADIR_MGWPATH}/idea_includes.txt; \\\n"; makefile+="\tdone\n"; STD_string idea_defines; // checking iPAT (parallel imaging) capability JDXfileName testfile(opts_cache.ideadir+"/n4/pkg/MrServers/MrImaging/seq/common/iPAT/iPAT.h"); if(testfile.exists()) idea_defines="-DHAVE_iPAT"; // checking whether standard STL header 'vector' is available (which is the case on VB13) testfile=opts_cache.ideadir+"/n4_opensource/STLport/stlport/vector"; if(testfile.exists()) idea_defines+=" -DHAVE_STL_VECTOR"; // Checking for MultiByteToWideChar in MrProt.h STD_list possible_mrprot; possible_mrprot.push_back(opts_cache.ideadir+"/n4/comp/Measurement/Sequence/Prot/MrProt.h"); possible_mrprot.push_back(opts_cache.ideadir+"/n4/pkg/MrServers/MrProtSrv/MrProt/MrProt.h"); int retval=find_in_alternatives("MultiByteToWideChar",possible_mrprot); if(retval<0) return; if(retval>0) idea_defines+=" -DHAVE_MULTIBYTETOWIDECHAR"; // Checking whether we have study index STD_list possible_measpatient; possible_measpatient.push_back(opts_cache.ideadir+"/n4/comp/Measurement/MeasPatient/MeasPatient.h"); possible_measpatient.push_back(opts_cache.ideadir+"/n4/pkg/MrServers/MrMeasSrv/MeasPatient/MeasPatient.h"); retval=find_in_alternatives("uiStudyIndex",possible_measpatient); if(retval<0) return; if(retval>0) idea_defines+=" -DHAVE_STUDYINDEX"; // Checking whether we have INC_16 STD_list possible_seqdefines; possible_seqdefines.push_back(opts_cache.ideadir+"/n4/comp/Measurement/Sequence/SeqDefines.h"); possible_seqdefines.push_back(opts_cache.ideadir+"/n4/pkg/MrServers/MrProtSrv/MrProt/SeqDefines.h"); retval=find_in_alternatives("INC_16",possible_seqdefines); if(retval<0) return; if(retval>0) idea_defines+=" -DHAVE_INC_16"; // Assume new Linux-based Ice reco is there if IceConfigurators are present STD_string icecmd="MakeIcePrg"; testfile=opts_cache.ideadir+"/n4/pkg/MrServers/MrVista/Config/IceConfigurators"; if(testfile.exists()) { idea_defines+=" -DHAVE_ICE_CONFIGURATOR"; icecmd="mi"; } // checking whether libGTR is there testfile=opts_cache.ideadir+"/n4/x86/delivery/lib/libGTR.lib"; bool has_libgtr=testfile.exists(); // Creating batch script for Makefiles makefile+=mprefix+"cat ${ARCHNAME}/platforms/IDEA_n4/MakSeq.bat | \\\n"; makefile+="\tsed s/_VXWORKS_EXT_TAG_/"+opts_cache.get_vxworks_ext()+"/g \\\n"; makefile+="\t> ${ODIN2IDEADIR_MGWPATH}/MakSeq.bat\n"; // creating VA*/VB12 Makefile for vxworks makefile+=mprefix+"cat ${ARCHNAME}/platforms/IDEA_n4/"+opts_cache.get_vxworks_Makefile()+" | \\\n"; makefile+="\tawk -v repl=${ODIN2IDEA_LABEL} '{gsub(\"_ODIN2IDEA_TAG_\",repl); print; }' | \\\n"; makefile+="\tawk -v repl=\"`cat ${ODIN2IDEADIR_MGWPATH}/idea_includes.txt`\" '{gsub(\"_IDEA_INCLUDES_TAG_\",repl); print; }' | \\\n"; makefile+="\tawk -v repl=\""+odindir_slash+"/vxworks\" '{gsub(\"_ODINDIR_TAG_\",repl); print; }' | \\\n"; makefile+="\tawk -v repl=\""+idea_defines+"\" '{gsub(\"_CPPFLAGS_TAG_\",repl); print; }' \\\n"; makefile+="\t> ${ODIN2IDEADIR_MGWPATH}/"+opts_cache.get_vxworks_Makefile()+"\n"; // creating VA*/VB12 Makefiles for host(d) STD_string idea_libdir_backslash=replaceStr(idea_libdir,"\\","\\\\\\\\"); // double protect backslash from shell makefile+=mprefix+"for HOSTLETTER in \"d\" \"\" ; do \\\n"; makefile+="\t cat ${ARCHNAME}/platforms/IDEA_n4/MakHost.txt | \\\n"; makefile+="\t awk -v repl=\"$$HOSTLETTER\" '{gsub(\"_DEBUGLETTER_TAG_\",repl); print; }' | \\\n"; makefile+="\t awk -v repl=${ODIN2IDEA_LABEL} '{gsub(\"_ODIN2IDEA_TAG_\",repl); print; }' | \\\n"; makefile+="\t awk -v repl=\""+idea_defines+"\" '{gsub(\"_CPPFLAGS_TAG_\",repl); print; }' | \\\n"; makefile+="\t awk -v repl=\""+idea_libdir_backslash+"\" '{gsub(\"_IDEA_LIBDIR_TAG_\",repl); print; }' | \\\n"; if(has_libgtr) makefile+="\t awk '{gsub(\"#REM_IF_HAS_LIBGTR \",\"\"); print; }' | \\\n"; makefile+="\t awk -v repl=\"`cat ${ODIN2IDEADIR_MGWPATH}/libs_host$${HOSTLETTER}.txt`\" '{gsub(\"_IDEA_HOST_LIBS_TAG_\",repl); print; }' | \\\n"; makefile+="\t awk -v repl=\"`cat ${ODIN2IDEADIR_MGWPATH}/idea_includes.txt`\" '{gsub(\"_IDEA_INCLUDES_TAG_\",repl); print; }' | \\\n"; makefile+="\t awk -v repl=\""+odindir_slash+"/host$${HOSTLETTER}\" '{gsub(\"_ODINDIR_TAG_\",repl); print; }' \\\n"; makefile+="\t > ${ODIN2IDEADIR_MGWPATH}/MakHost$${HOSTLETTER}.txt; \\\n"; makefile+="\tdone\n"; // creating Makefile for VB13 makefile+=mprefix+"cat ${ARCHNAME}/platforms/IDEA_n4/odin.mk | \\\n"; makefile+="\tawk -v repl=${ODIN2IDEA_LABEL} '{gsub(\"_ODIN2IDEA_TAG_\",repl); print; }' | \\\n"; makefile+="\tawk -v repl=\"`cat ${ODIN2IDEADIR_MGWPATH}/idea_includes.txt`\" '{gsub(\"_IDEA_INCLUDES_TAG_\",repl); print; }' | \\\n"; makefile+="\tawk -v repl=\""+idea_defines+"\" '{gsub(\"_CPPFLAGS_TAG_\",repl); print; }' | \\\n"; makefile+="\tawk -v repl=\""+odindir_slash+"\" '{gsub(\"_ODINDIR_TAG_\",repl); print; }' \\\n"; makefile+="\t> ${ODIN2IDEADIR_MGWPATH}/${ODIN2IDEA_LABEL}.mk\n\n"; // Set up Ice STD_string iceodindir="\""+mgwpath(opts_cache.icedir)+"/IceOdin\""; makefile+="ice:\n"; makefile+=mprefix+"mkdir -p ${ICEODINDIR}\n"; // makefile+=mprefix+"cat ${ARCHNAME}/platforms/IDEA_n4/Ice/IceOdin.evp | sed s/ODINRECO_FLAG/false/ > ${ICEODINDIR}/IceOdin.evp\n"; // makefile+=mprefix+"cat ${ARCHNAME}/platforms/IDEA_n4/Ice/IceOdin.evp | sed s/ODINRECO_FLAG/true/ > ${ICEODINDIR}/IceOdinOnline.evp\n"; makefile+=mprefix+"cp ${ARCHNAME}/platforms/IDEA_n4/Ice/IceOdin.evp ${ICEODINDIR}\n"; makefile+=mprefix+"cp ${ARCHNAME}/platforms/IDEA_n4/Ice/*.h ${ICEODINDIR}\n"; makefile+=mprefix+"cp ${ARCHNAME}/platforms/IDEA_n4/Ice/*.cpp ${ICEODINDIR}\n"; makefile+=mprefix+"cp ${ARCHNAME}/platforms/IDEA_n4/Ice/MakeRelease.X86 ${ICEODINDIR}\n\n"; makefile+=mprefix+"cp ${ARCHNAME}/platforms/IDEA_n4/Ice/Makefile.imk ${ICEODINDIR}\n\n"; STD_string makefilename=opts_cache.odindir+SEPARATOR_STR+"Makefile"; write(makefile, makefilename); STD_string msg=justificate("A Makefile to build and install ODIN for IDEA has been stored under "+makefilename+". Execute this Makefile now?"); if(!message_question(msg.c_str(), "Execute Makefile?", GuiDialog::get_widget(),true)) return; // set environment variables which would be set by cygwin.bat otherwise #ifdef USING_WIN32 /* STD_string oldpath=secure_getenv("PATH"); if(oldpath.find(cygnus_bin) != 0) { // add only if cygnus_bin is not already 1st entry STD_string path="PATH="+cygnus_bin+";"+oldpath; ODINLOG(odinlog,normalDebug) << "oldpath/path=" << oldpath << "/" << path << STD_endl; _putenv(path.c_str()); } */ _putenv("MAKE_MODE=UNIX"); #endif STD_string target="rebuild"; if(opts_cache.make_clean) target+="-clean"; if(!execute_make(make,target)) return; msg=justificate("Congratulations! You have sucessfully compiled ODIN for IDEA. Includes and libraries have been installed under "+opts_cache.odindir); message_question(msg.c_str(), "Build complete", GuiDialog::get_widget()); if(!execute_make(make,"ideaseq")) return; msg=justificate("An IDEA sequence '"+opts_cache.odin2idea_label+"' which holds the ODIN methods has been " "installed under "+opts_cache.seqdir+". " "You can now open the SDE shell and change to the newly " "created sequence by using the 'cs' command. " "Then type 'odin' to start the ODIN graphical user interface. " "After creating/editing your ODIN methods, you can create the " "DLLs via the 'Siemens' menu."); message_question(msg.c_str(), "Sequence setup complete", GuiDialog::get_widget()); if(!execute_make(make,"ice")) return; msg=justificate("An ICE reconstruction 'IceOdin' which writes the raw data to disk has been " "installed under "+opts_cache.icedir+". " "You can now use the ICE shell to compile the ICE " "reconstruction using the command '"+icecmd+"'."); message_question(msg.c_str(), "ICE setup complete", GuiDialog::get_widget()); } bool IdeaDialog::execute_make(const STD_string& make, const STD_string& target) { Log odinlog("IdeaDialog","execute_make"); svector cmd_chain; cmd_chain.resize(1); cmd_chain[0]="\""+make+"\" -C "+opts_cache.odindir+" "+target; ProcessDialog makedlg(GuiDialog::get_widget()); int waitstate=makedlg.execute_cmds(cmd_chain,false); // log to console bool status=(!waitstate); ODINLOG(odinlog,normalDebug) << "status / waitstate = " << status << " / " << waitstate << STD_endl; if(!status && waitstate!=-2) { error_msg("Make "+target+" failed"); return false; } if(waitstate==-2) { // code for cancel return false; } return true; } void IdeaDialog::update() { Log odinlog("IdeaDialog","update"); // check for space characters if(opts_cache.odindir.find(" ") != STD_string::npos) { error_msg("Please do not use space characters in installation path, otherwise compilation fails"); } // set compilers and path of tools opts_cache.win_cxx=opts_cache.msvcdir+"/VC98/Bin/cl.exe"; STD_list vxworks_dir_alternatives; vxworks_dir_alternatives.push_back(opts_cache.ideadir+"/n4_fsp/tornado/i86/host/x86-win32"); vxworks_dir_alternatives.push_back(opts_cache.ideadir+"/n4_fsp/tornado/ppc/host/x86-win32"); select_alternative(opts_cache.vxworks_dir, vxworks_dir_alternatives); STD_list vxworks_path_alternatives; vxworks_path_alternatives.push_back(opts_cache.vxworks_dir+"/lib/gcc-lib/powerpc-wrs-vxworks/cygnus-2.7.2-960126"); vxworks_path_alternatives.push_back(opts_cache.vxworks_dir+"/bin"); // for VB12 select_alternative(opts_cache.vxworks_path, vxworks_path_alternatives); STD_string global_includes; STD_string global_defines; // set includes STD_list possible_includepaths; possible_includepaths.push_back("n4/x86/delivery/include"); // pre VA25 possible_includepaths.push_back("n4/comp"); possible_includepaths.push_back("n4/comp/Measurement/Sequence/libRT"); possible_includepaths.push_back("n4/comp/Measurement/Sequence/libSBB"); // for fSBBECGFillTimeRun possible_includepaths.push_back("n4/comp/Measurement/Sequence/SeqBuffer"); possible_includepaths.push_back("n4/comp/Measurement/Sequence/Prot"); // for MrProt.h // VA25/VB* possible_includepaths.push_back("n4/pkg"); possible_includepaths.push_back("n4/pkg/MrServers/MrMeasSrv/SeqIF/libRT"); possible_includepaths.push_back("n4/pkg/MrServers/MrImaging/libSBB"); // for fSBBECGFillTimeRun possible_includepaths.push_back("n4/pkg/MrServers/MrMeasSrv/SeqIF/SeqBuffer"); possible_includepaths.push_back("n4/pkg/MrServers/MrProtSrv/MrProt"); // for MrProt.h possible_includepaths.push_back("n4/x86/delivery/include/MrServers/MrMeasSrv/SeqIF/libRT"); // for libRTmsg.h select_idea_include_dirs(global_includes, possible_includepaths, opts_cache); // extra includes for VxWorks JDXfileName vxworks_target_includes; vxworks_target_includes.set_dir(true); STD_list vxworks_target_includes_alternatives; vxworks_target_includes_alternatives.push_back(opts_cache.ideadir+"/n4/pkg/MrServers/MrMPCUSystem/Tornado_i86/target/h"); vxworks_target_includes_alternatives.push_back(opts_cache.ideadir+"/n4_fsp/tornado/ppc/target/h"); select_alternative(vxworks_target_includes, vxworks_target_includes_alternatives); // checking for presence of sGRAD_PULSE_ARB class in sGRAD_PULSE.h STD_list sGRAD_PULSE_h_alternatives; sGRAD_PULSE_h_alternatives.push_back(opts_cache.ideadir+"/n4/pkg/MrServers/MrMeasSrv/SeqIF/libRT/sGRAD_PULSE.h"); sGRAD_PULSE_h_alternatives.push_back(opts_cache.ideadir+"/n4/comp/Measurement/Sequence/libRT/sGRAD_PULSE.h"); int retval=find_in_alternatives("sGRAD_PULSE_ARB",sGRAD_PULSE_h_alternatives); if(retval<0) return; if(retval>0) global_defines+="-DHAVE_sGRAD_PULSE_ARB"; // checking for presence of FFTScale in MrCoilSelect.h STD_list MrCoilSelect_h_alternatives; MrCoilSelect_h_alternatives.push_back(opts_cache.ideadir+"/n4/comp/Measurement/Sequence/CoilSelect/MrCoilSelect.h"); MrCoilSelect_h_alternatives.push_back(opts_cache.ideadir+"/n4/pkg/MrServers/MrProtSrv/MrProt/CoilSelect/MrCoilSelect.h"); retval=find_in_alternatives("FFTScale",MrCoilSelect_h_alternatives); if(retval<0) return; if(retval>0) global_defines+=" -DHAVE_MRCOILSELECT_FFTSCALE"; opts_cache.vxworks_flags=global_includes+" -I"+replaceStr(vxworks_target_includes,"\\","/")+" "+global_defines+" -DVXWORKS -DCPU="+opts_cache.vxworks_cpu.JDXenum::operator STD_string(); opts_cache.vxworks_opts="-ansi"; if(tolowerstr(opts_cache.vxworks_cpu).find("pentium")!=STD_string::npos) { opts_cache.vxworks_opts+=" -O1"; // -O2 causes the compiler to enter inifinite loop ... opts_cache.vxworks_opts+=" -mcpu=pentium -march=pentium -fvolatile -nostdlib -fno-builtin -fno-defer-pop -malign-double"; } else { opts_cache.vxworks_opts+=" -O2"; } STD_list possible_hostall_includepaths; possible_hostall_includepaths.push_back("n4/comp/STLport"); // VA* path possible_hostall_includepaths.push_back("n4_opensource/STLport/stlport"); // VB* path, if this path is absent, the MSVC iostream would be used which fails possible_hostall_includepaths.push_back("n4_extsw/x86/extsw/MedCom/include"); // VA* path possible_hostall_includepaths.push_back("n4/x86/extsw/MedCom/include"); // VB* path STD_string hostall_idea_includes; select_idea_include_dirs(hostall_idea_includes, possible_hostall_includepaths, opts_cache); STD_string hostall_defines=global_defines+" -DWIN32 -D_AFXDLL -DCSA_HAS_DLL -D_MBCS -DAFX_NOVTABLE= -D_RWTOOLSDLL -D_UNICODE -DUNICODE -DO_DLL_PCLASS_ONLY -D_CONSOLE -D_WINDLL -DACE_HAS_DLL"; STD_string hostall_includes=global_includes+" "+hostall_idea_includes; STD_string hostall_opts="-nologo -Z7 -O2 -GR -GX -G5 -GF"; opts_cache.hostd_flags=hostall_defines+" "+hostall_includes+" "+hostall_opts+" -MDd"; opts_cache.host_flags= hostall_defines+" "+hostall_includes+" "+hostall_opts+" -MD"; optswidget->updateWidget(); emit changed(); } IdeaDialog::~IdeaDialog() { delete pb_compile; delete optswidget; delete grid; } //////////////////////////////////////////////////////////////////////////////////////// IdeaMethodDialog::IdeaMethodDialog(const STD_string& methdir, sarray& selectedMethods, const STD_string& install_prefix, const IdeaOpts& ideaopts, QWidget *parent) : GuiDialog(parent,"Select Methods",false), selMeth(selectedMethods), methrootdir(methdir), install_dir(install_prefix), ideaopts_cache(ideaopts) { Log odinlog("IdeaMethodDialog","IdeaMethodDialog"); svector subdirs(browse_dir(methdir,true,true)); ODINLOG(odinlog,normalDebug) << "subdirs=" << subdirs.printbody() << STD_endl; grid = new GuiGridLayout( GuiDialog::get_widget(), 3, 1 ); svector collabel; collabel.resize(1); collabel[0]="Method"; method_list=new GuiListView (GuiDialog::get_widget(), collabel, 100, 300); for(unsigned int i=0; iadd_widget( method_list->get_widget(), 0, 0 ); pb_make = new GuiButton( GuiDialog::get_widget(), this, SLOT(make()), "Make" ); grid->add_widget( pb_make->get_widget(), 1, 0, GuiGridLayout::Center ); pb_cancel = new GuiButton( GuiDialog::get_widget(), this, SLOT(emitDone()), "Cancel" ); grid->add_widget( pb_cancel->get_widget(), 2, 0, GuiGridLayout::Center ); GuiDialog::show(); } IdeaMethodDialog::~IdeaMethodDialog() { for(STD_list::iterator dirit=method_checks.begin();dirit!=method_checks.end();++dirit) { delete (*dirit); } delete method_list; delete pb_make; delete pb_cancel; delete grid; } void IdeaMethodDialog::make() { Log odinlog("IdeaMethodDialog","make"); STD_list methlist; for(STD_list::const_iterator dirit=method_checks.begin();dirit!=method_checks.end();++dirit) { if((*dirit)->is_checked()) methlist.push_back((*dirit)->get_text()); } if(!methlist.size()) { message_question("Please select at least one method", "No Method(s) Selected", GuiDialog::get_widget(),false,true); return; } selMeth.resize(methlist.size()); unsigned int index=0; for(STD_list::const_iterator it=methlist.begin(); it!=methlist.end(); ++it) { selMeth[index]=(*it); ODINLOG(odinlog,normalDebug) << "selMeth[" << index << "]=" << (*it) << STD_endl; SeqMakefile mf(selMeth[index],install_dir); STD_string methdir=methrootdir+SEPARATOR_STR+selMeth[index]+SEPARATOR_STR; svector cmd_chain; cmd_chain=mf.get_odin4idea_method_compile_chain(methdir, ideaopts_cache.odindir, ideaopts_cache.vxworks_path, ideaopts_cache.get_vxworks_cxx(), ideaopts_cache.vxworks_flags+" "+ideaopts_cache.vxworks_opts, ideaopts_cache.win_cxx, ideaopts_cache.hostd_flags, ideaopts_cache.host_flags); ProcessDialog makedlg(GuiDialog::get_widget()); int waitstate=makedlg.execute_cmds(cmd_chain); bool status=(!waitstate); ODINLOG(odinlog,normalDebug) << "status / waitstate = " << status << " / " << waitstate << STD_endl; if(!status && waitstate!=-2) { message_question("An error occured during method compilation", "Make Failed", GuiDialog::get_widget(),false,true); this->emitDone(); return; } index++; } unsigned int imeth; STD_string methods_decls,methods_inits,methods_objs; for(imeth=0; imethemitDone(); return; } void IdeaMethodDialog::emitDone() { GuiDialog::done(); } odin-1.8.5/odin/odincomp.cpp0000644000175000017500000000020611322062346012641 00000000000000#include "odincomp.h" #include const char* OdinComp::get_compName() {return "Odin";} LOGGROUNDWORK(OdinComp) odin-1.8.5/odin/odinconf.cpp0000644000175000017500000003062411455553540012647 00000000000000#include "odinconf.h" #include "odincomp.h" #include #include // for message_question #include #ifdef USING_WIN32 #include #include #include #endif OdinConf::OdinConf(const STD_string& label, bool ignore_environment) : JcampDxBlock(label), sourcecode("","SourceCode",true,notBroken,hidden), editor(DEFAULT_EDITOR,"SourceCodeEditor",true,notBroken), browser(DEFAULT_BROWSER,"WebBrowser",true,notBroken), methroot(get_homedir()+SEPARATOR_STR+DEFAULT_METH_ROOT+SEPARATOR_STR,"MethodsRootDir",true,notBroken), smpfile(get_samplesdir(),"SampleFile",true,notBroken), protfile(get_homedir(),"ProtocolFile",true,notBroken), compiler(CXX,"Compiler",true,notBroken), linker(CXX,"Linker",true,notBroken), compiler_flags(CXXFLAGS,"CompilerOptions",true,notBroken), extra_includes("","ExtraIncludes",true,notBroken), extra_libs("","ExtraLibraries",true,notBroken), selectedMethods(sarray(0),"SelectedMethods",true,notBroken), attachDebugger(false,"AttachDebugger") { Log odinlog("OdinConf","OdinConf"); ignore_env=ignore_environment; sourcecode.set_defaultdir(get_homedir()); sourcecode.set_suffix("cpp"); methroot.set_dir(true); #ifdef USING_WIN32 // compiler=WIN_CXX; // linker=WIN_LD; #else editor.set_defaultdir("/usr/bin"); browser.set_defaultdir("/usr/bin"); #endif protfile.set_parmode(hidden); JcampDxBlock::append(sourcecode); JcampDxBlock::append(methroot); JcampDxBlock::append(smpfile); JcampDxBlock::append(protfile); if(!ignore_env) { JcampDxBlock::append(compiler_flags); JcampDxBlock::append(extra_includes); JcampDxBlock::append(extra_libs); } #ifdef HAVE_GDB_XTERM JcampDxBlock::append(attachDebugger); #endif JcampDxBlock::append(editor); JcampDxBlock::append(browser); JcampDxBlock::append(selectedMethods); } bool OdinConf::init(QWidget* parent) { Log odinlog("OdinConf","init"); #ifdef USING_WIN32 #ifdef USING_GCC // Assume MinGW STD_string instprefix(get_installdir()); compiler=instprefix+SEPARATOR_STR+"bin"+SEPARATOR_STR+"g++"; linker=STD_string(compiler); // the same for GCC // Try to find and use notepad2 STD_string notepad2_fname=instprefix+SEPARATOR_STR+"bin"+SEPARATOR_STR+"notepad2.exe"; if(filesize(notepad2_fname.c_str())>0) editor=notepad2_fname; #else // Assume Visual C++ 6 STD_string keyname("SOFTWARE\\Microsoft\\VisualStudio\\6.0\\Setup\\Microsoft Visual C++"); STD_string valname("ProductDir"); STD_string vcreg(get_registryvalue(keyname,valname)); // retrieve VC++ installation path from registry ODINLOG(odinlog,normalDebug) << "vcreg=" << vcreg << STD_endl; STD_string msg; if(vcreg=="") { msg=justificate("Visual C++ 6.0 is required for compiling ODIN sequences. I cannot find the path of the Visual C++ installation under the registry key-value pair "+keyname+"-"+valname+". Please install Visual C++ 6.0 and re-install ODIN."); message_question(msg.c_str(), "Cannot find Visual C++", parent, false, true); return false; } else { STD_string compiler_fname=vcreg+SEPARATOR_STR+"bin"+SEPARATOR_STR+"cl.exe"; if(filesize(compiler_fname.c_str())<=0) { msg=justificate("Visual C++ 6.0 is installed but I cannot find the compiler cl.exe under the path "+compiler_fname+". Please make sure that it is installed together with Visual C++ 6.0 and re-install ODIN."); message_question(msg.c_str(), "Cannot find Visual C++ Compiler", parent, false, true); return false; } else { compiler=compiler_fname; // and set it as the initial value, if found ODINLOG(odinlog,normalDebug) << "compiler=" << compiler << STD_endl; } STD_string linker_fname=vcreg+SEPARATOR_STR+"bin"+SEPARATOR_STR+"link.exe"; if(filesize(linker_fname.c_str())<=0) { msg=justificate("Visual C++ 6.0 is installed but I cannot find the linker link.exe under the path "+linker_fname+". Please make sure that it is installed together with Visual C++ 6.0 and re-install ODIN."); message_question(msg.c_str(), "Cannot find Visual C++ Linker", parent, false, true); return false; } else { linker=linker_fname; // and set it as the initial value, if found ODINLOG(odinlog,normalDebug) << "linker=" << linker << STD_endl; } extra_includes="-I\""+vcreg+SEPARATOR_STR+"Include\""; // and set it as the initial value, if found extra_libs="/LIBPATH:\""+vcreg+SEPARATOR_STR+"lib\" "; } vcreg=get_registryvalue("SOFTWARE\\Microsoft\\VisualStudio\\6.0\\Setup","VsCommonDir"); if(vcreg!="") { editor=vcreg+SEPARATOR_STR+"MSDev98"+SEPARATOR_STR+"Bin"+SEPARATOR_STR+"msdev.exe"; } #endif #endif return true; } svector OdinConf::get_method_compile_chain() const { Log odinlog("OdinConf","get_method_compile_chain"); STD_string methlabel(sourcecode.get_basename_nosuffix()); ODINLOG(odinlog,normalDebug) << "methlabel=" << methlabel << STD_endl; if(methlabel=="") return svector(); SeqMakefile mf(methlabel,get_installdir(),compiler,compiler_flags,linker,extra_includes,extra_libs); return mf.get_method_compile_chain(false,true); // Only shared object } STD_string OdinConf::get_registryvalue(const STD_string& keyname, const STD_string& valuename) { Log odinlog("OdinConf","get_registryvalue"); STD_string result; #ifdef USING_WIN32 HKEY reghandle=0; LONG openresult=RegOpenKeyEx(HKEY_LOCAL_MACHINE,keyname.c_str(),0,KEY_READ,®handle); ODINLOG(odinlog,normalDebug) << "reghandle/openresult=" << reghandle << "/" << openresult << STD_endl; if(reghandle) { if(openresult==ERROR_SUCCESS) { unsigned char buff[ODIN_MAXCHAR]; DWORD buffsize=ODIN_MAXCHAR-1; buff[0]='\0'; LONG queryresult=RegQueryValueEx(reghandle,valuename.c_str(),NULL,NULL,buff,&buffsize); ODINLOG(odinlog,normalDebug) << "buffsize/queryresult=" << buffsize << "/" << queryresult << STD_endl; if(queryresult==ERROR_SUCCESS && buffsize<(ODIN_MAXCHAR-1)) { buff[buffsize]='\0'; result=(const char *)buff; } else ODINLOG(odinlog,normalDebug) << "unable to get registry value " << valuename << STD_endl; } else ODINLOG(odinlog,normalDebug) << "unable to open registry key " << keyname << STD_endl; LONG closeresult=RegCloseKey(reghandle); ODINLOG(odinlog,normalDebug) << "closeresult=" << closeresult << STD_endl; } else ODINLOG(odinlog,normalDebug) << "unable to get handle for registry key " << keyname << ", openresult=" << openresult << STD_endl; #endif ODINLOG(odinlog,normalDebug) << "result(" << keyname << "\\" << valuename << ")=" << result << STD_endl; return result; } STD_string OdinConf::get_installdir() { Log odinlog("OdinConf","get_installdir"); JDXfileName result; // create normalized file name STD_string reg; if(!ignore_env) reg=get_registryvalue("SOFTWARE\\Odin","Install_Dir"); if(reg!="") result=reg; else result=INSTALL_PREFIX; ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } STD_string OdinConf::get_binprefix() { Log odinlog("OdinConf","get_binprefix"); STD_string result; // default: empty string -> use PATH #ifdef USING_WIN32 result=get_installdir()+SEPARATOR_STR+"bin"+SEPARATOR_STR; // Append separator (won't work with JDXfileName) so that prefix can either be directory or empty #endif ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } STD_string OdinConf::get_homedir() { Log odinlog("OdinConf","get_homedir"); JDXfileName result(secure_getenv("HOME")); #ifdef USING_WIN32 result=secure_getenv("USERPROFILE"); // the windows 'home' directory #endif if(result=="") ODINLOG(odinlog,warningLog) << "Cannot determine homedir" << STD_endl; ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } STD_string OdinConf::get_datadir() { Log odinlog("OdinConf","get_datadir"); JDXfileName result=get_installdir()+SEPARATOR_STR+"share"+SEPARATOR_STR+"odin"; ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } STD_string OdinConf::get_seqexamplesdir() { Log odinlog("OdinConf","get_seqexamplesdir"); JDXfileName result=get_datadir()+SEPARATOR_STR+"sequences"; ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } STD_string OdinConf::get_samplesdir() { Log odinlog("OdinConf","get_samplesdir"); JDXfileName result=get_datadir()+SEPARATOR_STR+"samples"; return result; } STD_string OdinConf::get_coilsdir() { Log odinlog("OdinConf","get_coilsdir"); JDXfileName result=get_datadir()+SEPARATOR_STR+"coils"; return result; } STD_string OdinConf::get_confdir() { Log odinlog("OdinConf","get_confdir"); STD_string confdir(get_homedir()+SEPARATOR_STR+".odin"); ODINLOG(odinlog,normalDebug) << "confdir=" << confdir << STD_endl; createdir(confdir.c_str()); return confdir; } STD_string OdinConf::get_tmpdir() { Log odinlog("OdinConf","get_tmpdir"); JDXfileName tmpdir(get_confdir()+SEPARATOR_STR+"tmp"); createdir(tmpdir.c_str()); return tmpdir; } STD_string OdinConf::get_manual_location() { Log odinlog("OdinConf","get_manual_location"); STD_string wwwloc("http://od1n.sourceforge.net/manual/html/"); STD_string instloc(get_installdir()+SEPARATOR_STR+"share"+SEPARATOR_STR+"doc"+SEPARATOR_STR+"odin"+SEPARATOR_STR+"manual"+SEPARATOR_STR+"html"+SEPARATOR_STR); STD_string result=wwwloc; if(filesize((instloc+"index.html").c_str())>0) result="file://"+instloc; ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } #ifdef USING_WIN32 bool open_file_in_win32(const STD_string& location, const STD_string& prog) { Log odinlog("OdinConf","open_file_in_win32"); const char* args[4]; STD_string exe; if(prog=="") { args[0]="rundll32.exe"; args[1]="url.dll,FileProtocolHandler"; args[2]=location.c_str(); args[3]=0; } else { args[0]=prog.c_str(); args[1]=location.c_str(); args[2]=0; args[3]=0; } int spawnpid=_spawnvp( _P_NOWAIT, args[0], args); if (spawnpid == -1) { if(errno==E2BIG) ODINLOG(odinlog,errorLog) << "exe to big" << STD_endl; if(errno==EINVAL) ODINLOG(odinlog,errorLog) << "mode invalid" << STD_endl; if(errno==ENOENT) ODINLOG(odinlog,errorLog) << "file not found" << STD_endl; if(errno==ENOEXEC) ODINLOG(odinlog,errorLog) << "exe not found" << STD_endl; if(errno==ENOMEM) ODINLOG(odinlog,errorLog) << "no mem" << STD_endl; } return true; } #endif #ifdef MACOS bool open_file_in_macos(const STD_string& location, STD_list& subprocs) { Log odinlog("OdinConf","open_file_in_macos"); return OdinConf::start_proc("open", location, subprocs); } #endif bool OdinConf::display_html(const STD_string& location, STD_list& subprocs) { Log odinlog("OdinConf","display_html"); bool result=true; #ifdef USING_WIN32 result=open_file_in_win32(location,""); #else #ifdef MACOS result=open_file_in_macos(location, subprocs); #else result=OdinConf::start_proc(browser, location, subprocs); #endif #endif if(!result) { STD_string msg=justificate("Cannot open URL "+location+" using "+browser+". Please change the browser under Preferences->Settings."); message_question(msg.c_str(), "Browser not found", 0, false, true); } return result; } bool OdinConf::open_ascfile(const STD_string& filename, STD_list& subprocs) { Log odinlog("OdinConf","open_ascfile"); bool result=true; #ifdef USING_WIN32 result=open_file_in_win32(filename,editor); #else #ifdef MACOS result=open_file_in_macos(filename, subprocs); #else result=OdinConf::start_proc(editor, filename, subprocs); #endif #endif if(!result) { STD_string msg=justificate("Cannot open ASCII file "+filename+" using "+editor+". Please change the editor under Preferences->Settings."); message_question(msg.c_str(), "Editor not found", 0, false, true); } return result; } #ifndef USING_WIN32 bool OdinConf::start_proc(const STD_string& program, const STD_string& filename, STD_list& subprocs) { Log odinlog("OdinConf","start_proc"); bool result=true; STD_string cmd(program+" \""+STD_string(filename)+"\""); Process proc; result=proc.start(cmd); sleep_ms(1000); // wait for error int retval=0; bool finished=proc.finished(retval); if(finished && retval) result=false; if(!finished) subprocs.push_back(proc); return result; } #endif bool OdinConf::ignore_env; odin-1.8.5/odin/main.cpp0000644000175000017500000000161211322062346011757 00000000000000#include "odin.h" #include "odinview.h" int main(int argc, char *argv[]) { // do this here so we do not have to query X server in order to get usage for manual if(hasHelpOption(argc, argv)) {OdinView::usage();exit(0);} bool has_debug_cmdline=isCommandlineOption(argc,argv,"-d",false); // Do this here before -d option is removed from argv GuiApplication a(argc, argv); // debug handler will be initialized here Log odinlog("","main"); ODINLOG(odinlog,normalDebug) << "GuiApplication::argc/argv()=" << GuiApplication::argc() << "/" << GuiApplication::argv() << STD_endl; Odin* odin =new Odin(); odin->initOdin(&a,has_debug_cmdline); int result=a.start(odin->get_widget()); ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; Static::destroy_all(); // free resources ODINLOG(odinlog,normalDebug) << "destroy_all done" << STD_endl; return result; } odin-1.8.5/odin/odinplot_vtk.cpp0000644000175000017500000000705511322062346013556 00000000000000#include "odinplot_vtk.h" #include "odincomp.h" #ifdef VTKSUPPORT #include #include #include #include #include #include #include #include #include #include #include #include #include #endif VtkMagnPlotter::VtkMagnPlotter() { renderer=0; renWin=0; iren=0; magnArrow=0; magnMapper=0; magnActor=0; magnGradActor=0; axes=0; axesTubes=0; axesMapper=0; axesActor=0; } void VtkMagnPlotter::start() { Log odinlog("VtkMagnPlotter","start"); #ifdef VTKSUPPORT magnArrow=vtkArrowSource::New(); magnMapper = vtkPolyDataMapper::New(); magnMapper->SetInput(magnArrow->GetOutput()); magnActor = vtkActor::New(); magnActor->SetMapper(magnMapper); magnActor->GetProperty()->SetColor(1,1,1); magnGradActor = vtkActor::New(); magnGradActor->SetMapper(magnMapper); magnGradActor->GetProperty()->SetColor(1,1,50); // Axes axes = vtkAxes::New(); // axes->SetOrigin(bounds[0], bounds[2], bounds[4]); // axes->SetScaleFactor(0.01); axesTubes = vtkTubeFilter::New(); axesTubes->SetInput(axes->GetOutput()); axesTubes->SetRadius(axes->GetScaleFactor()/100.0); axesTubes->SetNumberOfSides(6); axesMapper = vtkPolyDataMapper::New(); axesMapper->SetInput(axesTubes->GetOutput()); vtkActor *axesActor = vtkActor::New(); axesActor->SetMapper(axesMapper); // Create the usual rendering stuff renderer = vtkRenderer::New(); renWin = vtkRenderWindow::New(); renWin->AddRenderer(renderer); renderer->AddActor(magnActor); magnGradActor_added=false; renderer->AddActor(axesActor); // renderer->SetBackground(1,1,1); renderer->GetActiveCamera()->Roll(-120.0); // renderer->GetActiveCamera()->Azimuth(120.0); renderer->GetActiveCamera()->Elevation(-70.0); renderer->GetActiveCamera()->Zoom(0.25); renWin->SetSize(500,500); #else ODINLOG(odinlog,errorLog) << "vtk support is disabled, recompile with --enable-vtksupport" << STD_endl; #endif } void VtkMagnPlotter::plot_vector(float M[3], float* dM) { #ifdef VTKSUPPORT double Mnorm=norm3(M[0],M[1],M[2]); double heightAngle=180.0/PII*acos(secureDivision(M[2],Mnorm)); double azimuthAngle=180.0/PII*atan2(M[1],M[0]); magnActor->SetScale(Mnorm); magnActor->SetOrientation(0.0,heightAngle-90.0,azimuthAngle); if(dM) { // add magnGradActor if we have MagnGrads if(!magnGradActor_added) { renderer->AddActor(magnGradActor); magnGradActor_added=true; } // magnGradActor->SetOrigin(M[0],M[1],M[2]); Mnorm=norm3(dM[0],dM[1],dM[2]); heightAngle=180.0/PII*acos(secureDivision(dM[2],Mnorm)); azimuthAngle=180.0/PII*atan2(dM[1],dM[0]); magnGradActor->SetScale(0.02*Mnorm); magnGradActor->SetOrientation(0.0,heightAngle-90.0,azimuthAngle); } if(renWin) renWin->Render(); #endif } void VtkMagnPlotter::interact() { #ifdef VTKSUPPORT if(!iren) iren = vtkRenderWindowInteractor::New(); iren->SetRenderWindow(renWin); // interact with data if(iren) iren->Start(); #endif } VtkMagnPlotter::~VtkMagnPlotter() { #ifdef VTKSUPPORT if(axes) axes->Delete(); if(axesTubes) axesTubes->Delete(); if(axesMapper) axesMapper->Delete(); if(axesActor) axesActor->Delete(); if(magnArrow) magnArrow->Delete(); if(magnMapper) magnMapper->Delete(); if(magnActor) magnActor->Delete(); if(renderer) renderer->Delete(); if(iren) iren->Delete(); if(renWin) renWin->Delete(); #endif } odin-1.8.5/odin/odindialog_progress.cpp0000644000175000017500000000205711322062346015074 00000000000000#include "odindialog_progress.h" #include "odincomp.h" ProgressDisplayDialog::ProgressDisplayDialog(QWidget *parent, bool modal) : GuiProgressDialog(parent, modal, 0), counter(0) { // Non-percent display by default } void ProgressDisplayDialog::finish() { GuiProgressDialog::hide(); } void ProgressDisplayDialog::init(unsigned int nsteps, const char* txt) { Log odinlog("ProgressDisplayDialog","init"); ODINLOG(odinlog,normalDebug) << "nsteps/txt=" << nsteps << "/" << txt << STD_endl; if(txt) GuiProgressDialog::set_text(txt); GuiProgressDialog::set_total_steps(nsteps); GuiProgressDialog::reset(); GuiProgressDialog::show(); // Show dialog at this point, necessary for Bruker dialogs counter=0; } void ProgressDisplayDialog::increase(const char*) { counter++; // GuiProgressDialog expects [0...nsteps] GuiProgressDialog::set_progress( counter ); } bool ProgressDisplayDialog::refresh() { GuiApplication::process_events(); if(GuiProgressDialog::was_cancelled()) { throw OdinCancel(); return true; } return false; } odin-1.8.5/odin/odindialog_new.h0000644000175000017500000000304311322062346013462 00000000000000/*************************************************************************** odindialog_new.h - description ------------------- begin : Mon Oct 10 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_NEW_H #define ODINDIALOG_NEW_H #include #include class NewMethDialog : public QObject, public GuiDialog { Q_OBJECT public: NewMethDialog(QWidget *parent, JcampDxBlock& files); ~NewMethDialog(); public: void updateWidget(); signals: void valueChanged(); private slots: void done(); void cancel(); void emit_valueChanged(); private: GuiGridLayout* grid; GuiButton* pb_done; GuiButton* pb_cancel; JDXwidget* fileswidget; }; #endif odin-1.8.5/odin/odindialog_new.cpp0000644000175000017500000000237611322062346014025 00000000000000#include "odindialog_new.h" #include "odincomp.h" #include NewMethDialog::NewMethDialog(QWidget *parent, JcampDxBlock& files) : GuiDialog(parent,"Please select a template and a name for the new method",true) { Log odinlog("NewMethDialog","NewMethDialog"); grid=new GuiGridLayout(GuiDialog::get_widget(), 2, 2); fileswidget=new JDXwidget(files,1,GuiDialog::get_widget()); connect(fileswidget,SIGNAL(valueChanged()),this,SLOT(emit_valueChanged())); grid->add_widget( fileswidget, 0, 0, GuiGridLayout::Default, 1, 2 ); pb_cancel = new GuiButton( GuiDialog::get_widget(), this, SLOT(cancel()), "Cancel" ); grid->add_widget( pb_cancel->get_widget(), 1, 0, GuiGridLayout::Center ); pb_done = new GuiButton( GuiDialog::get_widget(), this, SLOT(done()), "Done" ); grid->add_widget( pb_done->get_widget(), 1, 1, GuiGridLayout::Center ); // GuiDialog::show(); } void NewMethDialog::updateWidget() { fileswidget->updateWidget(); } void NewMethDialog::done() { GuiDialog::done(); } void NewMethDialog::cancel() { GuiDialog::cancel(); } void NewMethDialog::emit_valueChanged() { emit valueChanged(); } NewMethDialog::~NewMethDialog() { delete pb_done; delete pb_cancel; delete fileswidget; delete grid; } odin-1.8.5/odin/odinplot.h0000644000175000017500000002104611363773556012354 00000000000000/*************************************************************************** odinplot.h - description ------------------- begin : Mon Jul 26 2004 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef OdinPlot_H #define OdinPlot_H #include #include #include #include #include #include #include "odinplot_vtk.h" #define MIN_HEIGHT_PER_CHAN 120 #define MIN_WIDTH_PER_CHAN 1000 #define CLOSEST_CURVE_MAX 30 #define PLOT_SYMBOLS_MAX_RANGE 10 #define MAX_HIGHRES_INTERVAL 1000.0 #define MAX_MARKER_INTERVAL 400.0 #define MAX_START_RANGE 10000 #define MAGN_PLOT_PAGE_DURATION 20.0 class RangeWidget; // forward declaration ///////////////////////////////////////////////////////////// class PlotView : public QWidget, public SeqSimFeedbackAbstract { Q_OBJECT public: PlotView(const char* method, const STD_string& nucleus, GuiMainWindow* parent); ~PlotView(); const SeqTimecourseData* get_timecourses(); const SeqTimecourseData* get_kspace_trajs(); bool simulate(const STD_string& fidfile, const STD_string& samplefile, ProgressMeter* progmeter); public slots: void replot(); void mouseMovedInPlot0(const QMouseEvent& e) {mouseMovedInPlot(0,e);} void mouseMovedInPlot1(const QMouseEvent& e) {mouseMovedInPlot(1,e);} void mouseMovedInPlot2(const QMouseEvent& e) {mouseMovedInPlot(2,e);} void mouseMovedInPlot3(const QMouseEvent& e) {mouseMovedInPlot(3,e);} void mouseMovedInPlot4(const QMouseEvent& e) {mouseMovedInPlot(4,e);} void mouseMovedInPlot5(const QMouseEvent& e) {mouseMovedInPlot(5,e);} void mouseMovedInPlot6(const QMouseEvent& e) {mouseMovedInPlot(6,e);} void mouseMovedInPlot7(const QMouseEvent& e) {mouseMovedInPlot(7,e);} void mouseMovedInPlot8(const QMouseEvent& e) {mouseMovedInPlot(8,e);} void mousePressedInPlot0(const QMouseEvent& e) {mousePressedInPlot(0,e);} void mousePressedInPlot1(const QMouseEvent& e) {mousePressedInPlot(1,e);} void mousePressedInPlot2(const QMouseEvent& e) {mousePressedInPlot(2,e);} void mousePressedInPlot3(const QMouseEvent& e) {mousePressedInPlot(3,e);} void mousePressedInPlot4(const QMouseEvent& e) {mousePressedInPlot(4,e);} void mousePressedInPlot5(const QMouseEvent& e) {mousePressedInPlot(5,e);} void mousePressedInPlot6(const QMouseEvent& e) {mousePressedInPlot(6,e);} void mousePressedInPlot7(const QMouseEvent& e) {mousePressedInPlot(7,e);} void mousePressedInPlot8(const QMouseEvent& e) {mousePressedInPlot(8,e);} void mouseReleasedInPlot0(const QMouseEvent& e) {mouseReleasedInPlot(0,e);} void mouseReleasedInPlot1(const QMouseEvent& e) {mouseReleasedInPlot(1,e);} void mouseReleasedInPlot2(const QMouseEvent& e) {mouseReleasedInPlot(2,e);} void mouseReleasedInPlot3(const QMouseEvent& e) {mouseReleasedInPlot(3,e);} void mouseReleasedInPlot4(const QMouseEvent& e) {mouseReleasedInPlot(4,e);} void mouseReleasedInPlot5(const QMouseEvent& e) {mouseReleasedInPlot(5,e);} void mouseReleasedInPlot6(const QMouseEvent& e) {mouseReleasedInPlot(6,e);} void mouseReleasedInPlot7(const QMouseEvent& e) {mouseReleasedInPlot(7,e);} void mouseReleasedInPlot8(const QMouseEvent& e) {mouseReleasedInPlot(8,e);} void autoscalePlot0() {autoscale_y(0);} void autoscalePlot1() {autoscale_y(1);} void autoscalePlot2() {autoscale_y(2);} void autoscalePlot3() {autoscale_y(3);} void autoscalePlot4() {autoscale_y(4);} void autoscalePlot5() {autoscale_y(5);} void autoscalePlot6() {autoscale_y(6);} void autoscalePlot7() {autoscale_y(7);} void autoscalePlot8() {autoscale_y(8);} void rescalePlot0(double val) {rescale_y(0,val);} void rescalePlot1(double val) {rescale_y(1,val);} void rescalePlot2(double val) {rescale_y(2,val);} void rescalePlot3(double val) {rescale_y(3,val);} void rescalePlot4(double val) {rescale_y(4,val);} void rescalePlot5(double val) {rescale_y(5,val);} void rescalePlot6(double val) {rescale_y(6,val);} void rescalePlot7(double val) {rescale_y(7,val);} void rescalePlot8(double val) {rescale_y(8,val);} void update_x_axes(); void autoscale_x(); void hide_and_show(); void set_rect_zoom_tool() {set_zoom_tool(rect);} void set_hort_zoom_tool() {set_zoom_tool(horizontal);} void set_vert_zoom_tool() {set_zoom_tool(vertical);} void change_toolbar(); void plot_all(); void osci(); void print(); void save(); void close(); void changeMode(int newmode); void settingsChanged(); void save_closest_curve_data(); void save_current_channel_data(); signals: void setMessage(const char* text); void closeMe(); private: friend class PlotWindow; double get_x(int iplot, int x_pixel); double get_y(int iplot, int y_pixel); void mouseMovedInPlot (int iplot, const QMouseEvent& e); void mousePressedInPlot (int iplot, const QMouseEvent& e); void mouseReleasedInPlot(int iplot, const QMouseEvent& e); void set_range_and_update_x_axes(double min, double max, bool discard_scrollbar=false); void autoscale_all_y(); void autoscale_y(int iplot); void rescale_y(int iplot, double val); void get_plot_label(int iplot, STD_string& label, STD_string& unit) const; void set_plot_labels(bool extra_space=false); void set_curve_pens(bool thick_lines=false); void create_baseline(); void add_plotcurve(const Curve4Qwt& curve); void create_plotcurves(); void add_marker(const Marker4Qwt& marker); void add_tc_marker(const TimecourseMarker4Qwt& marker); void create_markers(); void create_plotcurves_and_markers(); bool create_timecourses(timecourseMode type); void create_timecourse_markers(); void plot_timecourses(timecourseMode type); SeqPlotDataAbstract* plotdata; double totaldur; STD_string nuc; int plot_pressed,x_pressed,y_pressed; static int lastplot_old; double baseline_x[2]; double baseline_y[2]; long curveid_baseline[numof_plotchan]; int closest; int lastplot_closest; int lastcurve_closest; int iplot_cache; GuiToolBar* chan_toolbar; GuiToolBar* zoom_toolbar; GuiToolBar* settings_toolbar; GuiComboBox* plotmode; timecourseMode oldmode; GuiGridLayout* grid; GuiPlot* plotter[numof_plotchan]; GuiWheel* wheel[numof_plotchan]; GuiToolButton* plotflag[numof_plotchan]; // GuiButton* autoscalebutton[numof_plotchan]; GuiToolButton* oscibutton; GuiToolButton* printbutton; GuiToolButton* savebutton; GuiToolButton* closebutton; RangeWidget* x_range; GuiPrinter* printer; GuiToolButton* plotAxes; GuiToolButton* plotMarkers; GuiToolButton* plotGrid; enum zoomMode {rect=0, horizontal, vertical, numof_zoomModes}; void set_zoom_tool(zoomMode mode); GuiToolButton* zoomflag[numof_zoomModes]; long markid_vertzoom; long markid_hortzoom; STD_map curves_map[numof_plotchan]; long timecourse_curve_id[numof_tcmodes][numof_plotchan]; // Stuff for osci JDXenum TriggerType; JDXdouble TriggerWidth; JDXdouble RefreshRate; VtkMagnPlotter* active_magplot; long markid_magplot; int ipage; void plot_vector(double timepoint, float M[3], float* dM); // implementing virtual function of SeqSimFeedbackAbstract }; //////////////////////////////////////// class PlotWindow : public QObject, public GuiMainWindow { Q_OBJECT public: PlotWindow(const char* method, const STD_string& nucleus, QWidget *parent); ~PlotWindow(); const SeqTimecourseData* get_timecourses() {return view->get_timecourses();} const SeqTimecourseData* get_kspace_trajs() {return view->get_kspace_trajs();} bool simulate(const STD_string& fidfile, const STD_string& samplefile, ProgressMeter* progmeter) {return view->simulate(fidfile,samplefile,progmeter);} public slots: void statusBarMessage(const char* text); void close(); private: PlotView* view; }; #endif odin-1.8.5/odin/odindialog_kspace.cpp0000644000175000017500000000616511322062346014502 00000000000000#include #include #include "odindialog_kspace.h" #include "odincomp.h" KspaceDialog::KspaceDialog(QWidget *parent, float kmax, unsigned int nadc) : GuiDialog(parent,"k-Space",false), k0(kmax), progcount(0), canceled(false) { Log odinlog("KspaceDialog","KspaceDialog"); ODINLOG(odinlog,normalDebug) << "kmax/nadc=" << kmax << "/" << nadc << STD_endl; grid=new GuiGridLayout(GuiDialog::get_widget(), 3, 1); int pixsize=KSPACE_INPLANE_SIZE+2*KSPACE_BORDER_SIZE+2*KSPACE_THROUGHPLANE_SIZE; kspace_pixmap_buff=new QPixmap(pixsize, pixsize); kspace_pixmap_buff->fill(_ARRAY_BACKGROUND_COLOR_); painter=new GuiPainter(kspace_pixmap_buff); painter->setPen(_ARRAY_GRID_COLOR_); int rectoffset=KSPACE_BORDER_SIZE+KSPACE_THROUGHPLANE_SIZE; painter->drawRect(rectoffset, rectoffset, KSPACE_INPLANE_SIZE, KSPACE_INPLANE_SIZE); painter->setPen(_ARRAY_GRID_COLOR_, 1, true); painter->moveTo(rectoffset,rectoffset+KSPACE_INPLANE_SIZE/2); painter->lineTo(rectoffset+KSPACE_INPLANE_SIZE,rectoffset+KSPACE_INPLANE_SIZE/2); painter->moveTo(rectoffset+KSPACE_INPLANE_SIZE/2,rectoffset); painter->lineTo(rectoffset+KSPACE_INPLANE_SIZE/2,rectoffset+KSPACE_INPLANE_SIZE); painter->end(); kspace_label=new QLabel(GuiDialog::get_widget()); kspace_label->setPixmap(*kspace_pixmap_buff); grid->add_widget( kspace_label, 0, 0, GuiGridLayout::Center ); progbar=new GuiProgressBar (GuiDialog::get_widget(), nadc); progbar->set_min_width(pixsize); grid->add_widget( progbar->get_widget(), 1, 0, GuiGridLayout::Center ); pb_cancel = new GuiButton( GuiDialog::get_widget(), this, SLOT(cancel()), "Cancel/Close" ); grid->add_widget( pb_cancel->get_widget(), 2, 0, GuiGridLayout::Center ); GuiDialog::show(); } KspaceDialog::~KspaceDialog() { delete pb_cancel; delete kspace_label; delete kspace_pixmap_buff; delete progbar; delete grid; delete painter; } void KspaceDialog::draw_point(float kx, float ky, float kz) { Log odinlog("KspaceDialog","draw_point"); ODINLOG(odinlog,normalDebug) << "kx/ky/kz=" << kx << "/" << ky << "/" << kz << STD_endl; painter->begin(kspace_pixmap_buff); int xpos=kpos2index(kx); int ypos=kpos2index(ky); float relz=secureDivision(-kz,k0); // draw high kz in the foreground xpos+=int(relz*KSPACE_THROUGHPLANE_SIZE+0.5); ypos-=int(relz*KSPACE_THROUGHPLANE_SIZE+0.5); // Start in lower left corner painter->setPen(_ARRAY_FOREGROUND_COLOR1_, 1, false, -relz); // Make foreground brighter painter->drawRect(xpos-KSPACE_POINT_SIZE/2, ypos-KSPACE_POINT_SIZE/2, KSPACE_POINT_SIZE, KSPACE_POINT_SIZE); painter->end(); painter->repaint(kspace_label); progress(); } void KspaceDialog::repaint() { painter->repaint(kspace_label); } void KspaceDialog::progress() { progcount++; progbar->set_progress(progcount); GuiApplication::process_events(); if(canceled) throw OdinCancel(); } void KspaceDialog::cancel() { canceled=true; hide(); } int KspaceDialog::kpos2index(float kpos) const { float relpos=secureDivision(kpos,k0); return KSPACE_BORDER_SIZE+KSPACE_THROUGHPLANE_SIZE+int(0.5*(relpos+1.0)*KSPACE_INPLANE_SIZE); } odin-1.8.5/odin/odinview.h0000644000175000017500000000763311455553540012345 00000000000000/*************************************************************************** odinview.h - description ------------------- begin : Sun Sep 28 21:30:11 CEST 2003 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef OdinView_H #define OdinView_H #include #include #include #include "odinconf.h" #include "odindebugger.h" #include "odinmethod.h" #include "odinplot.h" #define ODIN_MINWIDTH 600 #define MESSAGES_HEIGHT 200 #define IMAGEVIEWER "miview" class ProgressDisplayDialog; // forward declaration class NewMethDialog; // forward declaration class IdeaOpts; // forward declaration class OdinView : public QWidget, public OdinMethodCallback { Q_OBJECT public: OdinView(QWidget *parent); ~OdinView(); void initOdinView(GuiToolBar* action_toolbar, bool has_debug_cmdline); static void usage(); public slots: void new_method(); void open_method(); void close_method(); void exit_odin(); void edit(); void recompile(); bool plot() {return create_seqplot();} void kspace(); void sim(); void geo(); void seqprops(); void seqtree(); void recoinfo(); void pulsars(); void pulsprog(); void gradprog(); void parx(); void pv_pilot(); void pv_scan(); void pv_rgscan(); void pv_howto(); void ideaevents(); void compile_idea(); void export_dlls(); void ideahowto(); void epiccode(); void edit_prefs(); void edit_system(); void load_system(); void edit_study(); void debug_opts(); void show_manual(); void show_apidoc(); void show_seqdoc(); void switch_to_platform_noask(odinPlatform pF); void recalc_method(); void new_geo_pars(); int load_prefs(bool ignore_debugLevels); int react_on_changed_prefs(); int save_prefs(); int save_protocol(); int load_protocol(); void newmeth_rels(); // void changeMethod(int index); signals: void newCaption(const char* text); void newStatus(bool, const char* text); private: void bruker_scan(bool autorg); bool chsrcdir(); bool prepare_method(); bool prepare_acquisition(); bool do_odinreco(const STD_string& outprefix); void update_methodsel(); bool switch_to_platform(odinPlatform pF, bool ask=true); STD_string get_samplefile(); bool create_seqplot(bool for_simulation=false); // implementing virtual functions of OdinMethodCallback void report(bool status, const STD_string& trans_label, const STD_string& message); void create_widgets(); void delete_widgets(); static void odintracefunction(const LogMessage& msg); static GuiTextView* messages_ptr; OdinConf settings; IdeaOpts* ideaopts; OdinMethod method; SeqPlatformProxy platform; GuiGridLayout *grid; GuiComboBox* methodsel; GuiTextView* messages; JDXwidget* seqpars; JDXwidget* commpars; ProgressDisplayDialog* progress; PlotWindow* seqplot; double* signal_x; double* signal_y; JDXfileName templatemeth; JDXstring newmethlabel; NewMethDialog* mewmethwizzard; bool newmethlabel_modified; STD_list subprocs; OdinDebugger debugger; void change_debugger(); }; #endif odin-1.8.5/odin/Makefile.am0000644000175000017500000000301411322062346012361 00000000000000 if GUI_ENABLED INCLUDES = $(all_includes) # Auto-generate any needed moc files %_moc.cpp: %.h $(MOC) -o $@ $< bin_PROGRAMS = odin odin_SOURCES = \ odincomp.cpp odincomp.h \ odinconf.cpp odinconf.h \ odindebugger.cpp odindebugger.h \ odindialog_progress.cpp odindialog_progress.h \ odindialog_process.cpp odindialog_process.h \ odindialog_system.cpp odindialog_system.h odindialog_system_moc.cpp \ odindialog_debug.cpp odindialog_debug.h odindialog_debug_moc.cpp \ odindialog_idea.cpp odindialog_idea.h odindialog_idea_moc.cpp \ odindialog_pulsar.cpp odindialog_pulsar.h odindialog_pulsar_moc.cpp \ odindialog_tree.cpp odindialog_tree.h \ odindialog_kspace.cpp odindialog_kspace.h odindialog_kspace_moc.cpp \ odindialog_new.cpp odindialog_new.h odindialog_new_moc.cpp \ odinmethod.cpp odinmethod.h \ odinplot_range.cpp odinplot_range.h odinplot_range_moc.cpp \ odinplot_vtk.cpp odinplot_vtk.h \ odinplot.cpp odinplot.h odinplot_moc.cpp \ odinview.cpp odinview.h odinview_moc.cpp \ odin.cpp odin.h icons.h odin_moc.cpp \ main.cpp odin_LDADD = ../odinseq/libodinseq.la ../odinqt/libodinqt.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la odin_LDFLAGS = $(VTKLIBS) # Auto-generate manual pages, only if not in srcdir %.1: % if test ! -f $(srcdir)/$@ ; then $(HELP2MAN) --name="$$(./$< --help | grep $<: | sed s/'$<: '//)" ./$< > $@ ; fi # Manual pages for distribution dist_man_MANS = odin.1 dist-hook: -rm -rf $(distdir)/*_moc.cpp endif clean-local: -rm -f *_moc.cpp odin-1.8.5/odin/Makefile.in0000644000175000017500000006424011734622602012406 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ VPATH = @srcdir@ pkgdatadir = $(datadir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ pkglibexecdir = $(libexecdir)/@PACKAGE@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c install_sh_SCRIPT = $(install_sh) -c INSTALL_HEADER = $(INSTALL_DATA) transform = $(program_transform_name) NORMAL_INSTALL = : PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ @GUI_ENABLED_TRUE@bin_PROGRAMS = odin$(EXEEXT) subdir = odin DIST_COMMON = $(dist_man_MANS) $(srcdir)/Makefile.am \ $(srcdir)/Makefile.in ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/configure.in am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) mkinstalldirs = $(install_sh) -d CONFIG_HEADER = $(top_builddir)/tjutils/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(man1dir)" PROGRAMS = $(bin_PROGRAMS) am__odin_SOURCES_DIST = odincomp.cpp odincomp.h odinconf.cpp \ odinconf.h odindebugger.cpp odindebugger.h \ odindialog_progress.cpp odindialog_progress.h \ odindialog_process.cpp odindialog_process.h \ odindialog_system.cpp odindialog_system.h \ odindialog_system_moc.cpp odindialog_debug.cpp \ odindialog_debug.h odindialog_debug_moc.cpp \ odindialog_idea.cpp odindialog_idea.h 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versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/odin/odindialog_idea.h0000644000175000017500000000752311322062346013602 00000000000000/*************************************************************************** odindialog_idea.h - description ------------------- begin : Fri Mar 9 21:30:11 CEST 2007 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_IDEA_H #define ODINDIALOG_IDEA_H // Qt related headers first to avoid ambiguity with 'debug' #include #include #include #include #include #include "odinconf.h" struct IdeaOpts : JcampDxBlock { IdeaOpts(); void set_defaults(const OdinConf& conf, QWidget *parent); STD_string get_vxworks_postfix() const; STD_string get_vxworks_ext() const; STD_string get_vxworks_Makefile() const; STD_string get_vxworks_cxx() const {return odindir+"/bin/cxxwrapper.exe";} STD_string get_ideadir_slash() const {return replaceStr(ideadir,"\\","/");} STD_string get_odindir_slash() const {return replaceStr(odindir,"\\","/");} JDXfileName arch; JDXfileName ideadir; JDXfileName odindir; JDXfileName msvcdir; JDXfileName seqdir; JDXstring odin2idea_label; JDXfileName icedir; JDXenum vxworks_cpu; JDXint vxworks_heap_size; JDXbool debug_vxworks_host; JDXint make_jobs; JDXbool make_clean; // read-only settings JDXfileName vxworks_dir; JDXstring vxworks_flags; JDXstring vxworks_opts; JDXfileName vxworks_path; JDXfileName win_cxx; JDXstring hostd_flags; JDXstring host_flags; }; /////////////////////////////////////////////////////// class IdeaDialog : public QObject, public GuiDialog { Q_OBJECT public: IdeaDialog(QWidget *parent, IdeaOpts& opts, const OdinConf& conf); ~IdeaDialog(); signals: void changed(); private slots: void cancel(); void defaults(); void compile(); void update(); private: void do_compile(); void error_msg(const STD_string& msg); int find_in_alternatives(const STD_string& findstr, const STD_list& alternatives); bool execute_make(const STD_string& make, const STD_string& target); STD_string hosttarget(bool debug, const STD_string& build_includes, const STD_string& global_conf, const STD_string& mprefix, const STD_string& make_install) const; static STD_string errcodes_src(const STD_string& msgfile); IdeaOpts& opts_cache; const OdinConf& conf_cache; GuiGridLayout* grid; GuiButton* pb_cancel; GuiButton* pb_defaults; GuiButton* pb_compile; JDXwidget* optswidget; }; /////////////////////////////////////////////////////// class IdeaMethodDialog : public QObject, public GuiDialog { Q_OBJECT public: IdeaMethodDialog(const STD_string& methdir, sarray& selectedMethods, const STD_string& install_prefix, const IdeaOpts& ideaopts, QWidget *parent); ~IdeaMethodDialog(); private slots: void make(); void emitDone(); private: GuiButton* pb_make; GuiButton* pb_cancel; GuiGridLayout* grid; GuiListView* method_list; STD_list method_checks; sarray& selMeth; STD_string methrootdir; STD_string install_dir; const IdeaOpts& ideaopts_cache; }; #endif odin-1.8.5/odin/odindialog_process.h0000644000175000017500000000266211322062346014355 00000000000000/*************************************************************************** odindialog_process.h - description ------------------- begin : Sun Oct 2 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_PROCESS_H #define ODINDIALOG_PROCESS_H #include // for forkResult #include "odindialog_progress.h" #define TIMER_INTERVAL 100 class ProcessDialog : public ProgressDisplayDialog { public: ProcessDialog(QWidget *parent); int execute_cmds(const svector& command_chain, bool log_std_streams=true); private: void update_progbar(); int progcount; }; #endif odin-1.8.5/odin/odinmethod.cpp0000644000175000017500000001221711322062346013170 00000000000000#include "odinmethod.h" #include "odindialog_process.h" OdinMethod::OdinMethod(const OdinConf& conf, OdinMethodCallback* callback, QWidget* parent4dialog) : StateMachine(&clean), clean (this,"Clean", 0, &OdinMethod::make_clean), compiled(this,"Compiled",&clean, &OdinMethod::clean2compiled), linked (this,"Linked" ,&compiled,&OdinMethod::compiled2linked), settings(conf), cback(callback), parent(parent4dialog) { Log odinlog("OdinMethod","OdinMethod"); register_direct_trans(&linked,&compiled,&OdinMethod::linked2compiled); } bool OdinMethod::make_clean() { Log odinlog("OdinMethod","make_clean"); if(!check_srcdir()) return false; bool result=unlink(); cback->report(result, "make_clean", method.get_status_string()); return result; } bool OdinMethod::clean2compiled() { Log odinlog("OdinMethod","clean2compiled"); if(!check_srcdir()) return false; return make(); } bool OdinMethod::compiled2linked() { Log odinlog("OdinMethod","compiled2linked"); if(!check_srcdir()) return false; STD_string so_name(find_so()); ODINLOG(odinlog,normalDebug) << "so_name=" << so_name << STD_endl; if(!method.load_method_so(so_name)) { cback->report(false, "compiled2linked", "Failed linking shared object "+so_name); return false; } else ODINLOG(odinlog,normalDebug) << "loaded sequence plugin" << STD_endl; int nmeth=method.get_numof_methods(); ODINLOG(odinlog,normalDebug) << "nmeth=" << nmeth << STD_endl; if(nmeth) { if(!method->init()) { cback->report(false, "compiled2linked", method.get_status_string()); return false; } ODINLOG(odinlog,normalDebug) << "init method done" << STD_endl; method->load_sequencePars(seqParsFile()); ODINLOG(odinlog,normalDebug) << "loaded sequencePars" << STD_endl; if(!method->build()) { cback->report(false, "compiled2linked", method.get_status_string()); return false; } ODINLOG(odinlog,normalDebug) << "build method done" << STD_endl; cback->create_widgets(); } cback->report(true, "compiled2linked", method.get_status_string()); return true; } bool OdinMethod::linked2compiled() { Log odinlog("OdinMethod","linked2compiled"); if(!check_srcdir()) return false; return unlink(); } bool OdinMethod::relink() { Log odinlog("OdinMethod","relink"); if(compiled.obtain_state()) return linked.obtain_state(); return false; } STD_string OdinMethod::seqParsFile() { return settings.sourcecode.get_dirname()+SEPARATOR_STR+settings.sourcecode.get_basename_nosuffix()+"_sequencePars"; } bool OdinMethod::unlink() { Log odinlog("OdinMethod","unlink"); if(method.get_numof_methods()) method->write_sequencePars(seqParsFile()); ODINLOG(odinlog,normalDebug) << "sequencePars stored" << STD_endl; ODINLOG(odinlog,normalDebug) << "deleting widgets" << STD_endl; cback->delete_widgets(); ODINLOG(odinlog,normalDebug) << "deleting old methods" << STD_endl; method.delete_methods(); return true; } bool OdinMethod::check_srcdir() { Log odinlog("OdinMethod","check_srcdir"); if(settings.sourcecode=="") { cback->report(false, "check_srcdir", "No method specified"); return false; } STD_string dirname(settings.sourcecode.get_dirname()); ODINLOG(odinlog,normalDebug) << "sourcecode / dirname=" << settings.sourcecode << " / " << dirname << STD_endl; if(!browse_dir(dirname).size()) { ODINLOG(odinlog,normalDebug) << "length(dirname)=0" << STD_endl; cback->report(false, "check_srcdir", "Directory " + dirname + " is invalid"); return false; } if(chpwd(dirname.c_str())) { ODINLOG(odinlog,normalDebug) << "chpwd failed" << STD_endl; cback->report(false, "check_srcdir", "Cannot change directory to " + dirname); return false; } cback->report(true, "check_srcdir", "Ready"); return true; } bool OdinMethod::make() { Log odinlog("OdinMethod","make"); ProcessDialog makedlg(parent); int waitstate=makedlg.execute_cmds(settings.get_method_compile_chain()); bool status=!waitstate; if(waitstate==-2) { cback->report(true,"make","Compilation interrupted"); } if(waitstate==-1) { cback->report(false,"make","Cannot start compiler"); } if(waitstate>0) { cback->report(false,"make","Compilation failed"); } ODINLOG(odinlog,normalDebug) << "status / waitstate = " << status << " / " << waitstate << STD_endl; if(status) cback->report(true, "make_clean", "Compiled"); return status; } STD_string OdinMethod::find_so() { Log odinlog("OdinMethod","find_so"); STD_string result; STD_string methlabel(settings.sourcecode.get_basename_nosuffix()); svector filelist(browse_dir(settings.sourcecode.get_dirname(),false,true)); for(unsigned int i=0; i0) { result=curr_file; break; } } ODINLOG(odinlog,normalDebug) << "result = " << result << STD_endl; return settings.sourcecode.get_dirname()+SEPARATOR_STR+result; } odin-1.8.5/odin/odinplot_range.h0000644000175000017500000000367211322062346013514 00000000000000/*************************************************************************** odinplot_range.h - description ------------------- begin : Wed Oct 12 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINPLOT_RANGE_H #define ODINPLOT_RANGE_H #include #include class QScrollBar; // forward declaration class RangeWidget : public QWidget { Q_OBJECT public: RangeWidget(double total_min, double total_max, double start_min, double start_max, QWidget *parent); ~RangeWidget(); double get_min() {return min_x->get_value();} double get_max() {return max_x->get_value();} // public slots: void set_range(double min, double max, bool discard_scrollbar=false); signals: void new_range(); private slots: void new_scroll_val(int v); void new_minmax_val(float); private: friend class QScrollBar; friend class floatLineEdit; void check_and_set_range(double min, double max); void update_scrollbar(); GuiGridLayout* grid; GuiScrollBar* scrollbar; floatLineEdit *min_x, *max_x; double total_min_cache, total_max_cache; bool react_on_scrollbar_change; }; #endif odin-1.8.5/odin/odindialog_system.cpp0000644000175000017500000000331011322062346014545 00000000000000#include "odindialog_system.h" #include #include SystemDialog::SystemDialog(QWidget *parent) : GuiDialog(parent,"SystemDialog",false), sysInfo_widget(0) { grid = new GuiGridLayout( GuiDialog::get_widget(), 3, 2 ); svector poss_platforms(SeqPlatformProxy::get_possible_platforms()); odinPlatform current_pf=SeqPlatformProxy::get_current_platform(); pf=new enumBox(poss_platforms,GuiDialog::get_widget(),"Platform"); pf->setValue(current_pf); grid->add_widget( pf, 0, 0, GuiGridLayout::Center ); connect( pf, SIGNAL(newVal(int)), this,SLOT(change_platform(int)) ); create_systemInfo_widget(); pb_done = new GuiButton( GuiDialog::get_widget(), this, SLOT(emitDone()), "Done" ); grid->add_widget( pb_done->get_widget(), 2, 1, GuiGridLayout::Center ); // connect( pb_done->get_widget(), SIGNAL(clicked()), this,SLOT(emitDone()) ); this->show(); } SystemDialog::~SystemDialog() { if(sysInfo_widget) delete sysInfo_widget; delete pf; delete pb_done; delete grid; } void SystemDialog::create_systemInfo_widget() { if(sysInfo_widget) delete sysInfo_widget; SeqPlatformProxy platform; sysInfo_widget=new JDXwidget(platform->get_systemInfo(),1,GuiDialog::get_widget()); sysInfo_widget->show(); grid->add_widget( sysInfo_widget, 1, 0, GuiGridLayout::Center, 1, 2 ); connect( sysInfo_widget, SIGNAL(valueChanged()), this,SLOT(emitChanged()) ); } void SystemDialog::emitChanged() { emit new_setting(); } void SystemDialog::emitDone() { emit finished(); GuiDialog::done(); } void SystemDialog::change_platform(int pF) { emit new_platform(odinPlatform(pF)); // change platform before creating new widget create_systemInfo_widget(); } odin-1.8.5/odin/odindialog_process.cpp0000644000175000017500000000440711322062346014707 00000000000000#include "odindialog_process.h" #include #include "odincomp.h" ProcessDialog::ProcessDialog(QWidget *parent) : ProgressDisplayDialog(parent,false) { Log odinlog("ProcessDialog","ProcessDialog"); } void ProcessDialog::update_progbar() { GuiProgressDialog::set_progress(progcount); progcount++; GuiApplication::process_events(); } int ProcessDialog::execute_cmds(const svector& command_chain, bool log_std_streams) { Log odinlog("ProcessDialog","execute_cmds"); int status=0; bool firstcmd=true; progcount=0; if(!command_chain.size()) return status; Process* procs=new Process[command_chain.size()]; // ODINLOG(odinlog,infoLog) << STD_endl; // make sure we start a new line for(unsigned int icmd=0; icmd or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information odin-1.8.5/odin/odin.h0000644000175000017500000002000611322062346011427 00000000000000/*************************************************************************** odin.h - description ------------------- begin : Sun Sep 28 21:30:11 CEST 2003 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef Odin_H #define Odin_H #include "odinview.h" /** * \page odin_doc ODIN user interface for sequence design (odin binary) * * \image html http://od1n.sourceforge.net/screenshots/odin.jpg * * \section odin_intro Introduction * The ODIN user interface is an easy-to-use program to edit, compile, test, and * simulate NMR sequences interactively in a single window. * Thereby the NMR sequence is compiled as a plug-in (shared object on UNIX or DLL * on Windows) and linked into the user interface. After that, the sequence * can be analyzed in various ways (vizualisation, simulation). * This documentation will describe all elements of the user interface * and their functionality to accomplish this task. * * \section odin_qg Quick Guide * A typical session with the ODIN user interface involves the following steps * - Create a new sequence by File->New or open an existing sequence by File->Open * - Compile & Link the sequence by the 'recycling'-symbol in the tool bar (alternatively Action->Compile & Link) * - Edit the sequence paramers * - Visualize the sequence by the 'plot'-symbol in the tool bar (alternatively Action->Plot Sequence) * - Simulate the sequence by the 'oscilloscope'-symbol in the tool bar (alternatively Action->Simulate) * * * \section parfield Parameter Field * After successfully compiling and linking a sequence, the central part * will contain a grid of widgets which contain the sequence parameters. * Each time a parameter is changed, the sequence will be recalculated. * * \section msgbox Message Box * The lower part contains a text field which displays warning/error messages from the * current sequence, compiler errors, etc. * * \section statindicator Status Bar * At the very bottom, the current status of the user interface is indicated by * a green/red light and a short message. For example, if compilation of * the sequence fails, this will be indicated in the Status Bar. * * * \section fileMenu File Menu * \subsection fileMenu_new New * Creates a new sequence by taking the source code of another sequences as a template * \subsection fileMenu_open Open * Opens the source code of a previously used sequence * \subsection fileMenu_close Close * Closes the current sequence * \subsection fileMenu_save Save Settings * Saves the current state of the ODIN user interface (compiler settings, debug levels, sequence parameters, system configuration, ...) * \subsection fileMenu_storeprot Save Protocol * Saves the current measurement protocol in a single protocol file * \subsection fileMenu_loadprot Load Protocol * Loads the current measurement protocol from a single protocol file * \subsection fileMenu_quit Quit * Exit the ODIN user interface * * \section actionMenu Action Menu * All entries in this menu can also be found in the tool bar with the corresponding icon. * \subsection actionMenu_edit Edit * Opens an editor (customizable via Preferences->Settings) to edit the source code of the sequence * \subsection actionMenu_comp Compile & &Link * Compiles the current sequence, and if successful, links it into the ODIN user interface * \subsection actionMenu_geo Geometry * Opens a dialog to edit the current geometry, i.e. slice positioning * \subsection actionMenu_plot Plot Sequence * Plots the sequence using an embedded plotting window * \subsection actionMenu_kspace Acquisition k-Space * Shows the k-Space during acquisition * \subsection actionMenu_sim Simulate * Simulates the current sequence. First, a dialog will pop-up to ask you for * various simulation settings. Then, after loading a virtual sample, a virtual NMR * signal will be created which can then be viewed in the plotting window. The * simulated raw data together with the parameter files is stored under * $HOME/odin-methods//sim. After simulation, the reconstruction is started using the simulated raw data. * * \section infoMenu Info Menu * \subsection infoMenu_prop Sequence Properties * Shows the description of the sequence together with some additional information * \subsection infoMenu_tree Sequence Tree * Displays the sequence tree, i.e. the internal layout of the sequence * \subsection infoMenu_reco Reconstruction Parameters * Displays all parameters used for automatic reconstruction * \subsection infoMenu_pulsars Pulsar Pulses * Displays a list of used SeqPulsar pulses in the current sequence. * By clicking an item in the list, the Pulsar user interface will pop up to show the * parameters of the pulse. * * \section brukerMenu Bruker Menu * \subsection brukerMenu_ppg Pulse Program * Displays the pulse program * \subsection brukerMenu_gp Gradient Program * Displays the gradient program * \subsection brukerMenu_parx PARX parameters * Displays parameters in the PARX parameter space which are used by ODIN * \subsection brukerMenu_pilot Pilot * Start a pilot scan on the host where Paravision is running * \subsection brukerMenu_scan Scan * Start a scan (GOP) on host where Paravision is running using the current sequence settings * * \section siemensMenu Siemens Menu * \subsection siemensMenu_events Event Table * Displays the event blocks and the events therein of the current sequence * \subsection siemensMenu_idea Compile ODIN for IDEA * Compile the ODIN libraries for sequence design for IDEA so that IDEA DLLs can be exported * \subsection siemensMenu_dll Export Siemens DLLs * Create all files/objects necessary to create a Siemens sequence DLL which contains all previously selected ODIN sequences * * \section geMenu GE Menu * \subsection geMenu_events EPIC Code * Generates code for the EPIC framework * * \section prefMenu Preferences Menu * \subsection prefMenu_sett Settings * Edit the Settings of the ODIN user interface * \subsection prefMenu_sys System * Edit the system configuration * \subsection prefMenu_loadsys Load systemInfo * Load the system configuration from a file * \subsection prefMenu_debug Debugging/Tracing * Change the debugging/tracing settings * This option is not available if ODIN was compiled as a release * */ #define IDS_ODIN_ABOUT "ODIN user interface\nVersion " VERSION \ "\n(w) 2004 by Thies Jochimsen\n\n" \ "Compiled with the following plugins:\n" \ PLUGIN_LIBS class Odin : public QObject, public GuiMainWindow { Q_OBJECT public: Odin(); void initOdin(GuiApplication* a, bool has_debug_cmdline); public slots: void changeCaption(const char* text); void changeStatus(bool status, const char* text); private slots: void slotHelpAbout(); private: OdinView *view; GuiPopupMenu *fileMenu; GuiPopupMenu *actionMenu; GuiPopupMenu *infoMenu; GuiPopupMenu *brukerMenu; GuiPopupMenu *siemensMenu; GuiPopupMenu *geMenu; GuiPopupMenu *prefMenu; GuiPopupMenu *helpMenu; GuiToolBar *toolbar; bool old_status; bool first_status; }; #endif odin-1.8.5/odin/odindialog_progress.h0000644000175000017500000000333011322062346014534 00000000000000/*************************************************************************** odindialog_progress.h - description ------------------- begin : Sun Oct 2 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_PROGRESS_H #define ODINDIALOG_PROGRESS_H #include #include struct OdinCancel {}; // exception ///////////////////////////////////////////// class ProgressDisplayDialog : public GuiProgressDialog, public virtual ProgressDisplayDriver { public: ProgressDisplayDialog(QWidget *parent, bool modal = true); void finish(); private: // Implementing virtual functions of ProgressDisplayDriver void init(unsigned int nsteps, const char* txt); void increase(const char*); bool refresh(); int counter; // Getting current progress from GuiProgressDialog does not work in non-percent mode, so we need an extra counter }; #endif odin-1.8.5/odin/odindialog_system.h0000644000175000017500000000315311322062346014217 00000000000000/*************************************************************************** odindialog_system.h - description ------------------- begin : Sun Oct 2 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_SYSTEM_H #define ODINDIALOG_SYSTEM_H #include #include #include class SystemDialog : public QObject, public GuiDialog { Q_OBJECT public: SystemDialog(QWidget *parent); ~SystemDialog(); signals: void new_platform(odinPlatform pF); void new_setting(); void finished(); private slots: void emitDone(); void emitChanged(); void change_platform(int pF); private: void create_systemInfo_widget(); GuiGridLayout* grid; enumBox* pf; GuiButton* pb_done; JDXwidget* sysInfo_widget; }; #endif odin-1.8.5/odin/odindialog_tree.h0000644000175000017500000000321711322062346013633 00000000000000/*************************************************************************** odindialog_tree.h - description ------------------- begin : Mon Oct 10 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_TREE_H #define ODINDIALOG_TREE_H #include #include class TreeDialog : public GuiDialog, public SeqTreeCallbackAbstract { public: TreeDialog(QWidget *parent, const char* caption, const svector& column_labels); ~TreeDialog(); private: // virtual functions from SeqTreeCallbackAbstract void display_node(const SeqClass* thisnode, const SeqClass* parentnode, int treelevel, const svector& columntext); GuiGridLayout* grid; GuiListView* root; STD_map nodemap; STD_map lastitemmap; }; #endif odin-1.8.5/odin/icons.h0000644000175000017500000006351211322062346011622 00000000000000static const char *recompIcon[] = { /* columns rows colors chars-per-pixel */ "22 22 193 2", " c Gray0", ". c Transparent", "X c #010101", "o c Gray1", "O c #070707", "+ c #010801", "@ c #020900", "# c Gray3", "$ c Gray4", "% c #0b0b0b", "& c Gray5", "* c #041203", "= c #061902", "- c #121600", "; c #141400", ": c #161600", "> c #101800", ", c #111113", "< c Gray7", "1 c Gray8", "2 c #151515", "3 c Gray9", "4 c #17171b", "5 c #191919", "6 c Gray10", "7 c Gray11", "8 c #1d1d1d", "9 c Gray12", "0 c #02230b", "q c #082003", "w c #0b2a05", "e c #0d3306", "r c #0a3009", "t c #112405", "y c #142908", "u c #142b0a", "i c #192c0b", "p c #16310c", "a c #17320c", "s c #1a330d", "d c #1b3e0f", "f c #113d10", "g c #1c3f10", "h c #270708", "j c #230806", "k c #250904", "l c #212106", "z c #213b14", "x c Gray13", "c c #222222", "v c Gray14", "b c #252525", "n c Gray16", "m c #2a2a2a", "M c #2c2c2c", "N c Gray18", "B c #2f2f2f", "V c Gray20", "C c #343434", "Z c #353535", "A c #34343a", "S c Gray22", "D c Gray23", "F c #3c3c3c", "G c Gray24", "H c #3f3f47", "J c #15410c", "K c #1c4110", "L c #1d4613", "P c #1e4917", "I c #284919", "U c #215017", "Y c #225118", "T c #275225", "R c #2b5623", "E c #2d582b", "W c #305020", "Q c #315c27", "! c #217316", "~ c #25791e", "^ c #256022", "/ c #296c27", "( c #2a6f2b", ") c #2a732f", "_ c #2c7f39", "` c #366d2f", "' c #337f3a", "] c #490f0e", "[ c #446a3d", "{ c #417036", "} c #407438", "| c Gray25", " . c #414141", ".. c Gray26", "X. c #434343", "o. c Gray27", "O. c #464646", "+. c Gray28", "@. c #414149", "#. c #484848", "$. c #4b4b4b", "%. c #4c4c4c", "&. c Gray30", "*. c #4a4a52", "=. c #505050", "-. c #515151", ";. c #565656", ":. c Gray34", ">. c #52525a", ",. c Gray37", "<. c #426344", "1. c #406641", "2. c #477d40", "3. c #686868", "4. c Gray41", "5. c #6a6a6a", "6. c #6d6d6d", "7. c #6f6f6f", "8. c Gray44", "9. c #717171", "0. c Gray46", "q. c #797979", "w. c #2c813a", "e. c #2d823b", "r. c #2f833c", "t. c #31843e", "y. c #32843f", "u. c #3d8e35", "i. c #2f8b40", "p. c #2f8f46", "a. c #378843", "s. c #3d8f4b", "d. c #3a924c", "f. c #319e52", "g. c #2fa057", "h. c #32a65c", "j. c #32a85d", "k. c #33b364", "l. c #34b464", "z. c #48a92e", "x. c #49a23f", "c. c #52aa3f", "v. c #56ae3b", "b. c #46914f", "n. c #419652", "m. c #50854a", "M. c #46b670", "N. c #47b671", "B. c #55bd7a", "V. c #668a5f", "C. c #628663", "Z. c #63c284", "A. c #63c385", "S. c #64c280", "D. c #65c284", "F. c #6ac684", "G. c #6fc386", "H. c #7dcb8f", "J. c #c7371a", "K. c #818181", "L. c Gray51", "P. c #848484", "I. c #898989", "U. c #8d8d8d", "Y. c #8f8f97", "T. c #9a9a9a", "R. c Gray61", "E. c Gray63", "W. c Gray64", "Q. c #a5a5a5", "!. c #afafaf", "~. c #bcbcbc", "^. c #8ccb84", "/. c #82cd91", "(. c #9dc392", "). c #a3daae", "_. c #b3d7ac", "`. c #b0e1b5", "'. c #b2e0b8", "]. c #b8e2be", "[. c #b9e4bd", "{. c #bee5c1", "}. c #cacaca", "|. c #cbe9cb", " X c #ceecce", ".X c #d4f4d4", "XX c #d8f0d6", "oX c #dbf1d9", "OX c #dff3dd", "+X c #e0f3dd", "@X c #e2f4e1", "#X c #e4f4e1", "$X c None", /* pixels */ "$X$X$X$X$X$X$X$XU Y g K z s ; $X$X$X$X$X$X$X", "$X$X$X$X$X$XL ) D.XX[./.s.2.{ P d $X$X$X$X$X", "$X$X$X$X$XL j.oX].N.r.L t - l ; P y $X$X$X$X", "$X$X$X$X$X) @X'.N.m.; ; $X$X$X$X; y > $X$X$X", "$X$X$X$XL D.|.A.' a $X$X$X$X$X$X$X$Xy ; $X$X", "$X$X$X$X( #X).y.; $X$X$X$X$X$X$X$X$X$X; $X$X", "$X$X$X$X/ +XA.b.y $X$X$X$X$X$X$X$X$X$X$X$X$X", "; d I W g.{.B.y.i ; ; ; $X$X$X$X$X$X$X$X$X$X", "; _ `.OX.XG.n.a.H. Xw.a $X$X$X. 1 $X$X$X$X$X", "$X; ` h.l.f.d.S.w.^ ; $X$X$X. E.o.5 $X$X$X$X", "$X$X; ` p.k.F.w.^ ; $X$X$X. ~.6.P.o.1 $X$X$X", "$X$X$X; } i.w.^ ; $X$X$X. }.6.S $.U.&.5 $X$X", "$X$X$X$X; ` ^ ; $X$X$X. ~.8.C c m &.U.o.1 $X", "$X$X$X$X$X; ; $X$X$XN E.4.o.o.m N N o.8.N % ", "$X$X$X$X$X$X$X$X$X$X. . . . 0.F =.b . . . . ", "$X$X$X$X$X$X$X$X$X$X$X$X$X. I. .;.b $X$X$X$X", "$X$X. $X$X$X$X$X$X$X$X$X$X. E.S =.5 $X$X$X$X", "$X$X. . $X$X$X$X$X$X$X$X. !.4. . .% $X$X$X$X", "$X$X$X. . . $X$X$X$X. . !.P. .$.1 $X$X$X$X$X", "$X$X$X$X% c % 9 . . q.!.K.=.=.N O $X$X$X$X$X", "$X$X$X$X$X. 9 $.4.K.Q.,. .=.& . $X$X$X$X$X$X", "$X$X$X$X$X$X$X% , 5 9 c 9 . $X$X$X$X$X$X$X$X" }; /* static const char *cleanIcon[] = { "22 22 9 1", " c black", ". c navy", "X c #800000", "o c #C00000", "O c #8080FF", "+ c #C0C0FF", "@ c #FFC0C0", "# c gray100", "$ c None", "$$$$$$$$$$$$$$$$+. $$$", "$$$$$$$$$$$$$$$+OO. $$", "$$$$$$$$$$$$$$+OOOO. $", "$$$$$$$$$$$$$+OOOOOO. ", "$$$$$$$$$$$$+OOOOOOOO.", "$$$$$$$$$$$+OOOOOOOOO.", "$$$$$$$$$$+OOOOOOOOO. ", "$$$$$$$$$+OOOOOOOOO. $", "$$$$$$$$+OOOOOOOOO. $$", "$$$$$$$@##OOOOOOO. $$$", "$$$$$$@oo##OOOOO. $$$$", "$$$$$@oooo##OOO. $$$$$", "$$$$@oooooo##O. $$$$$$", "$$$@oooooooo#. $$$$$$$", "$$@oooooooooX $$$$$$$$", "$@oooooooooX $$$$$$$$$", "@@@oooooooX $$$$$$$$$$", "@@@@oooooX $$$$$$$$$$$", "$@@@@oooX $$$$$$$$$$$$", "$$@@@@oX $$$$$$$$$$$$$", "$$$@@@X $$$$$$$$$$$$$$", "$$$$@X $$$$$$$$$$$$$$$" }; */ static const char *editIcon[] = { /* columns rows colors chars-per-pixel */ "22 22 187 2", " c Gray0", ". c #040404", "X c #090909", "o c Gray5", "O c #0e0e0e", "+ c #101010", "@ c #151515", "# c #161616", "$ c Gray9", "% c #32261e", "& c #2e2a22", "* c #36322e", "= c #363232", "- c #422e26", "; c #524636", ": c #5a4e36", "> c #5a4a3e", ", c #724e3a", "< c Gray31", "1 c #505050", "2 c #535353", "3 c #565252", "4 c Gray33", "5 c #565656", "6 c #585858", "7 c #5b5b5b", "8 c Gray37", "9 c #5f5f5f", "0 c #72664e", "q c #776a56", "w c #606060", "e c #626262", "r c Gray39", "t c Gray40", "y c #686868", "u c Gray41", "i c Gray42", "p c #6d6d6d", "a c Gray43", "s c #7e766b", "d c Gray44", "f c Gray45", "g c #747474", "h c #767676", "j c #777777", "k c Gray47", "l c #7b7b7b", "z c Gray", "x c #864a1e", "c c #9a4606", "v c #9e4a06", "b c #8e522a", "n c #8e5e36", "m c #965a3a", "M c #92622e", "N c #9a6636", "B c #a24e06", "V c #ae6232", "C c #ba7a3e", "Z c #877c6e", "A c #897960", "S c #c25e12", "D c #ca6206", "F c #ce6602", "G c #d66a06", "H c #da6e3e", "J c #f27e0e", "K c #e26a2e", "L c #908674", "P c #908675", "I c #938978", "U c #93897a", "Y c #998e7f", "T c #9d907d", "R c #a48f6f", "E c #b68a6a", "W c #b69e7a", "Q c #bc9d70", "! c #bd9f74", "~ c #bda176", "^ c #bda177", "/ c #bda27a", "( c #bea37b", ") c #f68606", "_ c #fa8606", "` c #fe8206", "' c #fe8602", "] c #fe8606", "[ c #fa820a", "{ c #fe8a02", "} c #fe8a06", "| c #fe9632", " . c #c28246", ".. c #ca825e", "X. c #da924e", "o. c #c68662", "O. c #ce8266", "+. c #ea8e5a", "@. c #e29a56", "#. c #ea9a6e", "$. c #faae5e", "%. c #eeb276", "&. c #808080", "*. c Gray51", "=. c #838383", "-. c #868686", ";. c #9d9382", ":. c #a39882", ">. c #a49985", ",. c #ac9d85", "<. c #aea28d", "1. c #afa38e", "2. c #b2a08a", "3. c #b2a38b", "4. c #bea680", "5. c #b9a688", "6. c #bfa885", "7. c #b8a88c", "8. c #beaa89", "9. c #bdaa8d", "0. c #bfab8d", "q. c #b2a690", "w. c #b5a593", "e. c #bbae9c", "r. c #bcb19c", "t. c #caae82", "y. c #c0b29b", "u. c #c8b79f", "i. c #d0ba9a", "p. c #c3b9a6", "a. c #c4bcac", "s. c #c3beb0", "d. c #c5bfb1", "f. c #f2b296", "g. c #f6b696", "h. c #c6c1b6", "j. c #c9c6bf", "k. c #d3c1a8", "l. c #dec6aa", "z. c #dbcbb1", "x. c #dacfbd", "c. c #e2caa2", "v. c #e0c9ae", "b. c #e4cca8", "n. c #e5cda9", "m. c #e6ceaa", "M. c #e7cfb3", "N. c #f6c6aa", "B. c #fecea6", "V. c #fed2b2", "C. c #fedaba", "Z. c #fedebe", "A. c #feeaae", "S. c #cfc9c2", "D. c Gray79", "F. c #d3ccc5", "G. c #d2cec8", "H. c #d3cfcf", "J. c Gray82", "K. c #d3d0d0", "L. c #d6d6d3", "P. c #d5d5d5", "I. c Gray84", "U. c #efe3d3", "Y. c #fee2c6", "T. c #fee6ca", "R. c #f2eada", "E. c #fae6d2", "W. c #feead2", "Q. c #f2eae2", "!. c #f6eee2", "~. c #f4ece4", "^. c #f7efe7", "/. c #f5f1e5", "(. c #f6f2e6", "). c #f7f3eb", "_. c #fef2e2", "`. c #faf2ea", "'. c #faf6ee", "]. c #f9f5f1", "[. c #faf6f6", "{. c #fafaf6", "}. c Gray98", "|. c #fefefa", " X c Gray99", ".X c #fefefe", "XX c None", /* pixels */ "XXXX-.-.=.z k h h d p u t e 9 7 7 2 2 b $.", "XXXX-.D.D.D.D.D.D.D.D.D.D.D.D.D.D.h.< b $.A.", "XXXX=.D..X.X.X.X.X.XI..X.X.X.X.X.Xs.b @.A.| ", "XXXX=.D..X.X.X.X.X.XI..X.X.X.X.X.Xn @.C.| } ", "XXXXz D..X.X.X.X.X.XI..X.X.X.X.XM @.C.| ` ' ", "XXXXk D.I.I.I.I.I.I.I.I.I.I.J.N @.B.| ` ' { ", "XXXXk D..X.X.X.X.X.XI..X.X.XC @.B.| _ ' ) G ", "XXXXh D..X.X.X.X.X.XI..X.X .X.B.| [ ' ) D B ", "XXXXd D..X.X.X.X.X.XI..Xg.%.B.| ' ] ) F v o ", "XXXXd D.I.I.I.I.I.I.I.g.Z.E.#.[ ' ) D v o ", "XXXXp D..X.X.X.X.X.XJ.B._.N.+.J [ F c o ", "XXXXu D..X.X.X.X.X].g.T.C.#.H K S c o ", "XXXXu D..X.X.X|.{.).B.W.g...V b x o $ ", "XXXXt D.I.I.L.H.G.g.Y.f...m b : o q $ ", "XXXXe D..X}.{.'.^.V.N.O.m : & * P A $ XX", "XXXXe D.|.[.`.^.0 E o., > * I T ,.R $ XXXX", "XXXX9 D.{.'./.t.0 % - 3 I ;.1.y.i.W + XXXXXX", "XXXX7 D.F.S.j.0 & = t.s P :.3.5.9.( o XXXXXX", "XXXX7 D./.!.U.; t.Y Z 1.u.z.M.b.c.^ X XXXXXX", "XXXX5 D.Q.R.U.x.e.w.>.k.v.b.b.c.l.! . 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TTTTTLHD Nvzgp95, !!", "! RWWRTILF Nv..pr5, !!", "! RWQWRILF N.zg.95, !!", "! TRWWTILF B.zg.r5, !!", "! .TRTIIHD .vlgp.5> !!", "! .IUILLFZ .vlsp.5> !!", "! L.LLHFZZ.vzkpr9.& !!", "! . . . !!", "! B.ZZZNNm.zkpr95.* !!", "! NN.NNmm. gsp95,&. !!", "! vv.mvvl. sp99<&*. !!", "! zzz.ll.g p965,*#O !!", "! sgg.gg.p 965,*#+X !!", "! pppp..rr 5,>&#+XX !!", "! rr9rr995 ,>&#+XXX !!", "!! !!!", "!!!!!!!!!!!!!!!!!!!!!!", "!!!!!!!!!!!!!!!!!!!!!!" }; static const char * redIcon[] = { "18 18 188 2", " c #FFFFFF", ". c #C2B6B6", "+ c None", "@ c #523030", "# c #371515", "$ c #331515", "% c #473232", "& c #736868", "* c #BAB7B7", "= c #DBD0D0", "- c #754A4A", "; c #4A0F0F", "> c #490F0F", ", c #480F0F", "' c #440F0F", ") c #401010", "! c #3A1010", "~ c #331111", "{ c #2B1212", "] c #594D4D", "^ c #D2D1D1", "/ c #CAB5B5", "( c #591212", "_ c #590E0E", ": c #5A0D0D", "< c #5A0E0E", "[ c #580E0E", "} c #540E0E", "| c #4F0E0E", "1 c #411010", "2 c #391010", "3 c #2F1111", "4 c #281616", "5 c #B9B7B7", "6 c #DFD0D0", "7 c #631111", "8 c #660C0C", "9 c #690C0C", "0 c #6B0C0C", "a c #6A0C0C", "b c #680C0C", "c c #640D0D", "d c #5F0D0D", "e c #500E0E", "f c #460F0F", "g c #3C1010", "h c #311111", "i c #8E4848", "j c #700C0C", "k c #760B0B", "l c #790B0B", "m c #7B0B0B", "n c #780B0B", "o c #740B0B", "p c #6E0C0C", "q c #5D0D0D", "r c #530E0E", "s c #3D1010", "t c #301111", "u c #D3B5B5", "v c #800A0A", "w c #860A0A", "x c #8A0909", "y c #8B0909", "z c #880A0A", "A c #830A0A", "B c #7D0B0B", "C c #600D0D", "D c #3B1010", "E c #2D1111", "F c #AB6363", "G c #8E0909", "H c #950808", "I c #9A0808", "J c #9C0808", "K c #9B0808", "L c #980808", "M c #930909", "N c #820A0A", "O c #770B0B", "P c #510E0E", "Q c #361111", "R c #756868", "S c #972B2B", "T c #A40707", "U c #AA0707", "V c #AC0606", "W c #AC0707", "X c #A80707", "Y c #A10707", "Z c #990808", "` c #4C0F0F", " . c #4A3131", ".. c #940D0D", "+. c #9F0808", "@. c #B30606", "#. c #BA0505", "$. c #BD0505", "%. c #BC0505", "&. c #B70606", "*. c #B00606", "=. c #A50707", "-. c #8D0909", ";. c #7F0A0A", ">. c #710C0C", ",. c #620D0D", "'. c #9D0C0C", "). c #A90707", "!. c #B60606", "~. c #C10505", "{. c #C90404", "]. c #CD0404", "^. c #CC0404", "/. c #C60404", "(. c #B10606", "_. c #960808", ":. c #870A0A", "<. c #3C1414", "[. c #AF2828", "}. c #B20606", "|. c #C00505", "1. c #D80303", "2. c #DE0202", "3. c #DC0202", "4. c #D40303", "5. c #C80404", "6. c #6D0C0C", "7. c #4D0F0F", "8. c #573030", "9. c #C76060", "0. c #B80606", "a. c #C70404", "b. c #D70303", "c. c #E50202", "d. c #EE0101", "e. c #EB0101", "f. c #DF0202", "g. c #D00303", "h. c #910909", "i. c #846666", "j. c #E5B3B3", "k. c #CA0404", "l. c #DB0303", "m. c #FB0000", "n. c #F50000", "o. c #C40505", "p. c #A30707", "q. c #920909", "r. c #610D0D", "s. c #C5B6B6", "t. c #CA4343", "u. c #E70202", "v. c #F10101", "w. c #E10202", "x. c #D20303", "y. c #C20505", "z. c #A20707", "A. c #810A0A", "B. c #7B4A4A", "C. c #F0CECE", "D. c #C30909", "E. c #AD0606", "F. c #9E0808", "G. c #7E0A0A", "H. c #611111", "I. c #DCD0D0", "J. c #E9B3B3", "K. c #C50808", "L. c #D10303", "M. c #BF0505", "N. c #A60707", "O. c #970808", "P. c #6C1010", "Q. c #CDB5B5", "R. c #F1CECE", "S. c #CD4343", "T. c #BB0505", "U. c #8F0909", "V. c #964747", "W. c #E1D0D0", "X. c #E7B3B3", "Y. c #CC6060", "Z. c #B62828", "`. c #A60B0B", " + c #9E0C0C", ".+ c #A02A2A", "++ c #B16262", "@+ c #D6B4B4", "+ + + + + . @ @ # $ % & * + + + + + ", "+ + + = - ; > , ' ) ! ~ { ] ^ + + + ", "+ + / ( _ : < [ } | > 1 2 3 4 5 + + ", "+ 6 7 8 9 0 a b c d [ e f g h 4 ^ + ", "+ i j k l m m n o p 8 q r , s t ] + ", "u n v w x y y z A B o 0 C } , D E * ", "F w G H I J K L M y N O 0 d P ' Q R ", "S M J T U V W X Y Z G N k b : ` s .", "..+.U @.#.$.%.&.*.=.I -.;.>.,.r ' # ", "'.).!.~.{.].^./.$.(.T _.:.n b _ > <.", "[.}.|.].1.2.3.4.5.#.W J -.B 6.q 7.8.", "9.0.a.b.c.d.e.f.g.~.(.Y h.v j C | i.", "j.#.k.l.e.m.n.c.4.o.@.p.q.N >.r.e s.", "+ t.5.1.u.v.d.w.x.y.}.z.h.A.>.C B.+ ", "+ C.D.g.l.w.f.b.k.%.E.F.G G.p H.I.+ ", "+ + J.K.].L.g.{.M.@.N.O.z l P.Q.+ + ", "+ + + R.S.|.|.T.@.X J U.A.V.W.+ + + ", "+ + + + + X.Y.Z.`. +.+++@++ + + + + "}; static const char * greenIcon[] = { "18 18 192 2", " c #FFFFFF", ". c #B6C2B9", "+ c None", "@ c #305239", "# c #15371E", "$ c #15331D", "% c #324737", "& c #68736B", "* c #B7BAB7", "= c #D0DBD3", "- c #4A7556", "; c #0F4A1F", "> c #0F491E", ", c #0F481E", "' c #0F441D", ") c #10401D", "! c #103A1B", "~ c #11331A", "{ c #122B18", "] c #4D5950", "^ c #D1D2D1", "/ c #B5CABB", "( c #125924", "_ c #0E5922", ": c #0D5A22", "< c #0E5A22", "[ c #0E5821", "} c #0E5421", "| c #0E4F20", "1 c #10411D", "2 c #10391B", "3 c #112F19", "4 c #16281B", "5 c #B7B9B7", "6 c #D0DFD4", "7 c #116326", "8 c #0C6624", "9 c #0C6925", "0 c #0C6B25", "a c #0C6A25", "b c #0C6825", "c c #0D6424", "d c #0D5F23", "e c #0E5020", "f c #0F461E", "g c #103C1C", "h c #11311A", "i c #488E5B", "j c #0C7026", "k c #0B7628", "l c #0B7928", "m c #0B7B29", "n c #0B7828", "o c #0B7427", "p c #0C6E26", "q c #0D5D23", "r c #0E5321", "s c #103D1C", "t c #113019", "u c #B5D3BD", "v c #0A802A", "w c #0A862B", "x c #098A2C", "y c #098B2C", "z c #0A882B", "A c #0A832A", "B c #0B7D29", "C c #0D6023", "D c #103B1B", "E c #112D19", "F c #B7BAB8", "G c #63AB76", "H c #098E2D", "I c #08952E", "J c #089A2F", "K c #089C2F", "L c #089B2F", "M c #08982F", "N c #09932D", "O c #0A822A", "P c #0B7728", "Q c #0E5120", "R c #11361A", "S c #68756B", "T c #2B9747", "U c #07A431", "V c #07AA32", "W c #06AC33", "X c #07AC33", "Y c #07A832", "Z c #07A130", "` c #08992F", " . c #0F4C1F", ".. c #314A38", "+. c #0D9430", "@. c #089F30", "#. c #06B334", "$. c #05BA35", "%. c #05BD36", "&. c #05BC36", "*. c #06B735", "=. c #06B033", "-. c #07A531", ";. c #098D2C", ">. c #0A7F29", ",. c #0C7127", "'. c #0D6224", "). c #0E5320", "!. c #0C9D32", "~. c #07A932", "{. c #06B635", "]. c #05C137", "^. c #04C939", "/. c #04CD39", "(. c #04CC39", "_. c #04C638", ":. c #06B134", "<. c #08962E", "[. c #0A872B", "}. c #143C1F", "|. c #28AF4C", "1. c #06B234", "2. c #05C037", "3. c #03D83C", "4. c #02DE3D", "5. c #02DC3C", "6. c #03D43B", "7. c #04C838", "8. c #05BA36", "9. c #0C6D26", "0. c #0F4D1F", "a. c #30573A", "b. c #60C77C", "c. c #06B835", "d. c #04C738", "e. c #03D73B", "f. c #02E53E", "g. c #01EE40", "h. c #01EB40", "i. c #02DF3D", "j. c #03D03A", "k. c #09912D", "l. c #66846E", "m. c #B3E5C0", "n. c #04CA39", "o. c #03DB3C", "p. c #00FB43", "q. c #00F542", "r. c #05C437", "s. c #07A331", "t. c #09922D", "u. c #0D6123", "v. c #B6C5BA", "w. c #43CA67", "x. c #02E73F", "y. c #01F141", "z. c #02E13D", "A. c #03D23A", "B. c #05C237", "C. c #07A231", "D. c #0A812A", "E. c #4A7B57", "F. c #CEF0D7", "G. c #09C33A", "H. c #02E13E", "I. c #06AD33", "J. c #089E30", "K. c #0A7E29", "L. c #116126", "M. c #D0DCD3", "N. c #B3E9C1", "O. c #08C53B", "P. c #03D13A", "Q. c #05BF37", "R. c #07A631", "S. c #08972E", "T. c #106C28", "U. c #B5CDBB", "V. c #CEF1D7", "W. c #43CD68", "X. c #05BB36", "Y. c #098F2D", "Z. c #47965C", "`. c #D0E1D4", " + c #B3E7C1", ".+ c #60CC7D", "++ c #28B64E", "@+ c #0BA634", "#+ c #0C9E32", "$+ c #2AA049", "%+ c #62B177", "&+ c #B4D6BD", "+ + + + + . @ @ # $ % & * + + + + + ", "+ + + = - ; > , ' ) ! ~ { ] ^ + + + ", "+ + / ( _ : < [ } | > 1 2 3 4 5 + + ", "+ 6 7 8 9 0 a b c d [ e f g h 4 ^ + ", "+ i j k l m m n o p 8 q r , s t ] + ", "u n v w x y y z A B o 0 C } , D E F ", "G w H I J K L M N y O P 0 d Q ' R S ", "T N K U V W X Y Z ` H O k b : .s ..", "+.@.V #.$.%.&.*.=.-.J ;.>.,.'.).' # ", "!.~.{.].^./.(._.%.:.U <.[.n b _ > }.", "|.1.2./.3.4.5.6.7.8.X K ;.B 9.q 0.a.", "b.c.d.e.f.g.h.i.j.].:.Z k.v j C | l.", "m.$.n.o.h.p.q.f.6.r.#.s.t.O ,.u.e v.", "+ w.7.3.x.y.g.z.A.B.1.C.k.D.,.C E.+ ", "+ F.G.j.o.H.i.e.n.&.I.J.H K.p L.M.+ ", "+ + N.O./.P.j.^.Q.#.R.S.z l T.U.+ + ", "+ + + V.W.2.2.X.#.Y K Y.D.Z.`.+ + + ", "+ + + + + +.+++@+#+$+%+&++ + + + + "}; /* static const char *recoIcon[] = { "22 22 178 2", " c #000000", ". c #010101", "X c #020202", "o c #030303", "O c #040404", "+ c #050505", "@ c #060606", "# c #080808", "$ c #0A0A0A", "% c #0B0B0B", "& c #0F0F0F", "* c #101010", "= c #111111", "- c #131313", "; c #141414", ": c #151515", "> c #161616", ", c #181818", "< c #191919", "1 c #1A1A1A", "2 c #1B1B1B", "3 c #1C1C1C", "4 c #1D1D1D", "5 c #1E1E1E", "6 c #1F1F1F", "7 c #202020", "8 c #212121", "9 c #222222", "0 c #242424", "q c #252525", "w c #262626", "e c #272727", "r c #282828", "t c #292929", "y c #2B2B2B", "u c #2C2C2C", "i c #2D2D2D", "p c #2E2E2E", "a c #2F2F2F", "s c #303030", "d c #313131", "f c #323232", "g c #333333", "h c #363636", "j c #373737", "k c #393939", "l c #3A3A3A", "z c #3C3C3C", "x c #3D3D3D", "c c #3E3E3E", "v c #3F3F3F", "b c #404040", "n c #414141", "m c #424242", "M c #434343", "N c #444444", "B c #454545", "V c #464646", "C c #474747", "Z c #484848", "A c #494949", "S c #4A4A4A", "D c #4C4C4C", "F c #4D4D4D", "G c #4E4E4E", "H c #4F4F4F", "J c #505050", "K c #515151", "L c #525252", "P c #535353", "I c #545454", "U c #555555", "Y c #575757", "T c #585858", "R c #595959", "E c #5A5A5A", "W c #5B5B5B", "Q c #5C5C5C", "! c #5D5D5D", "~ c #5F5F5F", "^ c #606060", "/ c #616161", "( c #626262", ") c #636363", "_ c #646464", "` c #656565", "' c #666666", "] c #676767", "[ c #686868", "{ c #696969", "} c #6A6A6A", "| c #6B6B6B", " . c #6C6C6C", ".. c #6D6D6D", "X. c #6E6E6E", "o. c #6F6F6F", "O. c #707070", "+. c #717171", "@. c #727272", "#. c #737373", "$. c #747474", "%. c #767676", "&. c #777777", "*. c #787878", "=. c #797979", "-. c #7A7A7A", ";. c #7B7B7B", ":. c #7C7C7C", ">. c #7D7D7D", ",. c #7E7E7E", "<. c #7F7F7F", "1. c #808080", "2. c #818181", "3. c #828282", "4. c #838383", "5. c #848484", "6. c #858585", "7. c #868686", "8. c #878787", "9. c #888888", "0. c #898989", "q. c #8A8A8A", "w. c #8C8C8C", "e. c #8D8D8D", "r. c #8F8F8F", "t. c #909090", "y. c #929292", "u. c #939393", "i. c #959595", "p. c #969696", "a. c #979797", "s. c #989898", "d. c #999999", "f. c #9A9A9A", "g. c #9B9B9B", "h. c #9C9C9C", "j. c #9E9E9E", "k. c #9F9F9F", "l. c #A2A2A2", "z. c #A3A3A3", "x. c #A4A4A4", "c. c #A5A5A5", "v. c #A6A6A6", "b. c #A7A7A7", "n. c #A8A8A8", "m. c #A9A9A9", "M. c #AAAAAA", "N. c #ABABAB", "B. c #ACACAC", "V. c #ADADAD", "C. c #AEAEAE", "Z. c #AFAFAF", "A. c #B0B0B0", "S. c #B1B1B1", "D. c #B2B2B2", "F. c #B4B4B4", "G. c #B5B5B5", "H. c #B6B6B6", "J. c #B7B7B7", "K. c #BABABA", "L. c #BBBBBB", "P. c #BDBDBD", "I. c #BEBEBE", "U. c #C1C1C1", "Y. c #C2C2C2", "T. c #C3C3C3", "R. c #C6C6C6", "E. c #C7C7C7", "W. c #C8C8C8", "Q. c #C9C9C9", "!. c #CECECE", "~. c #D0D0D0", "^. c #D1D1D1", "/. c #DDDDDD", "(. c #DEDEDE", "). c #F0F0F0", "_. c #F4F4F4", "`. c gray100", " O % ; 1 1 ; = O ", " & e r f f e e f f f 6 ", " e l a a a l e 6 e r a n l & ", " j B a C / L B c 8 e 8 f f B C % ", " 8 B r E ,.| | U C C l c C L B L C ", "O j 6 f O.,.%.%.` L ` Q L E / %.c C = ", "; e e B E ..O.2.c.C.F.F.b.%.,.7.a r 8 ", "e = j ..=.,.r.Y.Y.Y.b.2.W.i.f.7.8 C 6 ", "e 1 U 2.,.O.R.~.9.F.R.z.f.c.` 8 & ` f O ", "6 e O.7.,.E 9.b.P.(.C.f.b.C ; ; c U D C f ; ", "8 l ,.9.=.=.| O.(._.9.Q ..; r / %.E n E =.B ", "e l | 2...r.Z.f.~.`.F...j n =.O.%.D B ` D ; ", "r 8 B ` O.f.Y...c.).i.` 9.=.....L B Q i.=.6 ", "1 r f L ` f.C.=.C.W.U 7.Z.7.O.C.i.=.,.Q r.L ", "O n a e D %.2.,.2.j.2.Z.P.W.!.Y.z.F.F.O.2.=.", " 8 7.O.E n a f n E f.Z.b.F.R.j.r.r.j...r.f ", " r ,.c.9.=.7.i.=.` O.,.z.Y.f.f.C.W.%.P.` ", " O D J.r.C.9.O.%./ ,.f.F.9.r.Y.W.b.!.O.", " Q i.7.=.,.r.Q | | =.9.i.b.P.f.| 1 ", " & ,.%.2.=.f./ U E L ,.i./ j 6 ", " O E %.Q %.r.O...Q U i.U O ", " O n ` Q | ,.U E =.E =.1 " }; */ odin-1.8.5/odin/odinplot.cpp0000644000175000017500000012164711363773556012717 00000000000000#include // for QMouseEvent #include // for connecting signals #include #include "odinplot.h" #include "odinplot_range.h" #include "odindialog_progress.h" #include "odincomp.h" #include #include #include static const char *rectIcon[] = { "22 22 3 1", " c black", "# c white", "+ c yellow", /* pixels */ " # ", " ++++++++###+++++++++ ", " + ##### + ", " + # + ", " + # + ", " + # + ", " + # + ", " + # + ", " +# # #+ ", " ## # ## ", "######################", " ## # ## ", " +# # #+ ", " + # + ", " + # + ", " + # + ", " + # + ", " + # + ", " + # + ", " + ##### + ", " ++++++++###+++++++++ ", " # " }; static const char *hortIcon[] = { "22 22 3 1", " c black", "# c white", "+ c yellow", /* pixels */ " ", " + + ", " + + ", " + + ", " + + ", " + + ", " + + ", " + + ", " +# #+ ", " ## ## ", "######################", " ## ## ", " +# #+ ", " + + ", " + + ", " + + ", " + + ", " + + ", " + + ", " + + ", " + + ", " " }; static const char *vertIcon[] = { "22 22 3 1", " c black", "# c white", "+ c yellow", /* pixels */ " # ", " ++++++++###+++++++++ ", " ##### ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " # ", " ##### ", " ++++++++###+++++++++ ", " # " }; ////////////////////////////////////////////// /////////////////////////////////////////////// PlotView::PlotView(const char* method, const STD_string& nucleus, GuiMainWindow* parent ) : QWidget(parent->get_widget()), nuc(nucleus) { Log odinlog("PlotView","PlotView"); int iplot; for(iplot=0; iplotget_plot_data(); if(!plotdata) { ODINLOG(odinlog,errorLog) << "Unable to get plot_data" << STD_endl; return; } ODINLOG(odinlog,normalDebug) << "plotdata->n_frames()=" << plotdata->n_frames() << STD_endl; totaldur=plotdata->get_total_duration(); double min_x_cache=0.0; double max_x_cache=totaldur; if(max_x_cache>MAX_START_RANGE) max_x_cache=MAX_START_RANGE; ODINLOG(odinlog,normalDebug) << "min_x_cache/max_x_cache/totaldur=" << min_x_cache << "/" << max_x_cache << "/" << totaldur << STD_endl; baseline_x[0]=0.0; baseline_x[1]=totaldur; baseline_y[0]=0.0; baseline_y[1]=0.0; for(iplot=0; iplothas_curves_on_channel(plotChannel(iplot)); // default visibility if(iplot==B1re_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot0(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot0(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot0(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot0(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot0()), autoscale_txt); } if(iplot==B1im_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot1(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot1(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot1(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot1(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot1()), autoscale_txt); } if(iplot==rec_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot2(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot2(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot2(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot2(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot2()), autoscale_txt); cbon=false; // override visibilty } if(iplot==signal_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot3(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot3(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot3(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot3(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot3()), autoscale_txt); } if(iplot==freq_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot4(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot4(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot4(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot4(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot4()), autoscale_txt); } if(iplot==phase_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot5(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot5(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot5(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot5(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot5()), autoscale_txt); } if(iplot==Gread_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot6(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot6(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot6(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot6(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot6()), autoscale_txt); } if(iplot==Gphase_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot7(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot7(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot7(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot7(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot7()), autoscale_txt); } if(iplot==Gslice_plotchan) { connect( plotter[iplot], SIGNAL(plotMouseMoved(const QMouseEvent&)), SLOT(mouseMovedInPlot8(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot8(const QMouseEvent&)) ); connect( plotter[iplot], SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot8(const QMouseEvent&)) ); connect( wheel [iplot], SIGNAL(valueChanged(double)), SLOT(rescalePlot8(double)) ); // autoscalebutton[iplot]=new GuiButton(this, this, SLOT(autoscalePlot8()), autoscale_txt); } plotflag[iplot]=new GuiToolButton(chan_toolbar, 0, "", this, SLOT(hide_and_show()), true, cbon ); grid->add_widget( plotter[iplot]->get_widget(), iplot, 0); grid->add_widget( wheel[iplot]->get_widget(), iplot, 1); // grid->add_widget( autoscalebutton[iplot]->get_widget(), iplot, 2); } // canvas_framewidth=plotter[0]->canvas()->lineWidth(); // ODINLOG(odinlog,normalDebug) << "canvas_framewidth=" << canvas_framewidth << STD_endl; x_range=new RangeWidget(0.0,totaldur,min_x_cache,max_x_cache,this); connect( x_range, SIGNAL(new_range()),this, SLOT(update_x_axes()) ); grid->add_widget( x_range, numof_plotchan, 0, GuiGridLayout::Default, 1, 2); chan_toolbar->add_separator(); svector modelabel; modelabel.resize(numof_tcmodes); for(int imode=0; imodeset_current_item(tcmode_curves); oldmode=tcmode_curves; connect( plotmode->get_widget(), SIGNAL(activated(int)),this, SLOT(changeMode(int)) ); chan_toolbar->add_separator(); oscibutton=new GuiToolButton(chan_toolbar, 0, "Osci", this, SLOT(osci())); oscibutton->set_tooltip("Triggered oscilloscope"); printbutton=new GuiToolButton(chan_toolbar, 0, "Print", this, SLOT(print())); printbutton->set_tooltip("Print sequence plot"); savebutton=new GuiToolButton(chan_toolbar, 0, "Save", this, SLOT(save())); savebutton->set_tooltip("Save sequence plot as multi-column ASCII file"); closebutton=new GuiToolButton(chan_toolbar, 0, "Close", this, SLOT(close())); closebutton->set_tooltip("Close sequence plot"); plotAxes =new GuiToolButton(settings_toolbar, 0, "Axes", this, SLOT(settingsChanged()), true, true ); plotMarkers=new GuiToolButton(settings_toolbar, 0, "Markers", this, SLOT(settingsChanged()), true, false ); plotGrid =new GuiToolButton(settings_toolbar, 0, "Grid", this, SLOT(settingsChanged()), true, true ); for(int i=exttrigger_marker; i odinlog("PlotView","~PlotView()"); ODINLOG(odinlog,normalDebug) << "mem(pre )=" << Profiler::get_memory_usage() << STD_endl; plotdata->reset(); // free memory ODINLOG(odinlog,normalDebug) << "mem(post)=" << Profiler::get_memory_usage() << STD_endl; for(unsigned int iplot=0; iplot odinlog("PlotView","close()"); ODINLOG(odinlog,normalDebug) << "mem(pre )=" << Profiler::get_memory_usage() << STD_endl; plotdata->reset(); // free memory ODINLOG(odinlog,normalDebug) << "mem(post)=" << Profiler::get_memory_usage() << STD_endl; emit closeMe(); } void PlotView::changeMode(int newmode) { Log odinlog("PlotView","changeMode"); for(int iplot=0; iplotclear(); } if(newmode>tcmode_curves) { ODINLOG(odinlog,normalDebug) << "Creating timecourse for mode " << newmode << STD_endl; if(!create_timecourses(timecourseMode(newmode))) newmode=oldmode; } if(newmode==tcmode_curves) { ODINLOG(odinlog,normalDebug) << "Creating & Plotting curves" << STD_endl; create_plotcurves_and_markers(); } else { ODINLOG(odinlog,normalDebug) << "Plotting timecourse" << STD_endl; plot_timecourses(timecourseMode(newmode)); } plotmode->set_current_item(newmode); change_toolbar(); set_plot_labels(); bool do_autoscale=true; if(newmode==tcmode_plain && oldmode==tcmode_curves) do_autoscale=false; if(oldmode==tcmode_plain && newmode==tcmode_curves) do_autoscale=false; if(do_autoscale) { autoscale_y(Gread_plotchan); autoscale_y(Gphase_plotchan); autoscale_y(Gslice_plotchan); } replot(); oldmode=timecourseMode(newmode); } void PlotView::change_toolbar() { if(plotmode->get_current_item()==tcmode_curves) { savebutton->set_enabled(false); plotflag[freq_plotchan]->set_enabled(false); plotflag[phase_plotchan]->set_enabled(false); } else { savebutton->set_enabled(true); plotflag[freq_plotchan]->set_enabled(true); plotflag[phase_plotchan]->set_enabled(true); } } void PlotView::create_baseline() { int iplot; for(iplot=0; iplotinsert_curve(false, false, true); plotter[iplot]->set_curve_data(curveid_baseline[iplot],baseline_x,baseline_y,2); } } void PlotView::add_plotcurve(const Curve4Qwt& curve) { double minx=x_range->get_min(); double maxx=x_range->get_max(); if(curve.x[curve.size-1]>=minx && curve.x[0]<=maxx) { long curveid=plotter[curve.channel]->insert_curve(false,curve.spikes); curves_map[curve.channel][curveid]=curve; plotter[curve.channel]->set_curve_data(curveid,curve.x,curve.y,curve.size); } } void PlotView::create_plotcurves() { Log odinlog("PlotView","create_plotcurves"); int iplot; for(iplot=0; iplotclear(); curves_map[iplot].clear(); } create_baseline(); STD_list::const_iterator curves_begin; STD_list::const_iterator curves_end; STD_list::const_iterator curvit; plotdata->get_curves(curves_begin,curves_end,x_range->get_min(),x_range->get_max(),MAX_HIGHRES_INTERVAL); for(curvit=curves_begin; curvit!=curves_end; ++curvit) { add_plotcurve(*curvit); } plotdata->get_signal_curves(curves_begin, curves_end, x_range->get_min(), x_range->get_max()); for(curvit=curves_begin; curvit!=curves_end; ++curvit) { add_plotcurve(*curvit); } set_curve_pens(); } void PlotView::add_marker(const Marker4Qwt& marker) { Log odinlog("PlotView","add_marker"); double minx=x_range->get_min(); double maxx=x_range->get_max(); if(marker.x>=minx && marker.x<=maxx) { for(int iplot=0; iplotinsert_marker(marker.label,marker.x); } } } void PlotView::add_tc_marker(const TimecourseMarker4Qwt& marker) { double minx=x_range->get_min(); double maxx=x_range->get_max(); if(marker.x>=minx && marker.x<=maxx) { for(int iplot=0; iplotinsert_marker(ftos(marker.y[iplot]).c_str(),marker.x); } } } void PlotView::create_markers() { Log odinlog("PlotView","create_markers"); for(int iplot=0; iplotremove_markers(); if(!plotMarkers->is_on()) return; if((x_range->get_max()-x_range->get_min())>MAX_MARKER_INTERVAL) return; timecourseMode type=timecourseMode(plotmode->get_current_item()); if(type==tcmode_curves) { STD_list::const_iterator markers_begin; STD_list::const_iterator markers_end; plotdata->get_markers(markers_begin,markers_end,x_range->get_min(),x_range->get_max()); for(STD_list::const_iterator markit=markers_begin; markit!=markers_end; ++markit) { add_marker(*markit); } } else { STD_list::const_iterator tc_markers_begin; STD_list::const_iterator tc_markers_end; plotdata->get_timecourse_markers(type,tc_markers_begin,tc_markers_end,x_range->get_min(),x_range->get_max()); for(STD_list::const_iterator tc_markit=tc_markers_begin; tc_markit!=tc_markers_end; ++tc_markit) { add_tc_marker(*tc_markit); } } } void PlotView::create_plotcurves_and_markers() { create_plotcurves(); create_markers(); } void PlotView::plot_timecourses(timecourseMode type) { double min=x_range->get_min(); double max=x_range->get_max(); const SeqTimecourseData* subtimecourse=plotdata->get_subtimecourse(type,min, max); if(!subtimecourse) return; bool symbols=( (max-min) < PLOT_SYMBOLS_MAX_RANGE ); for(int iplot=0; iplotclear(); timecourse_curve_id[type][iplot]=plotter[iplot]->insert_curve(false,false); plotter[iplot]->set_curve_data(timecourse_curve_id[type][iplot],subtimecourse->x,subtimecourse->y[iplot],subtimecourse->size,symbols); } set_curve_pens(); create_markers(); } bool PlotView::create_timecourses(timecourseMode type) { Log odinlog("PlotView","create_timecourses"); bool do_plot=true; bool first_time=false; if(!plotdata->timecourse_created(type)) { ProgressDisplayDialog display(this); ProgressMeter progmeter(display); progmeter.new_task(plotdata->n_frames(),"Generating timecourse"); try { plotdata->create_timecourses(type,nuc,&progmeter); } catch(OdinCancel) { ODINLOG(odinlog,normalDebug) << " aborted" << STD_endl; do_plot=false; } display.finish(); first_time=true; } if(do_plot && first_time) { ODINLOG(odinlog,normalDebug) << "autoscaling freq/phase" << STD_endl; autoscale_y(freq_plotchan); autoscale_y(phase_plotchan); } return do_plot; } void PlotView::plot_all() { autoscale_x(); autoscale_all_y(); } void PlotView::autoscale_x() { set_range_and_update_x_axes(0.0,totaldur); replot(); } void PlotView::set_range_and_update_x_axes(double min, double max, bool discard_scrollbar) { x_range->set_range(min,max,discard_scrollbar); update_x_axes(); } void PlotView::autoscale_all_y() { for(int iplot=0; iplot odinlog("PlotView","autoscale_y"); double maxBound; plotter[iplot]->autoscale_y(maxBound); ODINLOG(odinlog,normalDebug) << "maxBound[" << iplot << "]=" << maxBound << STD_endl; wheel[iplot]->set_range(0.01*maxBound,10.0*maxBound); wheel[iplot]->set_value(maxBound); } void PlotView::rescale_y(int iplot, double val) { plotter[iplot]->rescale_y(val); } double PlotView::get_x(int iplot, int x_pixel) {return plotter[iplot]->get_x(x_pixel);} double PlotView::get_y(int iplot, int y_pixel) {return plotter[iplot]->get_y(y_pixel);} void PlotView::mouseMovedInPlot(int iplot, const QMouseEvent& e) { Log odinlog("PlotView","mouseMovedInPlot"); double xpos=get_x(iplot,e.x()); double ypos=get_y(iplot,e.y()); STD_string msg("x="+ftos(xpos)+"\t "+"y="+ftos(ypos)); if(plotmode->get_current_item()==tcmode_curves) { int dist; closest=plotter[iplot]->closest_curve(e.x(),e.y(),dist); // check whether we have a valid plotting curve for(int i=0; i=CLOSEST_CURVE_MAX) closest=0; bool do_replot=true; if(left_button(&e,true)) do_replot=false; ODINLOG(odinlog,normalDebug) << "closest/dist=" << closest << "/" << dist << STD_endl; // remove highlighting from last curve bool different_plot= (lastplot_closest!=iplot); bool different_curve=(lastcurve_closest!=closest); if(lastcurve_closest>0 && (different_plot || different_curve) ) { ODINLOG(odinlog,normalDebug) << "removing highlighting from last curve #" << lastcurve_closest << STD_endl; plotter[lastplot_closest]->highlight_curve(lastcurve_closest,false); if(do_replot) plotter[lastplot_closest]->replot(); } if(closest) { msg+="\t "; const char* curve_label=curves_map[iplot][closest].label; if(curve_label) msg+=curve_label; if(curves_map[iplot][closest].has_freq_phase) { msg+="\t "; msg+="freq="+ftos(curves_map[iplot][closest].freq)+ODIN_FREQ_UNIT; msg+="\t "; msg+="phase="+ftos(curves_map[iplot][closest].phase)+ODIN_ANGLE_UNIT; } if(curves_map[iplot][closest].gradmatrix) { msg+="\t "; msg+="gradmatrix="+curves_map[iplot][closest].gradmatrix->print(); } // highlight closest curve if(closest!=lastcurve_closest) { ODINLOG(odinlog,normalDebug) << "highlighting closest curve #" << closest << STD_endl; plotter[iplot]->highlight_curve(closest,true); if(do_replot) plotter[iplot]->replot(); } } lastplot_closest=iplot; lastcurve_closest=closest; } setMessage(msg.c_str()); } #define IMPOSSIBLE_PIXELVAL -100000 void PlotView::mousePressedInPlot (int iplot, const QMouseEvent& e) { Log odinlog("PlotView","mousePressedInPlot"); markid_vertzoom=0; markid_hortzoom=0; // for some reason, mouse release event is issued twice on MacOS/Qt4/qwt5 so we will process only matched mouse press-release events x_pressed=IMPOSSIBLE_PIXELVAL; y_pressed=IMPOSSIBLE_PIXELVAL; ODINLOG(odinlog,normalDebug) << "iplot=" << iplot << STD_endl; if(left_button(&e,false)) { ODINLOG(odinlog,normalDebug) << "left_button" << STD_endl; // plotter[iplot]->enable_outline(true); plot_pressed=iplot; x_pressed=e.x(); y_pressed=e.y(); if(zoomflag[horizontal]->is_on()) { markid_hortzoom=plotter[iplot]->insert_marker("",get_x(iplot,x_pressed),true,false); plotter[iplot]->replot(); } if(zoomflag[vertical]->is_on()) { markid_vertzoom=plotter[iplot]->insert_marker("",get_y(iplot,y_pressed),true,true); plotter[iplot]->replot(); } ODINLOG(odinlog,normalDebug) << "markid_hortzoom/markid_vertzoom=" << markid_hortzoom << "/" << markid_vertzoom << STD_endl; } if(right_button(&e,false)) { ODINLOG(odinlog,normalDebug) << "right_button" << STD_endl; // plotter[iplot]->enable_outline(false); GuiPopupMenu pm(this); pm.insert_item("Display All", this, SLOT(plot_all())); pm.insert_item("Autoscale x-Axis", this, SLOT(autoscale_x())); if(iplot==0) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot0())); if(iplot==1) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot1())); if(iplot==2) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot2())); if(iplot==3) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot3())); if(iplot==4) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot4())); if(iplot==5) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot5())); if(iplot==6) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot6())); if(iplot==7) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot7())); if(iplot==8) pm.insert_item("Autoscale y-Axis", this, SLOT(autoscalePlot8())); pm.insert_item("Refresh Plot", this, SLOT(replot())); if(closest) { iplot_cache=iplot; if(plotmode->get_current_item()==tcmode_curves) { pm.insert_item(("Save Curve \'"+STD_string(curves_map[iplot_cache][closest].label)+"\'").c_str(), this, SLOT(save_closest_curve_data())); } else { STD_string chanlabel, chanunit; get_plot_label(iplot, chanlabel, chanunit); pm.insert_item(("Save Channel \'"+chanlabel+"\'").c_str(), this, SLOT(save_current_channel_data())); } } ODINLOG(odinlog,normalDebug) << "e.pos=" << e.pos().x() << "/" << e.pos().y() << STD_endl; QPoint pos=plotter[iplot]->get_widget()->mapToGlobal(e.pos()); ODINLOG(odinlog,normalDebug) << "pos=" << pos.x() << "/" << pos.y() << STD_endl; pm.popup(pos); } } void PlotView::mouseReleasedInPlot(int iplot, const QMouseEvent& e) { Log odinlog("PlotView","mouseReleasedInPlot"); if(left_button(&e,false) && iplot==plot_pressed) { if(x_pressed!=IMPOSSIBLE_PIXELVAL && y_pressed!=IMPOSSIBLE_PIXELVAL) { int x_released=e.x(); int y_released=e.y(); int low_x=x_pressed; if(x_releasedupp_x) upp_x=x_released; int upp_y=y_pressed; if(y_released>upp_y) upp_y=y_released; ODINLOG(odinlog,normalDebug) << "low_x/low_y/upp_x/upp_y(" << iplot << ")=" << low_x << "/" << low_y << "/" << upp_x << "/" << upp_y << STD_endl; double y_axis_low=get_y(iplot,upp_y); double y_axis_upp=get_y(iplot,low_y); double x_axis_low=get_x(iplot,low_x); double x_axis_upp=get_x(iplot,upp_x); if(x_axis_lowis_on()) {rescale_y=true; rescale_x=true;} if(zoomflag[horizontal]->is_on()) {rescale_x=true;} if(zoomflag[vertical]->is_on()) {rescale_y=true;} if(rescale_y) plotter[iplot]->set_y_axis_scale(y_axis_low,y_axis_upp); if(rescale_x) set_range_and_update_x_axes(x_axis_low,x_axis_upp); } } if(markid_vertzoom) plotter[iplot]->remove_marker(markid_vertzoom); if(markid_hortzoom) plotter[iplot]->remove_marker(markid_hortzoom); replot(); } // reset x_pressed=IMPOSSIBLE_PIXELVAL; y_pressed=IMPOSSIBLE_PIXELVAL; markid_vertzoom=0; markid_hortzoom=0; } void PlotView::update_x_axes() { Log odinlog("PlotView","update_x_axes"); int iplot; if(plotmode->get_current_item()==tcmode_curves) { create_plotcurves_and_markers(); } else { timecourseMode type=timecourseMode(plotmode->get_current_item()); plot_timecourses(type); } for(iplot=0; iplotset_x_axis_scale(x_range->get_min(),x_range->get_max()); } replot(); } void PlotView::get_plot_label(int iplot, STD_string& label, STD_string& unit) const { STD_string gradunit(timecourseUnit[plotmode->get_current_item()]); STD_string gradprefix(timecoursePrefix[plotmode->get_current_item()]); if(iplot==B1re_plotchan) {label="B1re"; unit=ODIN_FIELD_UNIT;} if(iplot==B1im_plotchan) {label="B1im"; unit=ODIN_FIELD_UNIT;} if(iplot==rec_plotchan) {label="Rec"; unit="";} if(iplot==signal_plotchan) {label="Signal"; unit="";} if(iplot==freq_plotchan) {label="Freq"; unit=ODIN_FREQ_UNIT;} if(iplot==phase_plotchan) {label="Phase"; unit=ODIN_ANGLE_UNIT;} if(iplot==Gread_plotchan) {label=gradprefix+"read"; unit=gradunit;} if(iplot==Gphase_plotchan) {label=gradprefix+"phase"; unit=gradunit;} if(iplot==Gslice_plotchan) {label=gradprefix+"slice"; unit=gradunit;} } void PlotView::set_plot_labels(bool extra_space) { if(plotAxes->is_on()) { STD_string cbtext; STD_string plotunit; for(int iplot=0; iplotset_label(cbtext.c_str()); STD_string axtitle(cbtext); if(plotunit!="")axtitle+=" ["+plotunit+"]"; if(extra_space) axtitle+="\n\n\n\n"; plotter[iplot]->set_y_axis_label(axtitle.c_str()); } } } void PlotView::set_curve_pens(bool thick_lines) { int cpen_width=1; int bpen_width=1; if(thick_lines) { cpen_width=3; bpen_width=2; } for(unsigned iplot=0; iplotget_current_item()==tcmode_curves) { for(STD_map::const_iterator it=curves_map[iplot].begin(); it!=curves_map[iplot].end(); ++it) { plotter[iplot]->set_curve_pen(it->first,_ARRAY_FOREGROUND_COLOR1_,cpen_width); } if(curveid_baseline[iplot]) plotter[iplot]->set_curve_pen(curveid_baseline[iplot],_ARRAY_FOREGROUND_COLOR2_,bpen_width); } else { for(unsigned itc=0; itcset_curve_pen(timecourse_curve_id[itc][iplot],_ARRAY_FOREGROUND_COLOR1_,cpen_width); } } } } void PlotView::hide_and_show() { int lastplot=-1; for(int iplot=0; iplotis_on()) { plotter[iplot]->get_widget()->show(); wheel[iplot]->get_widget()->show(); // autoscalebutton[iplot]->get_widget()->show(); lastplot=iplot; grid->set_row_stretch(iplot,100); } else { plotter[iplot]->get_widget()->hide(); wheel[iplot]->get_widget()->hide(); // autoscalebutton[iplot]->get_widget()->hide(); grid->set_row_stretch(iplot,0); } plotter[iplot]->set_x_axis_label("",true); } // add axis label Time to last plotter if(lastplot>=0) { STD_string axtitle(STD_string("Time [")+ODIN_TIME_UNIT+"]"); plotter[lastplot]->set_x_axis_label(axtitle.c_str()); } if(lastplot_old!=lastplot) { if(lastplot_old>=0) plotter[lastplot_old]->replot(); if(lastplot>=0) plotter[lastplot]->replot(); } lastplot_old=lastplot; } void PlotView::set_zoom_tool(zoomMode mode) { for(int imode=0; imodeset_on(true); else zoomflag[imode]->set_on(false); } int iplot; if(zoomflag[rect]->is_on()) for(iplot=0; iplotset_rect_outline_style(); if(zoomflag[horizontal]->is_on()) for(iplot=0; iplotset_line_outline_style(false); if(zoomflag[vertical]->is_on()) for(iplot=0; iplotset_line_outline_style(true); } void PlotView::replot() { Log odinlog("PlotView","replot"); for(int iplot=0; iplotisOn())*/ plotter[iplot]->replot(); } } const SeqTimecourseData* PlotView::get_timecourses() { if(!create_timecourses(tcmode_plain)) return 0; return plotdata->get_timecourse(tcmode_plain); } const SeqTimecourseData* PlotView::get_kspace_trajs() { if(!create_timecourses(tcmode_kspace)) return 0; return plotdata->get_timecourse(tcmode_kspace); } bool PlotView::simulate(const STD_string& fidfile, const STD_string& samplefile, ProgressMeter* progmeter) { SeqSimFeedbackAbstract* feedback=0; VtkMagnPlotter magplot; // put it on stack so it gets deleted automatically on Cancel if(plotdata->monitor_simulation()) { active_magplot=&magplot; magplot.start(); feedback=this; ipage=-1; // trigger page zoom on first call of plot_vector } else active_magplot=0; if(!plotdata->simulate(fidfile,samplefile,progmeter,feedback)) return false; plotflag[signal_plotchan]->set_on(true); // make signal plotter visible create_plotcurves_and_markers(); // update to show simulated signal autoscale_y(signal_plotchan); hide_and_show(); // plotter[signal_plotchan]->replot(); return true; } void PlotView::plot_vector(double timepoint, float M[3], float* dM) { int iplot; if(active_magplot) { active_magplot->plot_vector(M,dM); bool change_page=false; while( ipage < int(timepoint/MAGN_PLOT_PAGE_DURATION) ) { ipage++; change_page=true; } if(change_page) { set_range_and_update_x_axes(ipage*MAGN_PLOT_PAGE_DURATION,(ipage+1)*MAGN_PLOT_PAGE_DURATION); for(iplot=0; iplotinsert_marker("Simulation",timepoint,false,false,true); } } for(iplot=0; iplotset_marker_pos(markid_magplot,timepoint); } replot(); } } void PlotView::settingsChanged() { for(int iplot=0; iplotenable_axes(plotAxes->is_on()); plotter[iplot]->enable_grid(plotGrid->is_on()); } create_markers(); replot(); } void PlotView::save_closest_curve_data() { if(!closest) return; STD_string fname=get_save_filename("Save Curve as ASCII", "", "", this); if(fname=="") return; STD_ofstream file(fname.c_str()); const Curve4Qwt& closcurve=curves_map[iplot_cache][closest]; if(!closcurve.size) return; double x0=closcurve.x[0]; // substract base time point to avoid round-off errors for(int i=0; iget_current_item()); if(!create_timecourses(type)) return; const SeqTimecourseData* timecourse=plotdata->get_timecourse(type); if(!timecourse) return; STD_string fname=get_save_filename("Save channel as ASCII", "", "", this); if(fname=="") return; STD_ofstream file(fname.c_str()); for(unsigned int i=0; isize; i++) { file << timecourse->x[i] << "\t" << timecourse->y[iplot_cache][i] << "\n"; } file.close(); } void PlotView::osci() { Log odinlog("PlotView","osci"); JcampDxBlock oscisettings("Settings for Oscilloscope"); oscisettings.append(TriggerType); oscisettings.append(TriggerWidth); oscisettings.append(RefreshRate); JDXwidgetDialog* dlg=new JDXwidgetDialog(oscisettings,1,this,true); markType marktype=markType(int(TriggerType)); timecourseMode tc_mode=timecourseMode(plotmode->get_current_item()); dvector timepoints; if(tc_mode==tcmode_curves) { STD_list::const_iterator markers_begin; STD_list::const_iterator markers_end; plotdata->get_markers(markers_begin,markers_end,0.0,totaldur); for(STD_list::const_iterator it=markers_begin; it!=markers_end; ++it) { if(it->type==marktype) timepoints.push_back(it->x); } } else { STD_list::const_iterator tc_markers_begin; STD_list::const_iterator tc_markers_end; plotdata->get_timecourse_markers(tc_mode,tc_markers_begin,tc_markers_end,0.0,totaldur); for(STD_list::const_iterator it=tc_markers_begin; it!=tc_markers_end; ++it) { if(it->type==marktype) timepoints.push_back(it->x); } } ODINLOG(odinlog,normalDebug) << "timepoints=" << timepoints.printbody() << STD_endl; if(timepoints.size()) { ProgressDisplayDialog display(this); ProgressMeter progmeter(display); progmeter.new_task(timepoints.size(),"Oscilloscope"); // cache min/max double minx=x_range->get_min(); double maxx=x_range->get_max(); try { for(unsigned int i=0; i odinlog("PlotView","print"); int iplot; int nplots=0; for(iplot=0; iplotis_on()) nplots++; if(!nplots) return; if(!printer->setup(this)) return; QPainter painter(printer->get_device()); int plotheight=paintdevice_height(printer->get_device())/nplots; int plotwidth =paintdevice_width(printer->get_device()); int hmargin=int(float(plotwidth)/20.0); plotwidth-=2*hmargin; int vmargin=-int(float(plotheight)/20.0); plotheight-=2*vmargin; ODINLOG(odinlog,normalDebug) << "plotheight/plotwidth=" << plotheight << "/" << plotwidth << STD_endl; ODINLOG(odinlog,normalDebug) << "hmargin/vmargin=" << hmargin << "/" << vmargin << STD_endl; // prepare printing set_plot_labels(true); set_curve_pens(true); int plotpos=0; for(iplot=0; iplotis_on()) { int left=hmargin; int top=plotpos*(2*vmargin+plotheight)+vmargin; int width=plotwidth; int height=plotheight; QRect rect( left, top, width, height); ODINLOG(odinlog,normalDebug) << "left/top/width/height[" << plotpos << "]=" << left << "/" << top << "/" << width << "/" << height << STD_endl; plotter[iplot]->print(&painter,rect); plotpos++; } } // reset after printing set_plot_labels(false); set_curve_pens(false); } void PlotView::save() { int iplot; if(plotmode->get_current_item()==tcmode_curves) return; timecourseMode type=timecourseMode(plotmode->get_current_item()); if(!create_timecourses(type)) return; const SeqTimecourseData* timecourse=plotdata->get_timecourse(type); if(!timecourse) return; STD_string fname=get_save_filename("Save plot as ASCII", "", "", this); if(fname=="") return; bool doplot[numof_plotchan]; for(iplot=0; iplotis_on()) doplot[iplot]=true; else doplot[iplot]=false; } STD_ofstream file(fname.c_str()); for(unsigned int i=0; isize; i++) { file << timecourse->x[i] << "\t"; for(iplot=0; iploty[iplot][i] << "\t"; } file << "\n"; } file.close(); } int PlotView::lastplot_old=-1; /////////////////////////////////////////////////////////// PlotWindow::PlotWindow(const char* method, const STD_string& nucleus, QWidget *parent) : GuiMainWindow(parent) { Log odinlog("PlotWindow","PlotWindow"); GuiMainWindow::set_caption(("Sequence Plot of "+STD_string(method)).c_str()); view=new PlotView(method, nucleus,this); connect(view, SIGNAL(setMessage(const char*)),this, SLOT (statusBarMessage(const char*))); connect(view, SIGNAL(closeMe()), this, SLOT (close())); GuiMainWindow::show(view,true); } PlotWindow::~PlotWindow() { Log odinlog("PlotWindow","~PlotWindow"); delete view; } void PlotWindow::statusBarMessage(const char* text) { GuiMainWindow::set_status_message(text); } void PlotWindow::close() { GuiMainWindow::close(); } odin-1.8.5/odin/odinplot_range.cpp0000644000175000017500000000663011322062346014044 00000000000000#include #include "odinplot_range.h" #include "odincomp.h" RangeWidget::RangeWidget(double total_min, double total_max, double start_min, double start_max, QWidget *parent) : QWidget(parent), total_min_cache(total_min), total_max_cache(total_max), react_on_scrollbar_change(true) { grid=new GuiGridLayout(this, 1, 3); grid->set_col_stretch(1,1000); scrollbar=new GuiScrollBar(this); connect(scrollbar->get_widget(), SIGNAL(valueChanged(int)), SLOT(new_scroll_val(int))); grid->add_widget( scrollbar->get_widget(), 0, 1 ); min_x=new floatLineEdit(total_min, total_max, start_min, 5, this, "min_x", 3*TEXTEDIT_WIDTH/2, TEXTEDIT_HEIGHT); max_x=new floatLineEdit(total_min, total_max, start_max, 5, this, "max_x", 3*TEXTEDIT_WIDTH/2, TEXTEDIT_HEIGHT); connect(min_x, SIGNAL(floatLineEditValueChanged(float)), SLOT(new_minmax_val(float))); connect(max_x, SIGNAL(floatLineEditValueChanged(float)), SLOT(new_minmax_val(float))); grid->add_widget( min_x->get_widget(), 0, 0, GuiGridLayout::Center ); grid->add_widget( max_x->get_widget(), 0, 2, GuiGridLayout::Center ); // setFixedHeight(2*min_x->sizeHint().height()); set_range(min_x->get_value(), max_x->get_value()); // initialize scrollbar } RangeWidget::~RangeWidget() { delete grid; } void RangeWidget::update_scrollbar() { Log odinlog("RangeWidget","update_scrollbar"); int scrollmin=int(total_min_cache); int scrollmax=int(total_max_cache); int linestep=int(max_x->get_value()-min_x->get_value())/10; int pagestep=int(max_x->get_value()-min_x->get_value()); int margin=pagestep/2; int value=int(0.5*(max_x->get_value()+min_x->get_value())); if(linestep<=0) linestep=1; if(pagestep<=0) pagestep=1; ODINLOG(odinlog,normalDebug) << "linestep/pagestep/value=" << linestep << "/" << pagestep << "/" << value << STD_endl; scrollbar->set_values(scrollmin+margin, scrollmax-margin, linestep, pagestep, value); } void RangeWidget::check_and_set_range(double min, double max) { Log odinlog("RangeWidget","check_and_set_range"); ODINLOG(odinlog,normalDebug) << "min/max/total_min_cache/total_max_cache=" << min << "/" << max << "/" << total_min_cache << "/" << total_max_cache << STD_endl; if(mintotal_max_cache) max=total_max_cache; if(maxset_value(min); max_x->set_value(max); } void RangeWidget::set_range(double min, double max, bool discard_scrollbar) { Log odinlog("RangeWidget","set_range"); check_and_set_range(min,max); if(!discard_scrollbar) update_scrollbar(); } void RangeWidget::new_scroll_val(int v) { Log odinlog("RangeWidget","new_scroll_val"); if(!react_on_scrollbar_change) return; double timepoint=double(v); double range_half=0.5*(max_x->get_value()-min_x->get_value()); if(timepoint<(total_min_cache+range_half)) timepoint=total_min_cache+range_half; if(timepoint>(total_max_cache-range_half)) timepoint=total_max_cache-range_half; double newmin=timepoint-range_half; double newmax=timepoint+range_half; ODINLOG(odinlog,normalDebug) << "newmin/newmax=" << newmin << "/" << newmax << STD_endl; check_and_set_range(newmin,newmax); emit new_range(); } void RangeWidget::new_minmax_val(float) { check_and_set_range(min_x->get_value(), max_x->get_value()); react_on_scrollbar_change=false; update_scrollbar(); react_on_scrollbar_change=true; emit new_range(); } odin-1.8.5/odin/odinview.cpp0000644000175000017500000006730111455553540012676 00000000000000#include "odinview.h" #include "odindialog_process.h" #include "odindialog_progress.h" #include "odindialog_system.h" #include "odindialog_debug.h" #include "odindialog_pulsar.h" #include "odindialog_tree.h" #include "odindialog_kspace.h" #include "odindialog_new.h" #include "odindialog_idea.h" #include "odincomp.h" #include #include #include //////////////////////////////////////////////////////////// void OdinView::usage() { STD_cout << "odin: Graphical user interface of ODIN" << STD_endl; STD_cout << "Usage: odin [options]" << STD_endl; STD_cout << "Options:" << STD_endl; STD_cout << "\t-c : Do not load configuration" << STD_endl; STD_cout << "\t-cl : Log to shell" << STD_endl; STD_cout << "\t-i : Ignore environment/registry settings" << STD_endl; STD_cout << "\t-m : Root directory of methods" << STD_endl; STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; } OdinView::OdinView(QWidget *parent) : QWidget(parent), settings("settings",isCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-i")), ideaopts(new IdeaOpts), method(settings, this, parent), grid(0), messages(0), seqpars(0), commpars(0), progress(0), seqplot(0),signal_x(0),signal_y(0) { Log odinlog("OdinView","OdinView"); newCaption("empty"); grid = new GuiGridLayout(this, 2, 2, false ); grid->set_row_minsize(0, 2*MESSAGES_HEIGHT); // reserve space for parameter widgets if(!isCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-cl")) { messages=new GuiTextView(this, ODIN_MINWIDTH, MESSAGES_HEIGHT); grid->add_widget( messages->get_widget(), 1, 0, GuiGridLayout::Default, 1, 2 ); messages_ptr=messages; LogBase::set_log_output_function(OdinView::odintracefunction); } } OdinView::~OdinView() { messages_ptr=0; delete ideaopts; } void OdinView::initOdinView(GuiToolBar* action_toolbar, bool has_debug_cmdline) { Log odinlog("OdinView","initOdinView"); // methodsel= new GuiComboBox(action_toolbar, svector() ); // connect( methodsel->get_widget(), SIGNAL(activated(int)),this, SLOT(changeMethod(int)) ); if(!settings.init(this)) { ODINLOG(odinlog,errorLog) << "Unable to initialize settings" << STD_endl; exit(-1); } ODINLOG(odinlog,normalDebug) << "GuiApplication::argc/argv()=" << GuiApplication::argc() << "/" << GuiApplication::argv() << STD_endl; char buff[ODIN_MAXCHAR]; if(!isCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-c")) { ODINLOG(odinlog,normalDebug) << "loading settings" << STD_endl; int loadresult=load_prefs(has_debug_cmdline); settings.set_label("General Settings"); ODINLOG(odinlog,normalDebug) << "loadresult=" << loadresult << STD_endl; if(getCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-m",buff,ODIN_MAXCHAR)) { settings.methroot=STD_string(buff)+SEPARATOR_STR; ODINLOG(odinlog,normalDebug) << "method root dir = >" << buff << "<" << STD_endl; } if( loadresult < 0 ) new_method(); else { //if(chsrcdir()) link(); // emit newStatus(chsrcdir(),SeqMethodProxy::get_status_string()); chsrcdir(); } } else { ODINLOG(odinlog,normalDebug) << "starting in clean mode" << STD_endl; new_method(); } } void OdinView::report(bool status, const STD_string& trans_label, const STD_string& message) { emit newStatus(status,message.c_str()); } void OdinView::create_widgets() { Log odinlog("OdinView","create_widgets"); commpars=new JDXwidget(method->get_commonPars(),1,this,false,(STD_string(method->get_label())+"_").c_str()); commpars->show(); grid->add_widget( commpars, 0, 0, GuiGridLayout::Center ); connect(commpars,SIGNAL(valueChanged()),this,SLOT(recalc_method())); seqpars=new JDXwidget(method->get_methodPars(),1,this,false,(STD_string(method->get_label())+"_").c_str()); seqpars->show(); grid->add_widget( seqpars, 0, 1, GuiGridLayout::Center ); connect(seqpars,SIGNAL(valueChanged()),this,SLOT(recalc_method())); } void OdinView::delete_widgets() { Log odinlog("OdinView","delete_widgets"); if(seqpars) { ODINLOG(odinlog,normalDebug) << "deleting seqpars" << STD_endl; seqpars->hide(); delete seqpars; seqpars=0; } if(commpars) { ODINLOG(odinlog,normalDebug) << "deleting commpars" << STD_endl; commpars->hide(); delete commpars; commpars=0; } } void OdinView::new_method() { Log odinlog("OdinView","new_method"); JcampDxBlock newmethfiles("NewSequence"); templatemeth.set_label("SequenceTemplate"); templatemeth.set_defaultdir(settings.get_seqexamplesdir()); templatemeth.set_suffix("cpp"); newmethlabel.set_label("NewSequenceLabel"); newmethlabel_modified=false; // start with empty fields templatemeth=""; newmethlabel=""; newmethfiles.append(templatemeth); newmethfiles.append(newmethlabel); mewmethwizzard=new NewMethDialog(this, newmethfiles); connect(mewmethwizzard,SIGNAL(valueChanged()),this,SLOT(newmeth_rels())); if(mewmethwizzard->exec()) { ODINLOG(odinlog,normalDebug) << "newmethlabel/templatemeth=" << newmethlabel << "/" << templatemeth << STD_endl; if( STD_string(newmethlabel)!="" && STD_string(templatemeth)!="" ) { createdir(settings.methroot.c_str()); createdir((settings.methroot+SEPARATOR_STR+newmethlabel).c_str()); settings.sourcecode=settings.methroot+SEPARATOR_STR+newmethlabel+SEPARATOR_STR+newmethlabel+".cpp"; ODINLOG(odinlog,normalDebug) << "settings.sourcecode=" << settings.sourcecode << STD_endl; copyfile(templatemeth.c_str(),settings.sourcecode.c_str()); // Create default Makefile SeqMakefile mf(newmethlabel,settings.get_installdir()); ::write(mf.get_Makefile("."),settings.methroot+SEPARATOR_STR+newmethlabel+SEPARATOR_STR+"Makefile"); if(chsrcdir()) { // Delete old sequencePars file STD_string seqparsfile(method.seqParsFile()); ODINLOG(odinlog,normalDebug) << "seqparsfile=" << seqparsfile << STD_endl; if(filesize(seqparsfile.c_str())) rmfile(seqparsfile.c_str()); method.link(); } } } } void OdinView::newmeth_rels() { Log odinlog("OdinView","newmeth_rels"); STD_string template_id=templatemeth.get_basename_nosuffix(); ODINLOG(odinlog,normalDebug) << "templatemeth/newmethlabel/template_id=" << templatemeth << "/" << STD_string(newmethlabel) << "/" << template_id << STD_endl; if(!newmethlabel_modified && STD_string(newmethlabel)=="" && template_id!="" ) { newmethlabel=template_id; ODINLOG(odinlog,normalDebug) << "newmethlabel(pre)=" << STD_string(newmethlabel) << STD_endl; mewmethwizzard->updateWidget(); ODINLOG(odinlog,normalDebug) << "newmethlabel(post)=" << STD_string(newmethlabel) << STD_endl; newmethlabel_modified=true; } } /* void OdinView::changeMethod(int index) { } */ void OdinView::update_methodsel() { /* int nmeth=method.get_numof_methods(); svector methlabel; methlabel.resize(nmeth); for(int i=0; iset_names(methlabel); */ } void OdinView::open_method() { Log odinlog("OdinView","open_method"); JDXfileName fname=get_open_filename("Open Method", settings.methroot.c_str(), (STD_string(settings.sourcecode.get_label())+" (*."+settings.sourcecode.get_suffix()+")").c_str(), this); if(fname!="") { method.clear(); settings.sourcecode=STD_string(fname); // Set methroot accordingly JDXfileName methdir=fname.get_dirname(); settings.methroot=STD_string(methdir.get_dirname()); if(chsrcdir()) method.link(); } } void OdinView::close_method() { Log odinlog("OdinView","close_method"); method.clear(); settings.sourcecode=""; save_prefs(); newCaption("empty"); } void OdinView::exit_odin() { Log odinlog("OdinView","exit_odin"); save_prefs(); // This must be executed before method.clear() so that linked in libs (odindata) still have their debug handler activated method.clear(); // Profiler::dump_final_result(); debugger.detach(); for(STD_list::iterator it=subprocs.begin(); it!=subprocs.end(); ++it) it->kill(); GuiApplication::quit(); } void OdinView::edit() { Log odinlog("OdinView","edit"); settings.open_ascfile(settings.sourcecode,subprocs); } void OdinView::recompile() { Log odinlog("OdinView","recompile"); method.clear(); if(method.compile()) method.link(); } bool OdinView::create_seqplot(bool for_simulation) { #ifdef STANDALONE_PLUGIN Log odinlog("OdinView","create_seqplot"); if(seqplot) delete seqplot; seqplot=0; if(!switch_to_platform(standalone)) return false; // ask for options prior to prepare_method because of coil selection SeqPlotDataAbstract* pd=SeqPlatformProxy()->get_plot_data(); if(!pd) { ODINLOG(odinlog,errorLog) << "Unable to get plot_data" << STD_endl; return false; } // load old config pd->set_coilsdir(settings.get_coilsdir()); pd->get_opts(true,true).load(settings.get_confdir()+SEPARATOR_STR+"plotsimopts"); JDXwidgetDialog* sidlg=new JDXwidgetDialog(pd->get_opts(true,for_simulation),1,this,true); ODINLOG(odinlog,normalDebug) << "sidlg=" << sidlg << STD_endl; // store new config pd->get_opts(true,true).write(settings.get_confdir()+SEPARATOR_STR+"plotsimopts"); if(!prepare_acquisition()) return false; ProgressDisplayDialog display(this); ProgressMeter progmeter(display); bool display_plot=true; try { SeqPlatformProxy()->create_plot_events(&progmeter); } catch(OdinCancel) { ODINLOG(odinlog,infoLog) << " aborted" << STD_endl; display_plot=false; } display.finish(); if(display_plot) { seqplot=new PlotWindow(method->get_label().c_str(), method->get_main_nucleus(), this); } return display_plot; #else return false; #endif } STD_string OdinView::get_samplefile() { Log odinlog("OdinView","get_samplefile"); STD_string fname=get_open_filename("Please select a virtual sample", settings.smpfile.c_str(), "Sample Files (*.smp)", this); if(fname=="") return ""; settings.smpfile=fname; return settings.smpfile; } bool OdinView::do_odinreco(const STD_string& outprefix) { Log odinlog("OdinView","do_odinreco"); STD_string scandir=method->get_systemInfo().get_scandir(); ODINLOG(odinlog,normalDebug) << "scandir=" << scandir << STD_endl; svector cmd_chain; cmd_chain.resize(1); cmd_chain[0]="\""+settings.get_binprefix()+"odinreco\" -ff Hamming -fp 0.8 -f jdx -v 1 -r \""+scandir+"/recoInfo\" -o \""+outprefix+"\""; ODINLOG(odinlog,normalDebug) << "cmd_chain=" << cmd_chain.printbody() << STD_endl; ProcessDialog recoproc(this); int waitstate=recoproc.execute_cmds(cmd_chain); bool status=(!waitstate); return status; } void OdinView::sim() { #ifdef STANDALONE_PLUGIN Log odinlog("OdinView","sim"); if(!create_seqplot(true)) return; STD_string methdir(settings.sourcecode.get_dirname()); STD_string simdir(methdir+SEPARATOR_STR+"sim"+SEPARATOR_STR); createdir(simdir.c_str()); STD_string fidfile(simdir+platform->get_rawfile()); STD_string outfile(simdir+"image"); STD_string sample=get_samplefile(); if(sample=="") return; ProgressDisplayDialog display(this); ProgressMeter progmeter(display); bool do_reco=true; try { if(!seqplot->simulate(fidfile,sample,&progmeter)) do_reco=false; } catch(OdinCancel) { ODINLOG(odinlog,infoLog) << " aborted" << STD_endl; do_reco=false; } display.finish(); Profiler::dump_final_result(); if(do_reco) { method->get_systemInfo().set_scandir(simdir); method->write_meas_contex(simdir); if(!do_odinreco(outfile)) return; Process proc; proc.start("\""+settings.get_binprefix()+IMAGEVIEWER+"\" \""+outfile+".jdx\""); subprocs.push_back(proc); } #endif } void OdinView::geo() { Log odinlog("OdinView","geo"); STD_string geoeditcmd="\""+settings.get_binprefix()+"geoedit\" "; STD_string pilot=platform->pv_pilot_scan(); if(pilot!="") { geoeditcmd+="-blowup 2 -pilot \""+pilot+"\" "; } else { STD_string sample=get_samplefile(); if(sample!="") geoeditcmd+="-sample \""+sample+"\" "; } STD_string geofile=settings.get_tmpdir()+SEPARATOR_STR+"geometryInfo"; geoeditcmd+="\""+geofile+"\""; ODINLOG(odinlog,normalDebug) << "geoeditcmd=" << geoeditcmd << STD_endl; method->write_geometry(geofile); Process proc; proc.start(geoeditcmd,true); // Block odin while geoedit is open subprocs.push_back(proc); method->load_geometry(geofile); new_geo_pars(); } void OdinView::new_geo_pars() { method->get_geometry().update(); recalc_method(); } void OdinView::seqprops() { Log odinlog("OdinView","seqprops"); if(!prepare_method()) return; STD_string msg; msg+=STD_string(method->get_label())+"\n\n"; msg+=STD_string(justificate(method->get_description())+"\n"); msg+="Total Duration : " + ftos(method->get_totalDuration()) + " min\n"; msg+="Number of Acquisitions : " + itos(method->get_numof_acquisitions()) + "\n"; msg+="RF Energy Deposition : "+ftos(method->get_rf_energy())+" a.u.\n"; message_question(msg.c_str(), "Sequence Properies", this); } void OdinView::seqtree() { Log odinlog("OdinView","seqtree"); if(!method.link()) return; svector column_labels; column_labels.resize(4); column_labels[0]="Label"; column_labels[1]="Type"; column_labels[2]="Duration[ms]"; column_labels[3]="Properties"; TreeDialog* treedlg=new TreeDialog(this,"Sequence Tree",column_labels); method->tree(treedlg); treedlg->show(); } void OdinView::recoinfo() { Log odinlog("OdinView","recoinfo"); if(!prepare_acquisition()) return; STD_string fname(settings.get_tmpdir()+SEPARATOR_STR+"recoInfo"); method->write_recoInfo(fname); settings.open_ascfile(fname,subprocs); } void OdinView::pulsars() { Log odinlog("OdinView","pulsars"); if(!prepare_method()) return; STD_string sifname(settings.get_tmpdir()+SEPARATOR_STR+"systemInfo4pulsar"); method->write_systemInfo(sifname); new PulsarDialog(method->get_active_pulsar_pulses(),settings.get_binprefix()+"pulsar",subprocs,settings.get_tmpdir(),sifname,this); } void OdinView::kspace() { #ifdef STANDALONE_PLUGIN Log odinlog("OdinView","kspace"); if(!create_seqplot()) return; const SeqTimecourseData* ktrajs=seqplot->get_kspace_trajs(); if(!ktrajs) return; float kmax=0.0; geometryMode geomode=method->get_geometry().get_Mode(); for(int i=0; iget_commonPars().get_MatrixSize(direction(i)); if(n>1) { float kmaxdir=secureDivision( PII * n , method->get_geometry().get_FOV(direction(i)) ); kmax=STD_max(kmax,kmaxdir); } } } ODINLOG(odinlog,normalDebug) << "kmax/n_rec_points=" << kmax << "/" << ktrajs->n_rec_points << STD_endl; KspaceDialog* kdlg=new KspaceDialog(this,kmax,ktrajs->n_rec_points); try { for(unsigned int i=0; i<(ktrajs->size); i++) { if((ktrajs->y[rec_plotchan][i])>0.0) { kdlg->draw_point(ktrajs->y[Gread_plotchan][i],ktrajs->y[Gphase_plotchan][i],ktrajs->y[Gslice_plotchan][i]); } } } catch(OdinCancel) { ODINLOG(odinlog,infoLog) << " aborted" << STD_endl; delete kdlg; } #endif } void OdinView::pulsprog() { Log odinlog("OdinView","pulsprog"); if(!switch_to_platform(paravision)) return; if(!prepare_method()) return; STD_string fname(settings.get_tmpdir()+SEPARATOR_STR+"pulsprog"); programContext context; context.mode=brukerPpg; STD_string file(platform->get_program(context)); ::write(file,fname); settings.open_ascfile(fname,subprocs); } void OdinView::gradprog() { Log odinlog("OdinView","gradprog"); if(!switch_to_platform(paravision)) return; if(!prepare_method()) return; STD_string fname(settings.get_tmpdir()+SEPARATOR_STR+"gradprog"); programContext context; context.mode=brukerGpg; STD_string file(platform->get_program(context)); ::write(file,fname); settings.open_ascfile(fname,subprocs); } void OdinView::parx() { Log odinlog("OdinView","parx"); if(!switch_to_platform(paravision)) return; if(!prepare_acquisition()) return; STD_string fname(settings.get_tmpdir()+SEPARATOR_STR+"parx"); programContext context; context.mode=brukerParx; STD_string file(platform->get_program(context)); ::write(file,fname); settings.open_ascfile(fname,subprocs); } void OdinView::pv_pilot() { Log odinlog("OdinView","pv_pilot"); method.clear(); // unlink current method if(!switch_to_platform(paravision)) return; ProgressDisplayDialog display(this); ProgressMeter progmeter(display); progmeter.new_task(0, "Pilot Scan"); bool success=false; try { success=platform->pv_pilot(&progmeter); } catch(OdinCancel) { ODINLOG(odinlog,infoLog) << " aborted" << STD_endl; platform->pv_stop(); } display.finish(); if(success) geo(); } void OdinView::bruker_scan(bool autorg) { Log odinlog("OdinView","pv_scan"); if(!switch_to_platform(paravision)) return; if(!prepare_acquisition()) return; ProgressDisplayDialog display(this); ProgressMeter progmeter(display); progmeter.new_task(0, "GOP Scan"); bool success=false; try { success=platform->pv_gop(autorg,&progmeter); } catch(OdinCancel) { ODINLOG(odinlog,infoLog) << " aborted" << STD_endl; platform->pv_stop(); } display.finish(); if(success) { STD_string outprefix=method->get_systemInfo().get_scandir()+"/image"; // Get prefix after clone in pv_gop if(!do_odinreco(outprefix)) return; Process proc; proc.start("\""+settings.get_binprefix()+IMAGEVIEWER+"\" -blowup 2 \""+outprefix+".jdx\""); subprocs.push_back(proc); } } void OdinView::pv_scan() {bruker_scan(false);} void OdinView::pv_rgscan() {bruker_scan(true);} void OdinView::pv_howto() { settings.open_ascfile(settings.get_installdir()+SEPARATOR_STR+"share"+SEPARATOR_STR+"doc"+SEPARATOR_STR+"odin"+SEPARATOR_STR+"Paravision"+SEPARATOR_STR+"HOWTO.txt",subprocs); } void OdinView::ideaevents() { Log odinlog("OdinView","ideaevents"); if(!switch_to_platform(numaris_4)) return; if(!prepare_acquisition()) return; svector column_labels; column_labels.resize(8); column_labels[0]="Event Block / Sequence Object"; column_labels[1]="NCO"; column_labels[2]="RF"; column_labels[3]="Gx"; column_labels[4]="Gy"; column_labels[5]="Gz"; column_labels[6]="ADC"; column_labels[7]="Sync"; TreeDialog* evdlg=new TreeDialog(this,"IDEA events",column_labels); eventContext context; context.action=seqRun; context.event_display=evdlg; method->event(context); evdlg->show(); } void OdinView::ideahowto() { settings.open_ascfile(settings.get_installdir()+SEPARATOR_STR+"share"+SEPARATOR_STR+"doc"+SEPARATOR_STR+"odin"+SEPARATOR_STR+"IDEA_n4"+SEPARATOR_STR+"HOWTO.txt",subprocs); } void OdinView::epiccode() { Log odinlog("OdinView","epiccode"); if(!switch_to_platform(epic)) return; if(!prepare_method()) return; STD_string fname(settings.get_tmpdir()+SEPARATOR_STR+"odin.e"); programContext context; context.mode=epicCode; STD_string file(platform->get_program(context)); ::write(file,fname); settings.open_ascfile(fname,subprocs); } void OdinView::edit_prefs() { Log odinlog("OdinView","edit_prefs"); JDXwidgetDialog* dlg=new JDXwidgetDialog(settings,2,this); connect(dlg,SIGNAL(finished()),this,SLOT(react_on_changed_prefs())); } void OdinView::edit_system() { Log odinlog("OdinView","edit_system"); SystemDialog* dlg=new SystemDialog(this); connect(dlg,SIGNAL(new_setting()),this,SLOT(recalc_method())); connect(dlg,SIGNAL(new_platform(odinPlatform)),this,SLOT(switch_to_platform_noask(odinPlatform))); connect(dlg,SIGNAL(finished()),this,SLOT(save_prefs())); } void OdinView::edit_study() { Log odinlog("OdinView","edit_study"); JDXwidgetDialog* dlg=new JDXwidgetDialog(method->get_studyInfo(),2,this); connect(dlg,SIGNAL(finished()),this,SLOT(react_on_changed_prefs())); } void OdinView::load_system() { Log odinlog("OdinView","load_system"); STD_string fname=get_open_filename("Load systemInfo", settings.get_homedir().c_str(), "", this); if(fname!="") { method->load_systemInfo(fname); recalc_method(); } } void OdinView::debug_opts() { Log odinlog("OdinView","debug_opts"); #ifdef ODIN_DEBUG DebugDialog* dlg=new DebugDialog(this); connect(dlg,SIGNAL(finished()),this,SLOT(save_prefs())); #endif } int OdinView::load_prefs(bool ignore_debugLevels) { Log odinlog("OdinView","load_prefs"); method->load_systemInfo(settings.get_confdir()+SEPARATOR_STR+"systemInfo"); method->load_geometry(settings.get_confdir()+SEPARATOR_STR+"geometryInfo"); method->get_studyInfo().load(settings.get_confdir()+SEPARATOR_STR+"studyInfo"); #ifdef ODIN_DEBUG if(!ignore_debugLevels) { STD_string debugLevels; ::load(debugLevels,settings.get_confdir()+SEPARATOR_STR+"debugLevels"); LogBase::set_levels(debugLevels.c_str()); } #endif int retval=settings.load(settings.get_confdir()+SEPARATOR_STR+"settings"); ODINLOG(odinlog,normalDebug) << "retval=" << retval << STD_endl; change_debugger(); ideaopts->set_defaults(settings,0); // do not ask for IDEA directory ideaopts->load(settings.get_confdir()+SEPARATOR_STR+"ideaopts"); return retval; } int OdinView::react_on_changed_prefs() { Log odinlog("OdinView","react_on_changed_prefs"); change_debugger(); return save_prefs(); } int OdinView::save_prefs() { Log odinlog("OdinView","save_prefs"); ODINLOG(odinlog,normalDebug) << "saving systemInfo" << STD_endl; method->write_systemInfo(settings.get_confdir()+SEPARATOR_STR+"systemInfo"); ODINLOG(odinlog,normalDebug) << "saving geometryInfo" << STD_endl; method->write_geometry(settings.get_confdir()+SEPARATOR_STR+"geometryInfo"); ODINLOG(odinlog,normalDebug) << "saving studyInfo" << STD_endl; method->get_studyInfo().write(settings.get_confdir()+SEPARATOR_STR+"studyInfo"); ODINLOG(odinlog,normalDebug) << "saving debugLevels" << STD_endl; STD_string debugLevels(LogBase::get_levels()); ::write(debugLevels,settings.get_confdir()+SEPARATOR_STR+"debugLevels"); ideaopts->write(settings.get_confdir()+SEPARATOR_STR+"ideaopts"); ODINLOG(odinlog,normalDebug) << "saving settings" << STD_endl; JcampDxBlock prefs; prefs.merge(settings); return prefs.write(settings.get_confdir()+SEPARATOR_STR+"settings"); } int OdinView::save_protocol() { Log odinlog("OdinView","save_protocol"); if(!method.link()) return -1; STD_string fname=get_save_filename("Store Protocol", settings.protfile.c_str(), "ODIN Protocols (*.pro)", this); if(fname=="") return 0; ODINLOG(odinlog,normalDebug) << "fname=" << fname << STD_endl; settings.protfile=fname; return method->write_protocol(fname); } int OdinView::load_protocol() { Log odinlog("OdinView","load_protocol"); if(!method.link()) return -1; STD_string fname=get_open_filename("Load Protocol", settings.protfile.c_str(), "ODIN Protocols (protocol *.pro)", this); if(fname=="") return 0; settings.protfile=fname; int result=method->load_protocol(fname); if(result>=0) method.relink(); return result; } void OdinView::compile_idea() { IdeaDialog* dlg=new IdeaDialog(this, *ideaopts, settings); connect(dlg,SIGNAL(changed()),this,SLOT(save_prefs())); } void OdinView::export_dlls() { JDXfileName testfile(ideaopts->odindir+SEPARATOR_STR+"build_complete_tag"); if(!testfile.exists()) { message_question(justificate("Cannot find compiled ODIN for IDEA installation under "+ideaopts->odindir+". Please create it first using the following dialog.").c_str(), "ODIN for IDEA not found", this, false, true); compile_idea(); } new IdeaMethodDialog(settings.methroot,settings.selectedMethods,settings.get_installdir(), *ideaopts, this); } void OdinView::show_manual() {settings.display_html(settings.get_manual_location()+"odin_doc.html",subprocs);} void OdinView::show_apidoc() {settings.display_html(settings.get_manual_location()+"index.html",subprocs);} void OdinView::show_seqdoc() {settings.display_html(settings.get_manual_location()+"group__odinseq.html",subprocs);} bool OdinView::chsrcdir() { Log odinlog("OdinView","chsrcdir"); method.clear(); bool result=method.check_srcdir(); if(result) { save_prefs(); newCaption(settings.sourcecode.get_basename_nosuffix().c_str()); } ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } bool OdinView::prepare_method() { Log odinlog("OdinView","prepare_method"); bool result=true; if(!method.link()) return result=false; else { method->clear(); if(!method->prepare()) result=false; } return result; } bool OdinView::prepare_acquisition() { Log odinlog("OdinView","prepare_acquisition"); bool result=prepare_method(); if(result) result=method->prep_acquisition(); return result; } void OdinView::recalc_method() { Log odinlog("OdinView","recalc_method"); if(!method.link()) return; if(seqplot) delete seqplot; seqplot=0; if(!method->clear()) { ODINLOG(odinlog,errorLog) << "clear() failed" << STD_endl; // emit newStatus(false,SeqMethodProxy::get_status_string()); return; } if(!method->build()) { ODINLOG(odinlog,errorLog) << "build() failed" << STD_endl; // emit newStatus(false,SeqMethodProxy::get_status_string()); return; } ODINLOG(odinlog,normalDebug) << "updating seqpars/commpars=" << seqpars << "/" << commpars << STD_endl; if(seqpars) seqpars->updateWidget(); if(commpars) commpars->updateWidget(); } void OdinView::odintracefunction(const LogMessage& msg) { if(messages_ptr) { // Do not use code in here which uses Log STD_string msgstr=msg.str(0, false); int msglength=msgstr.length(); if(msgstr[msglength-1]=='\n') msgstr=msgstr.substr(0,msglength-1); // remove endl because lines are wrapped by GuiTextView // catch compiler warnings logPriority level=msg.level; if(msgstr.find("warning:")!=STD_string::npos) level=warningLog; if(msgstr.find("error:") !=STD_string::npos) level=errorLog; // Replace any tag braces msgstr=replaceStr(msgstr, "<","<"); msgstr=replaceStr(msgstr, ">",">"); /* for(unsigned int i=0; i') msgstr[i]=']'; } */ // color-code log level if(level==errorLog) msgstr=""+msgstr+""; else if(level==warningLog) msgstr=""+msgstr+""; else msgstr=""+msgstr+""; messages_ptr->append_text(msgstr.c_str()); } else { default_tracefunction(msg); // fall back to console } } GuiTextView* OdinView::messages_ptr=0; void OdinView::switch_to_platform_noask(odinPlatform pF) { switch_to_platform(pF,false); } bool OdinView::switch_to_platform(odinPlatform pF, bool ask) { Log odinlog("OdinView","switch_to_platform"); bool result=true; if(ask) { if(method->get_systemInfo().get_platform()==pF) return true; STD_string pFstring(SeqPlatformProxy::get_possible_platforms()[pF]); STD_string msg=justificate("In order to perform the operation, the platform must be switched to "+pFstring+". Should it be switched now? (You can switch it back by the Preferences->System menu entry.)"); result=message_question(msg.c_str(), "Switching Platform", this, true); } if(result) { platform.set_current_platform(pF); method.relink(); } return result; } void OdinView::change_debugger() { Log odinlog("OdinView","change_debugger"); if(settings.attachDebugger) debugger.attach(); else debugger.detach(); } odin-1.8.5/odin/odinplot_vtk.h0000644000175000017500000000360711322062346013222 00000000000000/*************************************************************************** odinplot_vtk.h - description ------------------- begin : Tue Jul 26 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINPLOT_VTK_H #define ODINPLOT_VTK_H #include #include // forward declarations of vtk classes class vtkRenderer; class vtkRenderWindow; class vtkRenderWindowInteractor; class vtkPolyDataMapper; class vtkActor; class vtkAxes; class vtkTubeFilter; class vtkActor; class vtkArrowSource; ///////////////////////////////////////////////////// class VtkMagnPlotter { public: VtkMagnPlotter(); ~VtkMagnPlotter(); void start(); void plot_vector(float M[3], float* dM); void interact(); private: vtkRenderer* renderer; vtkRenderWindow* renWin; vtkRenderWindowInteractor* iren; vtkArrowSource* magnArrow; vtkPolyDataMapper* magnMapper; vtkActor* magnActor; vtkActor* magnGradActor; vtkAxes* axes; vtkTubeFilter* axesTubes; vtkPolyDataMapper* axesMapper; vtkActor* axesActor; bool magnGradActor_added; }; #endif odin-1.8.5/odin/odindialog_kspace.h0000644000175000017500000000371111322062346014141 00000000000000/*************************************************************************** odindialog_kspace.h - description ------------------- begin : Mon Oct 10 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_KSPACE_H #define ODINDIALOG_KSPACE_H #include #include #include "odindialog_progress.h" // for OdinCancel #define KSPACE_POINT_SIZE 3 #define KSPACE_INPLANE_SIZE 512 #define KSPACE_THROUGHPLANE_SIZE 128 #define KSPACE_BORDER_SIZE 50 class KspaceDialog : public QObject, public GuiDialog { Q_OBJECT public: KspaceDialog(QWidget *parent, float kmax, unsigned int nadc); ~KspaceDialog(); void draw_point(float kx, float ky, float kz); protected: void repaint(); // overloaded from GuiDialog void close() {canceled=true;} // overloaded from GuiDialog private slots: void cancel(); private: int kpos2index(float kpos) const; void progress(); GuiGridLayout* grid; GuiButton* pb_cancel; QLabel* kspace_label; QPixmap* kspace_pixmap_buff; GuiProgressBar* progbar; GuiPainter* painter; float k0; int progcount; bool canceled; }; #endif odin-1.8.5/odin/odinmethod.h0000644000175000017500000000717011322062346012637 00000000000000/*************************************************************************** odinmethod.h - description ------------------- begin : Sun Dec 25 21:30:11 CEST 2005 copyright : (C) 2005 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef OdinMethod_H #define OdinMethod_H #include #include #include "odincomp.h" #include "odinconf.h" class QWidget; // forward declaration ////////////////////////////////////////////////////////////////////// /* State diagram for OdinMethod, i.e. for compiling/linking of sequences: Possible transitions between states are indicated by the corresponding member functions that perform the transition. clean <-------\ | | | clear() | compile() | | | V | | compiled ------| /---------\ | | | | | | | | link() | | | relink() | | | | V | | | | V | linked --------' ---------' */ ////////////////////////////////////////////////////////////////////// /** * * Callback to report success/failure of state transitions * */ struct OdinMethodCallback { virtual void report(bool status, const STD_string& trans_label, const STD_string& message) = 0; virtual void create_widgets() = 0; virtual void delete_widgets() = 0; }; ////////////////////////////////////////////////////////////////////// /** * * State machine to handle compiling and linking of sequences * */ class OdinMethod : public StateMachine { public: OdinMethod(const OdinConf& conf, OdinMethodCallback* callback, QWidget* parent4dialog); /** * Performs state transition to 'clean' */ bool clear() {return clean.obtain_state();} /** * Performs state transition to 'compiled' */ bool compile() {return compiled.obtain_state();} /** * Performs state transition to 'linked' */ bool link() {return linked.obtain_state();} /** * Relinks the sequence into process space */ bool relink(); /** * Returns pointer to the encapsulated method */ SeqMethod* operator -> () {return method.get_current_method();} /** * Returns true if valid source code is present */ bool check_srcdir(); /** * Location of sequencePars file for this method */ STD_string seqParsFile(); private: // states and their transition functions: State clean; bool make_clean(); State compiled; bool clean2compiled(); State linked; bool compiled2linked(); bool linked2compiled(); // helpers: bool unlink(); bool make(); STD_string find_so(); SeqMethodProxy method; // stuff passed in during construction const OdinConf& settings; OdinMethodCallback* cback; QWidget* parent; }; #endif odin-1.8.5/odin/odindialog_debug.h0000644000175000017500000000277211322062346013767 00000000000000/*************************************************************************** odindialog_debug.h - description ------------------- begin : Sun Oct 3 21:30:11 CEST 2005 copyright : (C) 2003 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINDIALOG_DEBUG_H #define ODINDIALOG_DEBUG_H #include #include class DebugDialog : public QObject, public GuiDialog { Q_OBJECT public: DebugDialog(QWidget *parent); ~DebugDialog(); signals: void finished(); private slots: void emitDone(); void levelChanged(int); private: friend class QComboBox; friend class QPushButton; GuiGridLayout* grid; GuiButton* pb_done; STD_list debugenums; }; #endif odin-1.8.5/odin/odin.cpp0000644000175000017500000001352211455553540011777 00000000000000#include "odin.h" #include "icons.h" #include "odincomp.h" Odin::Odin() : old_status(true), first_status(true) { Log odinlog("Odin","Odin"); set_status_xpm(greenIcon); // init once view=new OdinView(GuiMainWindow::get_widget()); connect(view,SIGNAL(newCaption(const char*)),this,SLOT(changeCaption(const char*))); connect(view,SIGNAL(newStatus(bool,const char*)),this,SLOT(changeStatus(bool,const char*))); fileMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); fileMenu->insert_item("&New", view, SLOT(new_method()), Qt::CTRL+Qt::Key_N); fileMenu->insert_item("&Open", view, SLOT(open_method()), Qt::CTRL+Qt::Key_O); fileMenu->insert_item("&Close", view, SLOT(close_method()), Qt::CTRL+Qt::Key_W); fileMenu->insert_item("&Save Settings", view, SLOT(save_prefs()), Qt::CTRL+Qt::Key_S); fileMenu->insert_item("S&tore Protocol", view, SLOT(save_protocol()), Qt::CTRL+Qt::Key_T); fileMenu->insert_item("&Load Protocol", view, SLOT(load_protocol()), Qt::CTRL+Qt::Key_L); fileMenu->insert_item("&Quit", view, SLOT(exit_odin()), Qt::CTRL+Qt::Key_Q); toolbar = new GuiToolBar(this, "Action"); actionMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); new GuiToolButton(toolbar, editIcon, "Edit", view, SLOT(edit())); actionMenu->insert_item("Edit", view, SLOT(edit()), Qt::Key_F1); new GuiToolButton(toolbar, recompIcon, "Compile & Link", view, SLOT(recompile())); actionMenu->insert_item("Compile and &Link", view, SLOT(recompile()), Qt::Key_F2); new GuiToolButton(toolbar, geoIcon, "Geometry", view, SLOT(geo())); actionMenu->insert_item("Geometry", view, SLOT(geo()), Qt::Key_F3); #ifdef STANDALONE_PLUGIN new GuiToolButton(toolbar, plotIcon, "Plot Sequence", view, SLOT(plot())); actionMenu->insert_item("Plot Sequence", view, SLOT(plot()), Qt::Key_F4); new GuiToolButton(toolbar, kspaceIcon, "k-Space", view, SLOT(kspace())); actionMenu->insert_item("Acquisition k-Space", view, SLOT(kspace()), Qt::Key_F5); new GuiToolButton(toolbar, simIcon, "Simulate", view, SLOT(sim())); actionMenu->insert_item("Simulate", view, SLOT(sim()), Qt::Key_F6); #endif infoMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); infoMenu->insert_item("Sequence Properties", view, SLOT(seqprops())); infoMenu->insert_item("Sequence &Tree", view, SLOT(seqtree())); infoMenu->insert_item("Reconstruction Parameters", view, SLOT(recoinfo())); infoMenu->insert_item("P&ulsar Pulses", view, SLOT(pulsars())); brukerMenu=0; #ifdef PARAVISION_PLUGIN brukerMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); brukerMenu->insert_item("&Pulse Program", view, SLOT(pulsprog()), Qt::CTRL+Qt::Key_P); brukerMenu->insert_item("&Gradient Program", view, SLOT(gradprog()), Qt::CTRL+Qt::Key_G); brukerMenu->insert_item("P&ARX parameters", view, SLOT(parx()), Qt::CTRL+Qt::Key_A); brukerMenu->insert_item("Pilot", view, SLOT(pv_pilot())); brukerMenu->insert_item("Scan", view, SLOT(pv_scan())); brukerMenu->insert_item("AutoRG and Scan", view, SLOT(pv_rgscan())); brukerMenu->insert_item("&Show HOWTO", view, SLOT(pv_howto())); #endif siemensMenu=0; #ifdef IDEA_PLUGIN siemensMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); siemensMenu->insert_item("&Event Table", view, SLOT(ideaevents()), Qt::CTRL+Qt::Key_E); #ifdef USING_WIN32 siemensMenu->insert_item("&Compile ODIN for IDEA", view, SLOT(compile_idea())); siemensMenu->insert_item("E&xport DLLs", view, SLOT(export_dlls()), Qt::CTRL+Qt::Key_X); #endif siemensMenu->insert_item("&Show HOWTO", view, SLOT(ideahowto())); #endif geMenu=0; #ifdef EPIC_PLUGIN geMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); geMenu->insert_item("EPIC Code", view, SLOT(epiccode())); #endif prefMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); prefMenu->insert_item("Settings", view, SLOT(edit_prefs())); prefMenu->insert_item("System", view, SLOT(edit_system())); prefMenu->insert_item("Load systemInfo", view, SLOT(load_system())); prefMenu->insert_item("Study", view, SLOT(edit_study())); #ifdef ODIN_DEBUG prefMenu->insert_item("Debugging/Tracing", view, SLOT(debug_opts())); #endif helpMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); helpMenu->insert_item("User Manual", view, SLOT(show_manual())); helpMenu->insert_item("Programmers Manual", view, SLOT(show_apidoc())); helpMenu->insert_item("Documentation for Seq... Classes", view, SLOT(show_seqdoc())); helpMenu->insert_item("About...", this, SLOT(slotHelpAbout())); GuiMainWindow::insert_menu("File", fileMenu); GuiMainWindow::insert_menu("Action", actionMenu); GuiMainWindow::insert_menu("Info", infoMenu); if(brukerMenu) GuiMainWindow::insert_menu("Bruker", brukerMenu); if(siemensMenu) GuiMainWindow::insert_menu("Siemens", siemensMenu); if(geMenu) GuiMainWindow::insert_menu("GE", geMenu); GuiMainWindow::insert_menu("Preferences", prefMenu); GuiMainWindow::insert_menu_separator(); GuiMainWindow::insert_menu("Help", helpMenu); GuiMainWindow::show(view); } void Odin::initOdin(GuiApplication* a, bool has_debug_cmdline) { Log odinlog("Odin","initOdin"); view->initOdinView(toolbar,has_debug_cmdline); connect( a->get_object(),SIGNAL(aboutToQuit()), view,SLOT(exit_odin()) ); } void Odin::changeCaption(const char* text) { GuiMainWindow::set_caption((STD_string("Odin " VERSION) + " - " + text).c_str()); } void Odin::changeStatus(bool status, const char* text) { Log odinlog("OdinView","changeStatus"); old_status=status; first_status=false; if(status) { GuiMainWindow::set_status_xpm(greenIcon); if(text) GuiMainWindow::set_status_message(text); } else { STD_string msg="Error"; if(text && STD_string(text)!="") msg+=STD_string(" - ")+text; GuiMainWindow::set_status_xpm(redIcon); GuiMainWindow::set_status_message(msg.c_str()); } } void Odin::slotHelpAbout() { message_question(IDS_ODIN_ABOUT, "About...", GuiMainWindow::get_widget()); } odin-1.8.5/depcomp0000755000175000017500000004426711734622601010773 00000000000000#! /bin/sh # depcomp - compile a program generating dependencies as side-effects scriptversion=2009-04-28.21; # UTC # Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free # Software Foundation, Inc. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . case $1 in '') echo "$0: No command. Try \`$0 --help' for more information." 1>&2 exit 1; ;; -h | --h*) cat <<\EOF Usage: depcomp [--help] [--version] PROGRAM [ARGS] Run PROGRAMS ARGS to compile a file, generating dependencies as side-effects. Environment variables: depmode Dependency tracking mode. source Source file read by `PROGRAMS ARGS'. object Object file output by `PROGRAMS ARGS'. DEPDIR directory where to store dependencies. depfile Dependency file to output. tmpdepfile Temporary file to use when outputing dependencies. libtool Whether libtool is used (yes/no). Report bugs to . EOF exit $? ;; -v | --v*) echo "depcomp $scriptversion" exit $? ;; esac if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. depfile=${depfile-`echo "$object" | sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. We # parameterize here, but still list the modes in the big case below, # to make depend.m4 easier to write. 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However on # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c # ICC 7.0 will fill foo.d with something like # foo.o: sub/foo.c # foo.o: sub/foo.h # which is wrong. We want: # sub/foo.o: sub/foo.c # sub/foo.o: sub/foo.h # sub/foo.c: # sub/foo.h: # ICC 7.1 will output # foo.o: sub/foo.c sub/foo.h # and will wrap long lines using \ : # foo.o: sub/foo.c ... \ # sub/foo.h ... \ # ... "$@" -MD -MF "$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" # Each line is of the form `foo.o: dependent.h', # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process this invocation # correctly. 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"$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi # Remove `-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done test -z "$dashmflag" && dashmflag=-M # Require at least two characters before searching for `:' # in the target name. This is to cope with DOS-style filenames: # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise. "$@" $dashmflag | sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" rm -f "$depfile" cat < "$tmpdepfile" > "$depfile" tr ' ' ' ' < "$tmpdepfile" | \ ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; dashXmstdout) # This case only exists to satisfy depend.m4. 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"$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test "X$1" != 'X--mode=compile'; do shift done shift fi IFS=" " for arg do case "$arg" in -o) shift ;; $object) shift ;; "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift shift ;; *) set fnord "$@" "$arg" shift shift ;; esac done "$@" -E 2>/dev/null | sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" echo " " >> "$depfile" sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; msvcmsys) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; none) exec "$@" ;; *) echo "Unknown depmode $depmode" 1>&2 exit 1 ;; esac exit 0 # Local Variables: # mode: shell-script # sh-indentation: 2 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: odin-1.8.5/sequences/0000755000175000017500000000000011735135552011461 500000000000000odin-1.8.5/sequences/tj_gesse.cpp0000644000175000017500000003053511363773557013730 00000000000000 // include the headers of all sequence classes #include // The whole EPI sequence (including reco) is a C++ class class METHOD_CLASS : public SeqMethod { private: JDXint NumOfEchoes; JDXfloat PulseDur; JDXint NumOfSatPulses; JDXdoubleArr TEs; // sequence objects which are the elementary objects // to build the EPI sequence SeqPulsar exc; SeqPulsarReph exc_reph; SeqPulsar refoc; SeqSat fatsat; SeqAcqRead ge_acq; SeqAcqRead se_acq; SeqAcqDeph deph; SeqObjList ge_preacq; SeqObjList se_preacq; SeqAcqDeph reph; SeqDelay sedelay; SeqGradTrapezParallel rewind; SeqGradPhaseEnc pe,pe_rewind; SeqVecIter phaseiter; SeqObjLoop sliceloop; SeqObjLoop peloop; SeqObjLoop reploop; SeqObjLoop echoloop; SeqObjLoop dummyloop; SeqDelay trdelay; SeqObjVector gerewindvec; SeqObjList gepart; SeqDelay gepart_dummy; SeqObjVector serewindvec; SeqObjList separt; SeqDelay separt_dummy; SeqObjList scan; SeqObjList imagingpart; SeqObjList dummypart; SeqObjList slicepart; SeqObjList slicepart_dummy; SeqObjList preppart; SeqDelay exc2acq; SeqDelay exc2refoc; SeqDelay refoc2acq; SeqGradConstPulse spoiler; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; public: // This constructor creates an empty EPI sequence METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("GESSE sequence."); } void method_pars_init() { // In this function, parameters are initialized and default values are set commonPars->set_MatrixSize(readDirection,128); commonPars->set_MatrixSize(phaseDirection,128,noedit); commonPars->set_NumOfRepetitions(1); commonPars->set_RepetitionTime(1000.0); commonPars->set_AcqSweepWidth(100.0); // commonPars->set_ReductionFactor(3); NumOfEchoes=32; NumOfEchoes.set_description("Number of echoes per period"); append_parameter(NumOfEchoes,"NumOfEchoes"); PulseDur=4.0; // start with large duration so that sequence can be loaded PulseDur.set_unit(ODIN_TIME_UNIT); PulseDur.set_description("Pulse duration of excitation and refocusing pulse"); append_parameter(PulseDur,"PulseDur"); NumOfSatPulses=2; NumOfSatPulses.set_description("Number of consecutive saturation pulses"); append_parameter(NumOfSatPulses,"NumOfSatPulses"); TEs.resize(2*NumOfEchoes); TEs.set_description("Echo times"); append_parameter(TEs,"TEs"); } void method_seq_init() { Log odinlog(this,"method_seq_init"); if(NumOfEchoes<2) NumOfEchoes=2; ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float slicegap=geometryInfo->get_sliceDistance()-slicethick; // excitation pulse exc=SeqPulsarSinc("exc",slicethick,false,PulseDur,commonPars->get_FlipAngle()); dvector exclist=systemInfo->get_gamma() * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector(); ODINLOG(odinlog,normalDebug) << "exclist=" << exclist << STD_endl; exc.set_freqlist( exclist ); exc.set_pulse_type(excitation); exc_reph=SeqPulsarReph("exc_reph",exc); // Slightly thicker refocusing slice for better SNR // Since the same spatial resolution is used for exc and refoc, the gradient strengths will be the same float extra_slicethick_refoc=STD_min(0.5*slicethick, 0.3*slicegap); // refocusing pulse refoc=SeqPulsarSinc("refoc",slicethick+extra_slicethick_refoc,false,PulseDur,180.0); dvector refoclist=systemInfo->get_gamma() * refoc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector(); ODINLOG(odinlog,normalDebug) << "refoclist=" << refoclist << STD_endl; refoc.set_freqlist( refoclist ); if(!commonPars->get_RFSpoiling()) refoc.set_phase(90.0); refoc.set_pulse_type(refocusing); // fat saturation module fatsat=SeqSat("fatsat",fat,0.3,NumOfSatPulses); //////////////// Readout: ////////////////////////////// // set equivalent resolution in read and phase direction float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); int pelines=int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5); commonPars->set_MatrixSize(phaseDirection, pelines, noedit); float os_read=1.25; // slight oversampling to allow off-center FOV ge_acq=SeqAcqRead("ge_acq",commonPars->get_AcqSweepWidth(),commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection),readDirection,os_read); se_acq=ge_acq; // pre-dephase gradient deph=SeqAcqDeph("deph",ge_acq,FID); // post-rephase gradients reph=SeqAcqDeph("reph",ge_acq,rephase); // EPI rewinder after each echo fvector gradint(3); float rewind_strength=0.4*systemInfo->get_max_grad(); // OK for stimulation monitor gradint=reph.get_gradintegral()+deph.get_gradintegral(); // collapse rephase and dephase into one gradient pulse rewind=SeqGradTrapezParallel("rewind",gradint[0],gradint[1],gradint[2],rewind_strength); ODINLOG(odinlog,significantDebug) << "rewind.get_duration()=" << rewind.get_duration() << STD_endl; //////////////// Phase Encoding: ////////////////////////// pe=SeqGradPhaseEnc("pe",commonPars->get_MatrixSize(phaseDirection),geometryInfo->get_FOV(phaseDirection), phaseDirection,0.25*systemInfo->get_max_grad(), linearEncoding,noReorder,1, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, commonPars->get_PartialFourier()); pe_rewind=pe; pe_rewind.set_label("pe_rewind"); pe_rewind.invert_strength(); /////////////////// RF Spoiling /////////////////////////////////////////////////////// if(commonPars->get_RFSpoiling()) { // recommended by Goerke et al., NMR Biomed. 18, 534-542 (2005) // int plistsize=16; // double plistincr=45.0; // Handbook of MRI int plistsize=80; double plistincr=117.0; exc.set_phasespoiling(plistsize, plistincr); refoc.set_phasespoiling(plistsize, plistincr, 90.0); ge_acq.set_phasespoiling(plistsize, plistincr); se_acq.set_phasespoiling(plistsize, plistincr); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(refoc.get_phaselist_vector()); phaseiter.add_vector(ge_acq.get_phaselist_vector()); phaseiter.add_vector(se_acq.get_phaselist_vector()); } //////////////// Loops: ////////////////////////////// // loop to iterate over slices sliceloop=SeqObjLoop("sliceloop"); // loop to iterate over phase encoding peloop=SeqObjLoop("peloop"); // loop to iterate over repetitions reploop=SeqObjLoop("reploop"); // loop to iterate over EPI modules echoloop=SeqObjLoop("echoloop"); // loop to iterate over dummy cycles dummyloop=SeqObjLoop("dummyloop"); //////////////// Timing Delays: ////////////////////////////// // TR delay trdelay=SeqDelay("trdelay"); //////////////// Spoiler Gradient: ////////////////////////////// float spoiler_strength=0.5*systemInfo->get_max_grad(); float spoiler_integral=4.0*fabs(deph.get_gradintegral().sum()); float spoiler_dur=secureDivision(spoiler_integral,spoiler_strength); spoiler=SeqGradConstPulse("spoiler",sliceDirection,spoiler_strength,spoiler_dur); // zoomspoiler=SeqGradConstPulse("zoomspoiler",readDirection,spoiler_strength,0.5*spoiler_dur); //////////////// Crusher Gradient: ////////////////////////////// float crusher_strength=0.3*systemInfo->get_max_grad(); // Moderate strength to avoid problems with stimulation float crusher_integral=2.0*spoiler_integral; crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, crusher_strength); crusherdelay=SeqDelay("crusherdelay",1.0); // Small delay to avoid gradient-induced stimulation // add fat saturation to template and repetitions if(NumOfSatPulses>0) preppart += fatsat; // GE part ivector ge_iv(NumOfEchoes); int i; for(i=0; iget_RFSpoiling()) { slicepart += phaseiter; slicepart_dummy += phaseiter; } scan += dummyloop( slicepart_dummy )[3]; // actual scan loop scan+= reploop( peloop( slicepart )[pe][pe_rewind] )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } void method_rels() { Log odinlog(this,"method_rels"); double TEexc= exc.get_duration() - exc.get_magnetic_center(); ODINLOG(odinlog,significantDebug) << "TEexc=" << TEexc << STD_endl; // Fixed TE according to GE part double TEhalf = TEexc + gepart.get_duration() + refoc.get_magnetic_center(); commonPars->set_EchoTime(2.0*TEhalf); int nechoes_se=2*NumOfEchoes-1; // sample whole spin echo TEs.resize(NumOfEchoes+nechoes_se); double TEpreacq_ge=ge_preacq.get_duration(); double TEpreacq_se=se_preacq.get_duration(); double TEread=ge_acq.get_duration()+rewind.get_duration(); double TEacq=ge_acq.get_acquisition_center(); ODINLOG(odinlog,significantDebug) << "TEpreacq_ge/TEpreacq_se/TEread/TEacq=" << TEpreacq_ge << "/" << TEpreacq_se << "/" << TEread << "/" << TEacq << STD_endl; // GE echo times int i; for(i=0; iget_EchoTime()) << STD_endl; } } // middle readout samples SE double tediff=commonPars->get_EchoTime()-TEs[2*NumOfEchoes-1]; sedelay=tediff; ODINLOG(odinlog,normalDebug) << "tediff=" << tediff << STD_endl; for(i=0; iget_RepetitionTime()set_RepetitionTime(slicedur); trdelay=(commonPars->get_RepetitionTime()-slicedur)/double(geometryInfo->get_nSlices()); } void method_pars_set() { // extra information for the automatic reconstruction ge_acq.set_reco_vector(slice,exc); se_acq.set_reco_vector(slice,exc); ge_acq.set_reco_vector(line,pe); se_acq.set_reco_vector(line,pe); // Index for TEs ge_acq.set_reco_vector(userdef,gerewindvec); se_acq.set_reco_vector(userdef,serewindvec); recoInfo->set_DimValues(userdef,TEs); recoInfo->set_PostProc3D("usercoll | messer"); recoInfo->set_CmdLineOpts("-ff Hamming -fp 0.8"); } }; ///////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinspir.cpp0000644000175000017500000002221711322062347013731 00000000000000////////////////////////////////////////////////////////////////////////////// // // A simple spiral sequence // ////////////////////////////////////////////////////////////////////////////// // includes for the sequence objects #include ////////////////////////////////////////////////////////////////////////////// // The method itself is a class that is derived from // an abstract base class 'SeqMethod' that contains all // routines common to all methods: class METHOD_CLASS : public SeqMethod { public: // Constructor that takes the methods identifier (unique string) as its argument METHOD_CLASS(const STD_string& label); // virtual functions that are overwritten in this method to build the sequence, // calculate parameter relations, etc.: void method_pars_init(); void method_seq_init(); void method_rels(); void method_pars_set(); private: // Parameters for this method: JDXint SpiralSegments; JDXbool InOutSpiral; JDXfloat OptimizedPar; JDXtrajectory Trajectory; JDXbool FieldMap; JDXbool FatSaturation; JDXfloatArr DensityComp; JDXdouble ReadoutDuration; JDXint DisplaySegment; JDXfloatArr kx; JDXfloatArr ky; // Sequence objects for this method: SeqPulsar exc; SeqSat fatsat; SeqDelay echodelay; SeqDelay relaxdelay; SeqObjLoop sliceloop; SeqObjLoop segloop; SeqObjLoop reploop; SeqObjList kernel; SeqObjList segpart; SeqObjList scan; SeqAcqSpiral spiral; SeqFieldMap fmapscan; }; ////////////////////////////////////////////////////////////////////////////// METHOD_CLASS::METHOD_CLASS (const STD_string& label) : SeqMethod(label) { // Put in here all stuff that will once be initialised and // never changed // Specify a short description of the method set_description("A simple sequence with different spiral k-space trajectories. " "Optionally, a fieldmap can be acquired prior to the actual scan " "which will be used for conjugate-phase multi-frequency reconstruction. "); } ////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_init() { // In this function the methods parameters will be initialised // Assign default values: commonPars->set_RepetitionTime(1000.0); commonPars->set_EchoTime(0.0); commonPars->set_AcqSweepWidth(100.0); commonPars->set_MatrixSize(readDirection,64); commonPars->set_MatrixSize(phaseDirection,64,noedit); Trajectory.set_function_mode(twoDeeMode); Trajectory.set_funcpars("WrapSpiral(32,0.80)"); // Default trajectory Trajectory.set_description("Spiral trajectory"); append_parameter(Trajectory,"Trajectory"); // Make method specific parameters visible in the user interface SpiralSegments=8; SpiralSegments.set_description("Number of spiral interleaves"); append_parameter(SpiralSegments,"SpiralSegments"); InOutSpiral=false; InOutSpiral.set_description("Spiral-in spiral-out readout"); append_parameter(InOutSpiral,"InOutSpiral"); OptimizedPar=-1.0; OptimizedPar.set_description("Optimize trajectory for minimum readout length if trajectory has a free tunable parameter. Set this parameter to a negative value to trigger optimization."); append_parameter(OptimizedPar,"OptimizedPar"); ReadoutDuration.set_description("Total length of spiral readout"); append_parameter(ReadoutDuration,"ReadoutDuration",noedit); DensityComp.set_filemode(exclude); DisplaySegment.set_filemode(exclude); kx.set_filemode(exclude); ky.set_filemode(exclude); if(systemInfo->get_platform()!=numaris_4) { append_parameter(DensityComp,"DensityComp"); append_parameter(DisplaySegment,"DisplaySegment"); append_parameter(kx,"kx"); append_parameter(ky,"ky"); } FatSaturation=true; FatSaturation.set_description("Saturation of fat resonance prior to excitation"); append_parameter(FatSaturation,"FatSaturation"); FieldMap=true; FieldMap.set_description("Fieldmap pre-scan for distortion correction"); append_parameter(FieldMap,"FieldMap"); fmapscan.init("fmapscan"); append_parameter(fmapscan.get_parblock(),"FieldMapPars"); } ////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_seq_init() { // Put in here all stuff to create the layout of the sequence ///////////////// Excitation Pulse: ///////////////////// // Get the slice thickness from the global geometry handler 'geometryInfo': float slicethick=geometryInfo->get_sliceThickness(); // Create the sinc shaped excitation pulse. exc=SeqPulsarSinc("exc",slicethick,true,2.0,commonPars->get_FlipAngle()); // Set the frequency list of the excitation pulse so that we will excite all slices in the slicepack exc.set_freqlist( systemInfo->get_gamma("") * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); // This is useful for simulating/visualization of the sequence exc.set_pulse_type(excitation); // This loop object is used to loop over the slices sliceloop=SeqObjLoop("sliceloop"); ///////////////// Fat saturation Pulse: ///////////////////// fatsat=SeqSat("fatsat",fat); ////////////////// Geometry: ///////////////////////////////// float fov=geometryInfo->get_FOV(readDirection); unsigned int sizeRadial=commonPars->get_MatrixSize(readDirection); commonPars->set_MatrixSize(phaseDirection,sizeRadial,noedit); // check bounds if(SpiralSegments<1) SpiralSegments=1; if(SpiralSegments>int(sizeRadial/2)) SpiralSegments=sizeRadial/2; //////////////// Spiral Readout: ////////////////////////////// // Perform optimization only if requested manually, i.e. if OptimizedPar<0.0 bool optimize=(OptimizedPar<0.0); if(!optimize) Trajectory.set_parameter(_TRAJ_OPTIMIZE_PARLABEL_,ftos(OptimizedPar)); spiral=SeqAcqSpiral("spiral",commonPars->get_AcqSweepWidth(),fov,sizeRadial,SpiralSegments,Trajectory,InOutSpiral,optimize); // Cache calculated value (e.g. for calculation on VxWorks) if(optimize) OptimizedPar=atof(Trajectory.get_parameter(_TRAJ_OPTIMIZE_PARLABEL_).c_str()); //////////////// Delays: ////////////////////////////// // relaxation delay after each readout relaxdelay=SeqDelay("relaxdelay"); // delay to obtain correct TE echodelay=SeqDelay("echodelay"); //////////////// Loops: ////////////////////////////// // Construct a loop object to iterate through the phase encoding DisplaySegments segloop=SeqObjLoop("segloop"); // Construct a loop object to perform repetitions of the experiment reploop=SeqObjLoop("reploop"); //////////////// Field-map template: ////////////////////////////// if(FieldMap) { if(FatSaturation) fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0,fatsat); // pass fat saturation on to field-map scan else fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0); } //////////////// Build the Sequence: /////////////// // This sequence container will hold the objects for one readout: kernel=SeqObjList("kernel"); // This sequence container will hold the objects for one slicepack: segpart=SeqObjList("segpart"); scan=SeqObjList("scan"); if(FatSaturation) { kernel += fatsat; } kernel += exc + echodelay + spiral; segpart = segloop( sliceloop( kernel + relaxdelay )[exc] )[spiral.get_segment_vector()]; if(FieldMap) scan += fmapscan + relaxdelay; scan += reploop( segpart )[commonPars->get_NumOfRepetitions()]; // Finally, build the whole sequence set_sequence( scan ); } ////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_rels() { // Put in here all stuff that has to be performed whenever one of the sequence parameters // has been changed by the user // calculate relaxdelay to get the desired repetition time float scandur=kernel.get_duration()*float(geometryInfo->get_nSlices()); if(scandur>commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(scandur); relaxdelay.set_duration( (commonPars->get_RepetitionTime()-scandur)/float(geometryInfo->get_nSlices()) ); // set TE float min_echo_time=(exc.get_duration()-exc.get_magnetic_center())+(spiral.get_acquisition_center()); if (commonPars->get_EchoTime()set_EchoTime(min_echo_time); echodelay=commonPars->get_EchoTime()-min_echo_time; ReadoutDuration=secureDivision(double(spiral.get_npts()),commonPars->get_AcqSweepWidth()) ; if(systemInfo->get_platform()!=numaris_4) { DensityComp=spiral.get_denscomp(); kx=spiral.get_ktraj(DisplaySegment,readDirection); ky=spiral.get_ktraj(DisplaySegment,phaseDirection); } } ////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_set() { Log odinlog(this,"method_pars_set"); // Put in here all stuff that has to be performed after the parameters have been edited by the user // and before the sequence is played out spiral.set_reco_vector(slice,exc); } ////////////////////////////////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odindti.cpp0000644000175000017500000003744411455553544013557 00000000000000#include class METHOD_CLASS : public SeqMethod { private: JDXfloat bValue; JDXint NumOfDirections; JDXint b0Rate; JDXfloat GradStrength; JDXint Blades; JDXbool ShortAxis; JDXenum TemplateScan; JDXbool RampSampling; JDXenum RampMode; JDXfloat RampSteepness; JDXbool FatSaturation; JDXint DummyCycles; JDXint NumOfGradEchoes; JDXint NumOfSamples; JDXdouble PulseDur; JDXbool FieldMap; SeqPulsar exc; SeqPulsar refoc; SeqSat fatsat; SeqAcqEPI epiacq; SeqObjList epipart; SeqDelay epiacq_dummy; SeqObjList epipart_dummy; SeqAcqEPI epiacq_template; SeqObjList epipart_template; SeqAcqEPI epiacq_grappa; SeqObjList epipart_grappa; SeqAcqDeph deph; SeqAcqDeph deph_template; SeqAcqDeph deph_grappa; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop bladeloop; SeqObjLoop grappaloop; SeqObjLoop dummyloop; SeqObjLoop dwloop; SeqDelay trdelay; SeqObjList scan; SeqObjList dummypart; SeqObjList templatepart; SeqObjList grappapart; SeqObjList imagingpart; SeqObjList slicepart; SeqObjList slicepart_dummy; SeqObjList slicepart_template; SeqObjList slicepart_grappa; SeqObjList preppart; SeqDelay exc2refoc; SeqDelay refoc2acq; SeqTrigger trigger; SeqGradTrapezParallel spoiler; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; SeqFieldMap fmapscan; SeqVecIter phaseiter; SeqDiffWeight dw; SeqObjList midpart; SeqRotMatrixVector bladerot; SeqHalt physiotrigger; dvector bladeangels; public: // This constructor creates an empty EPI sequence METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("Diffusion tensor sequence based on PROPELLER-EPI. A simple Stejskal-Tanner gradient pair around the refocusing pulse is used for diffusion weighting."); } void method_pars_init() { // In this function, parameters are initialized and default values are set commonPars->set_MatrixSize(readDirection,128); commonPars->set_MatrixSize(phaseDirection,128,noedit); commonPars->set_NumOfRepetitions(1); commonPars->set_RepetitionTime(1000.0); commonPars->set_AcqSweepWidth(100.0); commonPars->set_PhysioTrigger(true); bValue=1000.0; bValue.set_unit("s/mm^2").set_description("Uniform b-value"); NumOfDirections=6; NumOfDirections.set_description("Number of uniformly distributed diffusion directions"); b0Rate=5; b0Rate.set_description("Rate of b0 scans interleaved wit diffusion weighting"); GradStrength=80.0; GradStrength.set_minmaxval(0.0,100.0).set_unit("%").set_description("Relative strength of diffusion-weighting gradients"); Blades=8; Blades.set_description("Number of PROPELLER blades"); ShortAxis=false; ShortAxis.set_description("Readout direction along short axis of blades"); TemplateScan.add_item("NoCorrection"); TemplateScan.add_item("PhaseCorrection"); TemplateScan.set_actual("PhaseCorrection"); TemplateScan.set_description("The type of template scan which is acquired beforehand"); RampSampling=false; RampSampling.set_description("Perform sampling during gradient ramps"); RampMode.add_item("linear",linear); RampMode.add_item("sinusoidal",sinusoidal); RampMode.add_item("half_sinusoidal",half_sinusoidal); RampMode.set_actual(linear); RampMode.set_description("The shape of the ramps of the read gradient"); RampSteepness=1.0; RampSteepness.set_description("Relative steepness (slew rate) of the EPI readout ramps"); FatSaturation=true; FatSaturation.set_description("Saturation of fat resonance prior to excitation"); DummyCycles=3; DummyCycles.set_description("Number of dummy shots before actual acquisition"); FieldMap=false; FieldMap.set_description("Fieldmap pre-scan for distortion correction"); PulseDur=4.0; // avoid initial high RF amplitude PulseDur.set_description("Pulse duration of excitation/refocusing pulse"); // register method parameters for user interface, parameter files, etc. append_parameter(bValue,"bValue"); append_parameter(NumOfDirections,"NumOfDirections"); append_parameter(b0Rate,"b0Rate"); append_parameter(GradStrength,"GradStrength"); append_parameter(Blades,"Blades"); append_parameter(ShortAxis,"ShortAxis"); append_parameter(DummyCycles,"DummyCycles"); append_parameter(TemplateScan,"TemplateScan"); append_parameter(RampSampling,"RampSampling"); append_parameter(FatSaturation,"FatSaturation"); append_parameter(FieldMap,"FieldMap"); fmapscan.init("fmapscan"); append_parameter(fmapscan.get_parblock(),"FieldMapPars"); append_parameter(PulseDur,"PulseDur"); if(systemInfo->get_platform()!=numaris_4) { append_parameter(RampMode,"RampMode"); append_parameter(RampSteepness,"RampSteepness"); append_parameter(NumOfGradEchoes,"NumOfGradEchoes",noedit); append_parameter(NumOfSamples,"NumOfSamples",noedit); } } void method_seq_init() { ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float slicegap=geometryInfo->get_sliceDistance()-slicethick; // excitation pulse exc=SeqPulsarSinc("exc",slicethick,true,PulseDur,commonPars->get_FlipAngle()); exc.set_rephased(true, 0.8*systemInfo->get_max_grad()); // short rephaser exc.set_freqlist( systemInfo->get_gamma() * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); exc.set_pulse_type(excitation); // Slightly thicker refocusing slice for better SNR // Since the same spatial resolution is used for exc and refoc, the gradient strengths will be the same float extra_slicethick_refoc=STD_min(0.5*slicethick, 0.3*slicegap); // refocusing pulse refoc=SeqPulsarSinc("refoc",slicethick+extra_slicethick_refoc,false,PulseDur,180.0); refoc.set_freqlist( systemInfo->get_gamma() * refoc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); if(!commonPars->get_RFSpoiling()) refoc.set_phase(90.0); refoc.set_pulse_type(refocusing); // fat saturation module fatsat=SeqSat("fatsat",fat); //////////////// EPI-Readout: ////////////////////////////// // square FOV int sizeRadial=commonPars->get_MatrixSize(readDirection); commonPars->set_MatrixSize(phaseDirection,sizeRadial,noedit); int readpts_blade=sizeRadial; int pelines_blade=sizeRadial; int bladewidth=sizeRadial; if(Blades>1) bladewidth=int(0.5*PII*sizeRadial/Blades+0.5); if(ShortAxis) readpts_blade=bladewidth; else pelines_blade=bladewidth; float os_read=2.0; // For reduced undersampling artifacts float fov=geometryInfo->get_FOV(readDirection); // uniform FOV epiacq=SeqAcqEPI("epiacq",commonPars->get_AcqSweepWidth(), readpts_blade, fov, pelines_blade, fov, 1, commonPars->get_ReductionFactor(), os_read, "", 0, 0, rampType(int(RampMode)), RampSampling, RampSteepness, commonPars->get_PartialFourier()); // display sampling extents in read/phase direction NumOfGradEchoes=epiacq.get_numof_gradechoes(); NumOfSamples=epiacq.get_npts_read(); // Template scan fo EPI, begin with copy of actual EPI epiacq_template=epiacq; epiacq_template.set_label("epiacq_template"); // 1D phase correction if(TemplateScan=="PhaseCorrection") { epiacq_template.set_template_type(phasecorr_template); } // Full multi-shot EPI readout as GRAPPA training data epiacq_grappa=epiacq; epiacq_grappa.set_label("epiacq_grappa"); epiacq_grappa.set_template_type(grappa_template); // Delay instead of actual EPI readout for dummy scans epiacq_dummy=SeqDelay("epiacq_dummy",epiacq.get_duration()); // EPI pre-dephase gradient deph=SeqAcqDeph("deph",epiacq); deph_template=SeqAcqDeph("deph_template",epiacq_template); deph_grappa=SeqAcqDeph("deph_grappa",epiacq_grappa); /////////////////// Rotation of Blades //////////////////////////////////////////////// bladerot=SeqRotMatrixVector("bladerot"); bladeangels.resize(Blades); for(int iblade=0; ibladeget_RFSpoiling()) { // Use defaults for phase spoiling int plistsize=80; double plistincr=117.0; exc.set_phasespoiling(plistsize, plistincr); refoc.set_phasespoiling(plistsize, plistincr, 90.0); epiacq.set_phasespoiling(plistsize, plistincr); epiacq_template.set_phasespoiling(plistsize, plistincr); epiacq_grappa.set_phasespoiling(plistsize, plistincr); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(refoc.get_phaselist_vector()); phaseiter.add_vector(epiacq.get_phaselist_vector()); phaseiter.add_vector(epiacq_template.get_phaselist_vector()); phaseiter.add_vector(epiacq_grappa.get_phaselist_vector()); } //////////////// Loops: ////////////////////////////// // loop to iterate over slices sliceloop=SeqObjLoop("sliceloop"); // loop to iterate over repetitions reploop=SeqObjLoop("reploop"); // loop to iterate over blades bladeloop=SeqObjLoop("bladeloop"); // loop to iterate over GRAPPA interleaves to obtain training data grappaloop=SeqObjLoop("grappaloop"); // loop to iterate over dummy scans dummyloop=SeqObjLoop("dummyloop"); // loop to iterate over diffusion weighting dwloop=SeqObjLoop("dwloop"); //////////////// Timing Delays: ////////////////////////////// trdelay=SeqDelay("trdelay"); //////////////// Spoiler Gradient: ////////////////////////////// double spoiler_strength=0.5*systemInfo->get_max_grad(); double spoiler_integral=2.0*fabs(deph.get_gradintegral().sum()); // on all three axes for uniform b-value spoiler=SeqGradTrapezParallel("spoiler",spoiler_integral,spoiler_integral,spoiler_integral, spoiler_strength); //////////////// Crusher Gradient: ////////////////////////////// float crusher_integral=2.0*spoiler_integral; crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, spoiler_strength); crusherdelay=SeqDelay("crusherdelay",0.1); // Small delay to avoid gradient-induced stimulation //////////////// Field-map template: ////////////////////////////// if(FieldMap) { if(FatSaturation) fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0,fatsat); // pass fat saturation on to field-map scan else fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0); } //////////////// Diffusion weighting: ////////////////////////////// fvector bvals(1); bvals[0]=1000.0*bValue; midpart = spoiler + refoc + spoiler; dw=SeqDiffWeight("dw", NumOfDirections, bvals, 0.01*GradStrength*systemInfo->get_max_grad(), midpart, b0Rate, true); //////////////// Build the sequence: ////////////////////////////// // add physiological trigger physiotrigger=SeqHalt("physiotrigger"); if(commonPars->get_PhysioTrigger()) preppart += physiotrigger; // add fat saturation to template and repetitions if(FatSaturation) preppart += fatsat; // Rotate deph and epi simultaneously epipart_dummy =SeqObjList("epipart_dummy"); epipart_template=SeqObjList("epipart_template"); epipart_grappa =SeqObjList("epipart_grappa"); epipart =SeqObjList("epipart"); epipart_dummy += deph + epiacq_dummy; epipart_template+= deph_template + epiacq_template; epipart_grappa += deph_grappa + epiacq_grappa; epipart += deph + epiacq; epipart_dummy .set_gradrotmatrixvector(bladerot); epipart_template.set_gradrotmatrixvector(bladerot); epipart_grappa .set_gradrotmatrixvector(bladerot); epipart .set_gradrotmatrixvector(bladerot); dummypart= preppart + exc + exc2refoc + dw + refoc2acq + epipart_dummy + crusherdelay + crusher; templatepart= preppart + exc + exc2refoc + dw + refoc2acq + epipart_template + crusherdelay + crusher; grappapart= preppart + exc + exc2refoc + dw + refoc2acq + epipart_grappa + crusherdelay + crusher; imagingpart= preppart + exc + exc2refoc + dw + refoc2acq + epipart + crusherdelay + crusher; slicepart_dummy = sliceloop( dummypart + trdelay )[exc][refoc]; slicepart_template = sliceloop( templatepart + trdelay )[exc][refoc]; slicepart_grappa = sliceloop( grappapart + trdelay )[exc][refoc]; slicepart += sliceloop( imagingpart + trdelay )[exc][refoc]; if(commonPars->get_RFSpoiling()) { slicepart += phaseiter; slicepart_dummy += phaseiter; slicepart_template += phaseiter; slicepart_grappa += phaseiter; } if(FieldMap) scan += fmapscan + trdelay; if(DummyCycles>0) { scan+= dummyloop( slicepart_dummy )[DummyCycles]; } if(TemplateScan=="PhaseCorrection") { scan += bladeloop( // Use b0 scan for phase correction of all slicepart_template )[bladerot]; } if(commonPars->get_ReductionFactor()>1) { // Fully sampled k-space scan+= grappaloop( // Use b0 scan for interpolation of all bladeloop( slicepart_grappa )[bladerot] )[deph_grappa.get_epi_reduction_vector()]; } scan+= reploop( dwloop( bladeloop( slicepart )[bladerot] )[dw] )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } void method_rels() { ////////////////// TE Timings: //////////////////////////////// double min_echo_time=0.0; //////////////// Duration from the middle of the excitation pulse /////////////////// //////////////// to the middle of the refocusing pulse: ///////////////////////////// double TE1=( exc.get_duration() - exc.get_magnetic_center() ) + dw.get_grad1_duration() + spoiler.get_duration() + refoc.get_magnetic_center(); if(min_echo_time<(2.0*TE1)) min_echo_time=2.0*TE1; //////////////// Duration from the middle of the refocusing pulse /////////////////// //////////////// to the middle of the acquisition window: /////////////////////////// double TE2=(refoc.get_duration() - refoc.get_magnetic_center()) + spoiler.get_duration() + dw.get_grad2_duration() + deph.get_duration() + epiacq.get_acquisition_center(); if(min_echo_time<(2.0*TE2)) min_echo_time=2.0*TE2; if (commonPars->get_EchoTime()set_EchoTime(min_echo_time); commonPars->set_EchoTime(min_echo_time); exc2refoc=commonPars->get_EchoTime()/2.0-TE1; refoc2acq=commonPars->get_EchoTime()/2.0-TE2; ////////////////// TR Timings: //////////////////////////////// // reset before recalculating timings trdelay=0.0; float slicedur=slicepart.get_duration(); if(commonPars->get_PhysioTrigger()) { commonPars->set_RepetitionTime(slicedur); // set to minimum TR } else { if(commonPars->get_RepetitionTime()set_RepetitionTime(slicedur); trdelay=(commonPars->get_RepetitionTime()-slicedur)/double(geometryInfo->get_nSlices()); } } void method_pars_set() { // extra information for the automatic reconstruction epiacq.set_reco_vector(slice,exc); epiacq_template.set_reco_vector(slice,exc); epiacq_grappa.set_reco_vector(slice,exc); epiacq.set_reco_vector(cycle,bladerot); epiacq_template.set_reco_vector(cycle,bladerot); epiacq_grappa.set_reco_vector(cycle,bladerot); recoInfo->set_DimValues(cycle,bladeangels); epiacq.set_reco_vector(dti, dw); epiacq_template.set_reco_vector(dti, dw); epiacq_grappa.set_reco_vector(dti, dw); recoInfo->set_DimValues(dti, dw.get_b_vectors()); } }; ///////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinepi.cpp0000644000175000017500000004155011322062347013532 00000000000000 // include the headers of all sequence classes #include // The whole EPI sequence is a C++ class class METHOD_CLASS : public SeqMethod { private: // this section contains the data elements of the sequence, // i.e. the sequence specific parameters and the sequence objects // the following parameters are specific to EPI sequences, // parameters common to all sequences can be accessed via the // 'commonPars' global object JDXbool TakeMinEchoTime; JDXenum SliceTimingMode; JDXenum TemplateScan; JDXbool RampSampling; JDXenum RampMode; JDXfloat RampSteepness; JDXbool FatSaturation; JDXenum EPIMode; JDXint Shots; JDXint DummyCycles; JDXint NumOfGradEchoes; JDXint NumOfSamples; JDXdouble PulseDur; JDXbool fMRITrigger; JDXint fMRIBlockSize; JDXbool FieldMap; // sequence objects which are the elementary objects // to build the EPI sequence SeqPulsar exc; SeqPulsar refoc; SeqSat fatsat; SeqAcqEPI epiacq; SeqDelay epiacq_dummy; SeqAcqEPI epiacq_template; SeqAcqEPI epiacq_grappa; SeqAcqDeph deph; SeqAcqDeph deph_template; SeqAcqDeph deph_grappa; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop segloop; SeqObjLoop grappaloop; SeqObjLoop dummyloop; SeqDelay delayuniform; SeqDelay delaybunched; SeqObjList scan; SeqObjList dummypart; SeqObjList templatepart; SeqObjList grappapart; SeqObjList imagingpart; SeqObjList slicepart; SeqObjList slicepart_dummy; SeqObjList slicepart_template; SeqObjList slicepart_grappa; SeqObjList preppart; SeqDelay exc2acq; SeqDelay exc2refoc; SeqDelay refoc2acq; SeqGradConstPulse spoiler; SeqTrigger trigger; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; SeqFieldMap fmapscan; SeqVecIter phaseiter; public: // This constructor creates an empty EPI sequence METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("This is a feature-rich multislice EPI method. " "The template scan for phase correction is sampled before the repetitions. " "A field-map scan can be acquired prior to the actual scan for distortion correction."); } unsigned int numof_testcases() const {return 3;} void method_pars_init() { // In this function, parameters are initialized and default values are set commonPars->set_MatrixSize(readDirection,64); commonPars->set_MatrixSize(phaseDirection,64,noedit); commonPars->set_NumOfRepetitions(1); commonPars->set_RepetitionTime(1000.0); commonPars->set_AcqSweepWidth(100.0); SliceTimingMode.add_item("EPIuniform"); SliceTimingMode.add_item("EPIbunchedEarly"); SliceTimingMode.set_actual("EPIuniform"); SliceTimingMode.set_description("Scanning of slices uniformly distributed over TR (EPIuniform) or bunched at the start (EPIbunchedEarly)"); EPIMode.add_item("FIDMode"); EPIMode.add_item("SEMode"); EPIMode.set_actual("FIDMode"); EPIMode.set_description("Gradient-echo EPI (FIDMode) or spin-echo EPI (SEMode)"); TemplateScan.add_item("NoCorrection"); TemplateScan.add_item("PhaseCorrection"); TemplateScan.set_actual("PhaseCorrection"); TemplateScan.set_description("The type of template scan which is acquired beforehand"); RampSampling=false; RampSampling.set_description("Perform sampling during gradient ramps"); RampMode.add_item("linear",linear); RampMode.add_item("sinusoidal",sinusoidal); RampMode.add_item("half_sinusoidal",half_sinusoidal); RampMode.set_actual(linear); RampMode.set_description("The shape of the ramps of the read gradient"); RampSteepness=1.0; RampSteepness.set_description("Relative steepness (slew rate) of the EPI readout ramps"); FatSaturation=true; FatSaturation.set_description("Saturation of fat resonance prior to excitation"); TakeMinEchoTime=true; TakeMinEchoTime.set_description("Use minimum possible TE"); Shots=1; Shots.set_description("Number of shots, multi-shot (segmented) EPI if Shots>1"); DummyCycles=3; DummyCycles.set_description("Number of dummy shots before actual acquisition"); fMRITrigger=true; fMRITrigger.set_description("External triggering"); fMRIBlockSize=0; fMRIBlockSize.set_description("If non-zero, fMRI analysis will be performed with this size for both stimulation and rest"); FieldMap=false; FieldMap.set_description("Fieldmap pre-scan for distortion correction"); PulseDur=4.0; // avoid initial high RF amplitude PulseDur.set_description("Pulse duration of excitation/refocusing pulse"); // alternative default settings for sequence test if(get_current_testcase()==1) { EPIMode.set_actual("SEMode"); RampSteepness=0.8; RampSampling=true; FatSaturation=false; DummyCycles=0; commonPars->set_PartialFourier(0.7); } if(get_current_testcase()==2) { TemplateScan.set_actual("NoCorrection"); Shots=3; FieldMap=true; commonPars->set_RFSpoiling(false); } // register method parameters for user interface, parameter files, etc. append_parameter(EPIMode,"EPIMode"); append_parameter(TakeMinEchoTime,"TakeMinEchoTime"); append_parameter(Shots,"Shots"); append_parameter(DummyCycles,"DummyCycles"); append_parameter(TemplateScan,"TemplateScan"); append_parameter(RampSampling,"RampSampling"); append_parameter(FatSaturation,"FatSaturation"); append_parameter(FieldMap,"FieldMap"); fmapscan.init("fmapscan"); append_parameter(fmapscan.get_parblock(),"FieldMapPars"); append_parameter(fMRITrigger,"fMRITrigger"); append_parameter(fMRIBlockSize,"fMRIBlockSize"); append_parameter(PulseDur,"PulseDur"); if(systemInfo->get_platform()!=numaris_4) { append_parameter(RampMode,"RampMode"); append_parameter(RampSteepness,"RampSteepness"); append_parameter(SliceTimingMode,"SliceTimingMode"); append_parameter(NumOfGradEchoes,"NumOfGradEchoes",noedit); append_parameter(NumOfSamples,"NumOfSamples",noedit); } } void method_seq_init() { ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float slicegap=geometryInfo->get_sliceDistance()-slicethick; // excitation pulse exc=SeqPulsarSinc("exc",slicethick,true,PulseDur,commonPars->get_FlipAngle()); exc.set_rephased(true, 0.8*systemInfo->get_max_grad()); // short rephaser exc.set_freqlist( systemInfo->get_gamma() * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); exc.set_pulse_type(excitation); // Slightly thicker refocusing slice for better SNR // Since the same spatial resolution is used for exc and refoc, the gradient strengths will be the same float extra_slicethick_refoc=STD_min(0.5*slicethick, 0.3*slicegap); // refocusing pulse refoc=SeqPulsarSinc("refoc",slicethick+extra_slicethick_refoc,false,PulseDur,180.0); refoc.set_freqlist( systemInfo->get_gamma() * refoc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); if(!commonPars->get_RFSpoiling()) refoc.set_phase(90.0); refoc.set_pulse_type(refocusing); // fat saturation module fatsat=SeqSat("fatsat",fat); //////////////// EPI-Readout: ////////////////////////////// // set equivalent resolution in read and phase direction float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); int pelines=int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5); float os_read=1.2; // slight oversampling to allow off-center FOV epiacq=SeqAcqEPI("epiacq",commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), pelines, geometryInfo->get_FOV(phaseDirection), Shots, commonPars->get_ReductionFactor(), os_read, "", 0, 0, rampType(int(RampMode)), RampSampling, RampSteepness, commonPars->get_PartialFourier()); // display sampling extents in read/phase direction NumOfGradEchoes=epiacq.get_numof_gradechoes(); commonPars->set_MatrixSize(phaseDirection,NumOfGradEchoes*Shots*commonPars->get_ReductionFactor(),noedit); NumOfSamples=epiacq.get_npts_read(); // Template scan fo EPI, begin with copy of actual EPI epiacq_template=epiacq; epiacq_template.set_label("epiacq_template"); // 1D phase correction if(TemplateScan=="PhaseCorrection") { epiacq_template.set_template_type(phasecorr_template); } // Full multi-shot EPI readout as GRAPPA training data epiacq_grappa=epiacq; epiacq_grappa.set_label("epiacq_grappa"); epiacq_grappa.set_template_type(grappa_template); // Delay instead of actual EPI readout for dummy scans epiacq_dummy=SeqDelay("epiacq_dummy",epiacq.get_duration()); // EPI pre-dephase gradient dephaseMode dephmode=FID; if (EPIMode=="SEMode") dephmode=spinEcho; deph=SeqAcqDeph("deph",epiacq,dephmode); deph_template=SeqAcqDeph("deph_template",epiacq_template,dephmode); deph_grappa=SeqAcqDeph("deph_grappa",epiacq_grappa,dephmode); /////////////////// RF Spoiling /////////////////////////////////////////////////////// if(commonPars->get_RFSpoiling()) { // recommended by Goerke et al., NMR Biomed. 18, 534-542 (2005) int plistsize=16; double plistincr=45.0; exc.set_phasespoiling(plistsize, plistincr); refoc.set_phasespoiling(plistsize, plistincr, 90.0); epiacq.set_phasespoiling(plistsize, plistincr); epiacq_template.set_phasespoiling(plistsize, plistincr); epiacq_grappa.set_phasespoiling(plistsize, plistincr); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(refoc.get_phaselist_vector()); phaseiter.add_vector(epiacq.get_phaselist_vector()); phaseiter.add_vector(epiacq_template.get_phaselist_vector()); phaseiter.add_vector(epiacq_grappa.get_phaselist_vector()); } //////////////// Loops: ////////////////////////////// // loop to iterate over slices sliceloop=SeqObjLoop("sliceloop"); // loop to iterate over repetitions reploop=SeqObjLoop("reploop"); // loop to iterate over segments (multi shot) segloop=SeqObjLoop("segloop"); // loop to iterate over GRAPPA interleaves to obtain training data grappaloop=SeqObjLoop("grappaloop"); // loop to iterate over dummy scans dummyloop=SeqObjLoop("dummyloop"); //////////////// Timing Delays: ////////////////////////////// // Delays uniform/bunched delayuniform=SeqDelay("delayuniform"); delaybunched=SeqDelay("delaybunched"); //////////////// Spoiler Gradient: ////////////////////////////// double spoiler_strength=0.5*systemInfo->get_max_grad(); double spoiler_integral=4.0*fabs(deph.get_gradintegral().sum()); double spoiler_dur=secureDivision(spoiler_integral,spoiler_strength); spoiler=SeqGradConstPulse("spoiler",readDirection,spoiler_strength,spoiler_dur); //////////////// Crusher Gradient: ////////////////////////////// float crusher_integral=2.0*spoiler_integral; crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, spoiler_strength); crusherdelay=SeqDelay("crusherdelay",0.1); // Small delay to avoid gradient-induced stimulation //////////////// fMRI trigger: ////////////////////////////// trigger=SeqTrigger("fmri_trigger",1.0); //////////////// Field-map template: ////////////////////////////// if(FieldMap) { if(FatSaturation) fmapscan.build_seq(commonPars->get_AcqSweepWidth(),os_read,fatsat); // pass fat saturation on to field-map scan else fmapscan.build_seq(commonPars->get_AcqSweepWidth(),os_read); } //////////////// Build the sequence: ////////////////////////////// // add fat saturation to template and repetitions if(FatSaturation) preppart += fatsat; if(fMRITrigger) slicepart += trigger; if (EPIMode=="FIDMode") { dummypart= preppart + exc + deph + exc2acq + epiacq_dummy + crusherdelay + crusher; templatepart= preppart + exc + deph_template + exc2acq + epiacq_template + crusherdelay + crusher; grappapart= preppart + exc + deph_grappa + exc2acq + epiacq_grappa + crusherdelay + crusher; imagingpart= preppart + exc + deph + exc2acq + epiacq + crusherdelay + crusher; slicepart_dummy = sliceloop( dummypart + delayuniform )[exc]; slicepart_template = sliceloop( templatepart + delayuniform )[exc]; slicepart_grappa = sliceloop( grappapart + delayuniform )[exc]; slicepart += sliceloop( imagingpart + delayuniform )[exc]; } if (EPIMode=="SEMode") { dummypart= preppart + exc + exc2refoc + deph + spoiler + refoc + spoiler + refoc2acq + epiacq_dummy + crusherdelay + crusher; templatepart= preppart + exc + exc2refoc + deph_template + spoiler + refoc + spoiler + refoc2acq + epiacq_template + crusherdelay + crusher; grappapart= preppart + exc + exc2refoc + deph_grappa + spoiler + refoc + spoiler + refoc2acq + epiacq_grappa + crusherdelay + crusher; imagingpart= preppart + exc + exc2refoc + deph + spoiler + refoc + spoiler + refoc2acq + epiacq + crusherdelay + crusher; slicepart_dummy = sliceloop( dummypart + delayuniform )[exc][refoc]; slicepart_template = sliceloop( templatepart + delayuniform )[exc][refoc]; slicepart_grappa = sliceloop( grappapart + delayuniform )[exc][refoc]; slicepart += sliceloop( imagingpart + delayuniform )[exc][refoc]; } if(commonPars->get_RFSpoiling()) { slicepart += phaseiter; slicepart_dummy += phaseiter; slicepart_template += phaseiter; slicepart_grappa += phaseiter; } if(FieldMap) scan += fmapscan + delayuniform + delaybunched; if(DummyCycles>0) { scan+= dummyloop( slicepart_dummy + delaybunched )[DummyCycles]; } if(TemplateScan=="PhaseCorrection") { scan += slicepart_template + delaybunched; // phasecorr requires only one shot from template } if(commonPars->get_ReductionFactor()>1) { // Fully sampled k-space scan+= grappaloop( segloop( slicepart_grappa + delaybunched )[deph_grappa.get_epi_segment_vector()] )[deph_grappa.get_epi_reduction_vector()]; } scan+= reploop( segloop( slicepart + delaybunched )[deph.get_epi_segment_vector()] )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } void method_rels() { ////////////////// TE Timings: //////////////////////////////// double min_echo_time=0.0; if (EPIMode=="FIDMode") { min_echo_time=(exc.get_duration()-exc.get_magnetic_center())+deph.get_duration()+epiacq.get_acquisition_center(); if(commonPars->get_EchoTime()set_EchoTime(min_echo_time); if(TakeMinEchoTime) commonPars->set_EchoTime(min_echo_time); exc2acq=commonPars->get_EchoTime()-min_echo_time; } if (EPIMode=="SEMode") { //////////////// Duration from the middle of the excitation pulse /////////////////// //////////////// to the middle of the refocusing pulse: ///////////////////////////// double TE1=( exc.get_duration() - exc.get_magnetic_center() ) + deph.get_duration() + spoiler.get_duration() + refoc.get_magnetic_center(); if(min_echo_time<(2.0*TE1)) min_echo_time=2.0*TE1; //////////////// Duration from the middle of the refocusing pulse /////////////////// //////////////// to the middle of the acquisition window: /////////////////////////// double TE2=(refoc.get_duration() - refoc.get_magnetic_center()) + spoiler.get_duration() + epiacq.get_acquisition_center(); if(min_echo_time<(2.0*TE2)) min_echo_time=2.0*TE2; if (commonPars->get_EchoTime()set_EchoTime(min_echo_time); if(TakeMinEchoTime) commonPars->set_EchoTime(min_echo_time); exc2refoc=commonPars->get_EchoTime()/2.0-TE1; refoc2acq=commonPars->get_EchoTime()/2.0-TE2; } ////////////////// TR Timings: //////////////////////////////// // reset before recalculating timings delayuniform=0.0; delaybunched=0.0; float slicedur=slicepart.get_duration(); if(commonPars->get_RepetitionTime()set_RepetitionTime(slicedur); if (SliceTimingMode=="EPIuniform") { delayuniform=(commonPars->get_RepetitionTime()-slicedur)/double(geometryInfo->get_nSlices()); delaybunched=0.0; } if (SliceTimingMode=="EPIbunchedEarly") { delaybunched=commonPars->get_RepetitionTime()-slicedur; delayuniform=0.0; } } void method_pars_set() { // extra information for the automatic reconstruction epiacq.set_reco_vector(slice,exc); epiacq_template.set_reco_vector(slice,exc); epiacq_grappa.set_reco_vector(slice,exc); if(fMRIBlockSize>0) recoInfo->set_PostProc3D("repcoll | fmri("+itos(fMRIBlockSize)+","+itos(fMRIBlockSize)+")"); } }; ///////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinonep.cpp0000644000175000017500000001070311322062347013712 00000000000000#include class METHOD_CLASS : public SeqMethod { public: METHOD_CLASS(const STD_string& label); void method_pars_init(); void method_seq_init(); void method_rels(); void method_pars_set(); private: JDXenum OnepulseMode; JDXint NumOfSamples; JDXdouble PulseDuration; JDXdouble FreqOffset; SeqPulsarBP exc; SeqPulsarBP refoc; SeqAcq acq; SeqDelay relaxdelay; SeqDelay exc2refoc; SeqDelay refoc2acq; SeqObjLoop acculoop; SeqObjList scanpart; SeqGradConstPulse spoiler; SeqVector averagevec; // index vector for averages SeqVecIter phaseiter; }; //////////////////////////////////////////////////////////////////////////// METHOD_CLASS::METHOD_CLASS (const STD_string& label) : SeqMethod(label) { set_description("A simple onepulse experiment (non-selective RF pulse + acquisition)."); } //////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_init() { OnepulseMode.add_item("FID"); OnepulseMode.add_item("SpinEcho"); OnepulseMode.set_actual("FID"); commonPars->set_EchoTime(0.0); NumOfSamples=1024; PulseDuration=1.0; FreqOffset=0.0; append_parameter(OnepulseMode,"OnepulseMode"); append_parameter(NumOfSamples,"NumOfSamples"); append_parameter(PulseDuration,"PulseDuration"); append_parameter(FreqOffset,"FreqOffset"); } //////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_seq_init() { exc=SeqPulsarBP("exc",PulseDuration,commonPars->get_FlipAngle(),systemInfo->get_main_nucleus()); exc.set_pulse_type(excitation); refoc=SeqPulsarBP("refoc",PulseDuration,180.0,systemInfo->get_main_nucleus()); refoc.set_pulse_type(refocusing); acq=SeqAcq("acq",(unsigned int)NumOfSamples,commonPars->get_AcqSweepWidth(),1.0,systemInfo->get_main_nucleus()); exc.set_freqoffset(FreqOffset); refoc.set_freqoffset(FreqOffset); acq.set_freqoffset(FreqOffset); if(commonPars->get_RFSpoiling()) { exc.set_phasespoiling(4, 90.0); acq.set_phasespoiling(4, 90.0); refoc.set_phasespoiling(4, 90.0, 90.0); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(acq.get_phaselist_vector()); phaseiter.add_vector(refoc.get_phaselist_vector()); } else { refoc.set_phase(90.0); } spoiler=SeqGradConstPulse("spoiler",sliceDirection,0.5*systemInfo->get_max_grad(),2.0); relaxdelay=SeqDelay("relaxdelay"); exc2refoc=SeqDelay("exc2refoc"); refoc2acq=SeqDelay("refoc2acq"); acculoop=SeqObjLoop("acculoop"); if(OnepulseMode=="SpinEcho") scanpart= exc + exc2refoc + spoiler + refoc + spoiler + refoc2acq + acq + relaxdelay; else scanpart= exc + acq + spoiler + relaxdelay; if(commonPars->get_RFSpoiling()) scanpart += phaseiter; averagevec=SeqVector("averagevec",commonPars->get_NumOfRepetitions()); set_sequence( acculoop(scanpart)[averagevec] ); } //////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_rels() { float min_echo_time1=0.0; float min_echo_time2=0.0; if(OnepulseMode=="SpinEcho") { min_echo_time1=(exc.get_duration()-exc.get_magnetic_center())+spoiler.get_duration()+refoc.get_magnetic_center(); min_echo_time2=(refoc.get_duration()-refoc.get_magnetic_center())+spoiler.get_duration()+acq.get_acquisition_center(); } else { min_echo_time1=(exc.get_duration()-exc.get_magnetic_center())+acq.get_acquisition_center(); } if(commonPars->get_EchoTime()set_EchoTime(min_echo_time1); if(commonPars->get_EchoTime()set_EchoTime(min_echo_time2); exc2refoc=commonPars->get_EchoTime()-min_echo_time1; refoc2acq=commonPars->get_EchoTime()-min_echo_time2; if(scanpart.get_duration()>commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(scanpart.get_duration()); relaxdelay.set_duration(commonPars->get_RepetitionTime()-scanpart.get_duration()); } //////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_set() { acq.set_reco_vector(average,averagevec); recoInfo->set_Recipe("averagecoll | averagesum | kspace | fft | slicecoll | image | store"); // Quick hack to display a single spectrum from multiple averages } //////////////////////////////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinfisp.cpp0000644000175000017500000001477011363773557013743 00000000000000#include class METHOD_CLASS : public SeqMethod { private: SeqPulsar exc; SeqPulsarReph exc_reph; SeqPulsar exc_prep; SeqGradTrapez exc_prep_reph; SeqDelay prepdelay; SeqDelay postdelay; SeqDelay relaxdelay; SeqDelay grechdummy; SeqGradEcho grech; SeqGradConstPulse crusher; SeqObjList kernel; SeqObjList dummykernel; SeqObjList readout; SeqObjList shot; SeqObjList scan; SeqObjLoop reploop; SeqObjLoop sliceloop; SeqObjLoop peloop; SeqObjLoop phaseloop; SeqObjLoop dummyloop; JDXint DummyCycles; JDXenum PhaseEncoding; public: //////////////////////////////////////////////////// METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("Single-shot TrueFISP (balanced SSFP) sequence. See for example Scheffler et.al. Eur Radiol (2003) 13:2409-2418 "); } //////////////////////////////////////////////////// void method_pars_init() { commonPars->set_EchoTime(0.0,noedit); commonPars->set_FlipAngle(60.0); DummyCycles=3; DummyCycles.set_description("Number of dummy cycles before actual acquisition"); PhaseEncoding.add_item("Linear",linearEncoding); PhaseEncoding.add_item("CenterOut",centerOutEncoding); PhaseEncoding=linearEncoding; PhaseEncoding.set_description("Phase encoding order"); append_parameter(DummyCycles,"DummyCycles"); append_parameter(PhaseEncoding,"PhaseEncoding"); } void method_seq_init(){ double gamma=systemInfo->get_gamma(); ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float spatres=slicethick/4.0; // Excitation Pulse exc=SeqPulsarSinc("exc",slicethick,false,2.0,commonPars->get_FlipAngle(),spatres); dvector freqlist=gamma * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector(); exc.set_freqlist(freqlist); exc.set_pulse_type(excitation); // +/- flipangles for FISP dvector phaselist(2); phaselist[0]=0.0; phaselist[1]=180.0; exc.set_phaselist(phaselist); // rephasing lobe for excitation pulse exc_reph=SeqPulsarReph("exc_reph",exc); // initial preparation pulse exc_prep=exc; exc_prep.set_label("exc_prep"); exc_prep.set_flipangle(0.5*commonPars->get_FlipAngle()); exc_prep.set_phase(180.0); exc_prep_reph=SeqGradTrapez("exc_prep_reph",2.0*exc_reph.get_gradintegral().sum(),0.8*systemInfo->get_max_grad(),sliceDirection); ////////////////// Geometry: ///////////////////////////////// // calculate the resolution in the read Channel and set the number of phase encoding // steps so that we will obtain a uniform resolution in read and phase Channel: float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5),noedit); //////////////// Balanced Gradient Echo Module: ////////////// grech=SeqGradEcho("grech", exc, commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), encodingScheme(int(PhaseEncoding)), interleavedSegmented, 2, commonPars->get_ReductionFactor(),DEFAULT_ACL_BANDS,true,commonPars->get_PartialFourier()); grech.set_phaselist(phaselist); // +/- phase switching for SSFP //////////////// crusher Gradient: ////////////////////////////// double crusher_strength=0.5*systemInfo->get_max_grad(); double crusher_dur=4.0; crusher=SeqGradConstPulse("crusher",readDirection,crusher_strength,crusher_dur); //////////////// Loops //////////////////// reploop=SeqObjLoop("reploop"); sliceloop=SeqObjLoop("sliceloop"); peloop=SeqObjLoop("peloop"); phaseloop=SeqObjLoop("phaseloop"); //////////////// Timing Delays //////////////////// prepdelay=SeqDelay("prepdelay"); postdelay=SeqDelay("postdelay"); relaxdelay=SeqDelay("relaxdelay"); grechdummy=SeqDelay("grechdummy",grech.get_duration()-exc.get_duration()-exc_prep_reph.get_duration()); //////////////// building the sequence ////////////////////////////// kernel=SeqObjList("kernel"); kernel= grech + postdelay; dummykernel=SeqObjList("dummykernel"); dummykernel = exc + exc_prep_reph + grechdummy + postdelay; readout=SeqObjList("readout"); readout = dummyloop ( phaseloop( dummykernel )[exc.get_phaselist_vector()] )[DummyCycles] + peloop( phaseloop( kernel )[exc.get_phaselist_vector()][grech.get_phaselist_vector()][grech.get_pe_reorder_vector()] )[grech.get_pe_vector()]; shot=SeqObjList("shot"); shot = exc_prep + exc_prep_reph + prepdelay + readout + crusher; scan=SeqObjList("scan"); scan += reploop( sliceloop( shot + relaxdelay )[exc][exc_prep] )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } ////////////////////////////////////////////////// void method_rels(){ Log odinlog(this,"method_rels"); // TrueFISP timings, use minimum TE double TEprep=exc_prep.get_duration()-exc_prep.get_magnetic_center()+ exc_prep_reph.get_duration()+ exc.get_magnetic_center(); double TEpre=grech.get_acquisition_center()-exc.get_magnetic_center(); double TEpost=grech.get_duration()-grech.get_acquisition_center()+ exc.get_magnetic_center(); double TEmax=maxof3(TEprep,TEpre,TEpost); ODINLOG(odinlog,significantDebug) << "TEprep/pre/post/max=" << TEprep << "/" << TEpre << "/" << TEpost << "/" << TEmax << STD_endl; prepdelay=TEmax-TEprep; postdelay=TEmax-TEpost; commonPars->set_EchoTime(TEmax,noedit); // calculate relaxdelay to get the desired repetition time float scandur=shot.get_duration()*float(geometryInfo->get_nSlices()); if(scandur>commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(scandur); relaxdelay=(commonPars->get_RepetitionTime()-scandur)/float(geometryInfo->get_nSlices()); } ////////////////////////////////////////////////// void method_pars_set(){ } }; ////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinswi.cpp0000644000175000017500000001665311322062347013565 00000000000000#include class METHOD_CLASS : public SeqMethod { private: SeqPulsar exc; SeqPulsarReph exc_reph; SeqPulsarReph exc_reph_neg; SeqAcqRead acqread; SeqAcqRead negacqread; // need separate object since calling SeqAcqDeph on the same object with different polarity does not work SeqAcqDeph readdeph; SeqAcqDeph negreaddeph; SeqGradPhaseEncFlowComp pe; SeqGradPhaseEncFlowComp pe3d; SeqGradConstPulse crusher; SeqDelay exc2acq; SeqDelay relaxdelay; SeqObjList gradpart; SeqObjList scan; SeqObjList readout; SeqObjLoop peloop; SeqObjLoop peloop3d; SeqObjLoop reploop; SeqVecIter phaseiter; JDXfloat T1Ernst; public: METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("Fully flow-compensated FLASH sequence for Susceptibility Weighted Imaging. "); } void method_pars_init() { geometryInfo->set_Mode(voxel_3d); commonPars->set_MatrixSize(readDirection,256); commonPars->set_MatrixSize(phaseDirection,256,noedit); commonPars->set_RepetitionTime(50.0); commonPars->set_EchoTime(28.0); T1Ernst=1300.0; T1Ernst.set_minmaxval(0.0,5000.0).set_description("For optimum SNR, the flip angle will be set to the Ernst angle using this T1"); append_parameter(T1Ernst,"T1Ernst"); // fmapscan.init("fmapscan"); // append_parameter(fmapscan.get_parblock(),"FieldMapPars"); } void method_seq_init(){ Log odinlog(this,"method_seq_init"); ///////////////// Pulses: ///////////////////// // Excitation Pulse float spatres=3.0; float slicethick=geometryInfo->get_FOV(sliceDirection)-2.0*spatres; if(slicethickget_FlipAngle(), spatres, 512); exc.set_filter("Gauss"); exc.set_freqoffset(systemInfo->get_gamma() * exc.get_strength() / (2.0*PII) * geometryInfo->get_offset(sliceDirection) ); exc.set_pulse_type(excitation); // ODINLOG(odinlog,significantDebug) << "exc.rel_magnetic_center/get_pulsduration" << exc.get_rel_magnetic_center() << "/" << exc.get_pulsduration() << STD_endl; // ODINLOG(odinlog,significantDebug) << "exc.get_Gz()" << exc.get_Gz() << STD_endl; // rephasing lobe for excitation pulse exc_reph=SeqPulsarReph("exc_reph",exc); exc_reph_neg=SeqPulsarReph("exc_reph",exc); exc_reph_neg.invert_strength(); ////////////////// Geometry: ///////////////////////////////// // calculate the resolution in the read Channel and set the number of phase encoding // steps so that we will obtain a uniform resolution in read and phase Channel: float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5),noedit); commonPars->set_MatrixSize(sliceDirection,int(secureDivision(geometryInfo->get_FOV(sliceDirection),resolution)+0.5),noedit); //////////////// Phase Encoding: ////////////////////////// float t0=exc.get_duration()-exc.get_magnetic_center()+ exc_reph.get_duration()+ exc_reph.get_duration()+ exc_reph_neg.get_duration(); pe=SeqGradPhaseEncFlowComp("pe", t0, commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), phaseDirection, 0.25*systemInfo->get_max_grad(), linearEncoding, noReorder, 1, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, commonPars->get_PartialFourier()); //////////////// Phase Encoding (3D): ////////////////////////// pe3d=SeqGradPhaseEncFlowComp("pe3d", t0, commonPars->get_MatrixSize(sliceDirection),geometryInfo->get_FOV(sliceDirection), sliceDirection, pe.get_strength(), linearEncoding, noReorder, 1, commonPars->get_ReductionFactor()); //////////////// Readout: ////////////////////////////// acqread=SeqAcqRead("acqread",commonPars->get_AcqSweepWidth(),commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection),readDirection); negacqread=acqread; readdeph=SeqAcqDeph("readdeph", acqread); negreaddeph=SeqAcqDeph("negreaddeph", negacqread, spinEcho); //////////////// RF Spoiling: ////////////////////////////// if(commonPars->get_RFSpoiling()) { exc.set_phasespoiling(); acqread.set_phasespoiling(); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(acqread.get_phaselist_vector()); } //////////////// Crusher: ////////////////////////////// double crusher_strength=0.5*systemInfo->get_max_grad(); double crusher_integral=4.0*fabs(readdeph.get_gradintegral().sum()); double crusher_dur=secureDivision(crusher_integral, crusher_strength); crusher=SeqGradConstPulse("crusher",readDirection,crusher_strength,crusher_dur); //////////////// Field-map template: ////////////////////////////// // fmapscan.build_seq(100.0, SeqObjList(), commonPars->get_RepetitionTime()); //////////////// several padding delays //////////////////// exc2acq=SeqDelay("exc2acq"); relaxdelay=SeqDelay("relaxdelay"); //////////////// total sequence: ////////////////////////////// gradpart=SeqObjList("gradpart"); scan=SeqObjList("scan"); readout=SeqObjList("readout"); peloop=SeqObjLoop("peloop"); peloop3d=SeqObjLoop("peloop3d"); reploop=SeqObjLoop("reploop"); gradpart = (negreaddeph+readdeph)/pe/pe3d; readout = exc + exc_reph + exc_reph + exc_reph_neg + gradpart + exc2acq + readdeph + acqread + crusher; if(commonPars->get_RFSpoiling()) readout += phaseiter; // scan += fmapscan + relaxdelay; scan+= reploop( peloop3d( peloop( readout + relaxdelay )[pe] )[pe3d] )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } void method_rels(){ // TE double minTE=exc.get_duration()-exc.get_magnetic_center()+ exc_reph.get_duration()+ exc_reph.get_duration()+ exc_reph_neg.get_duration()+ gradpart.get_duration()+ readdeph.get_duration()+ acqread.get_acquisition_center(); if(commonPars->get_EchoTime()set_EchoTime(minTE); exc2acq=commonPars->get_EchoTime()-minTE; // TR // calculate relaxdelay to get the desired repetition time float readoutdur=readout.get_duration(); if(readoutdur > commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(readoutdur); relaxdelay.set_duration( commonPars->get_RepetitionTime()-readoutdur ); // calculate Ernst angle accordng to TR float flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), T1Ernst) ) ); commonPars->set_FlipAngle( flipangle, noedit ); exc.set_flipangle( flipangle ); } void method_pars_set(){ // inform the readout about the used phase encoding and slice vector (for automatic reconstruction) acqread.set_reco_vector(line,pe); acqread.set_reco_vector(line3d,pe3d); recoInfo->set_PreProc3D("swi"); recoInfo->set_PostProc3D("mip"); // recoInfo->set_CmdLineOpts("-ff CosSq -fp 0.5"); } }; // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/tj_messer.cpp0000644000175000017500000005311511455553544014111 00000000000000 // include the headers of all sequence classes #include // The whole EPI sequence (including reco) is a C++ class class METHOD_CLASS : public SeqMethod { private: JDXint NumOfEchoes; JDXbool SEAcquisition; JDXint Blades; JDXint Shots; JDXfloat PulseDur; JDXbool RampSampling; JDXbool FatSaturation; JDXbool fMRITrigger; JDXfloat FWbVal; JDXbool FieldMap; JDXdoubleArr TEs; // sequence objects which are the elementary objects // to build the EPI sequence SeqPulsar exc; SeqPulsar refoc; SeqSat fatsat; SeqAcqEPI ge_epi; SeqAcqEPI ge_epi_template; SeqAcqEPI ge_epi_grappa; SeqAcqEPI se_epi; SeqAcqEPI se_epi_template; SeqAcqEPI se_epi_grappa; SeqAcqDeph ge_deph; SeqAcqDeph se_deph; SeqAcqDeph deph_template; // one for both GE and SE SeqAcqDeph ge_deph_grappa; SeqAcqDeph se_deph_grappa; SeqAcqDeph ge_reph; SeqAcqDeph se_reph; SeqAcqDeph reph_template; // one for both GE and SE SeqAcqDeph ge_reph_grappa; SeqAcqDeph se_reph_grappa; SeqDelay sedelay; SeqGradTrapezParallel rewind; SeqGradTrapezParallel rewind_template; SeqDelay rewind_paddelay; SeqVecIter phaseiter; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop segloop; SeqObjLoop grappaloop; SeqObjLoop echoloop; SeqObjLoop dummyloop; SeqDelay trdelay; SeqObjVector gerewindvec; SeqObjVector gerewindvec_template; SeqObjVector gerewindvec_grappa; SeqObjList gepart; SeqObjList gepart_template; SeqObjList gepart_grappa; SeqDelay gepart_dummy; SeqObjVector serewindvec; SeqObjVector serewindvec_template; SeqObjVector serewindvec_grappa; SeqObjList separt; SeqObjList separt_template; SeqObjList separt_grappa; SeqDelay separt_dummy; SeqObjList scan; SeqObjList templatepart; SeqObjList grappapart; SeqObjList imagingpart; SeqObjList dummypart; SeqObjList slicepart; SeqObjList slicepart_dummy; SeqObjList slicepart_template; SeqObjList slicepart_grappa; SeqObjList preppart; SeqDelay exc2acq; SeqDelay exc2refoc; SeqDelay refoc2acq; SeqGradConstPulse spoiler; SeqTrigger trigger; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; SeqDiffWeight fw; SeqGradTrapez fw1st; SeqGradTrapezParallel fw2nd_reph; SeqObjList fwpart; SeqDelay fwmid; SeqObjLoop bladeloop; SeqRotMatrixVector bladerot; dvector bladeangels; SeqFieldMap fmapscan; public: // This constructor creates an empty EPI sequence METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("Multi-gradient-Echo Single-shot Sampling of Echo Refocussing (MESSER), a combined gradient- and spin-echo sequence using parallel imaging."); } void method_pars_init() { // In this function, parameters are initialized and default values are set commonPars->set_MatrixSize(readDirection,64); commonPars->set_MatrixSize(phaseDirection,64,noedit); commonPars->set_NumOfRepetitions(1); commonPars->set_RepetitionTime(1000.0); commonPars->set_AcqSweepWidth(100.0); commonPars->set_ReductionFactor(3); NumOfEchoes=3; NumOfEchoes.set_description("Number of echoes per period"); append_parameter(NumOfEchoes,"NumOfEchoes"); SEAcquisition=true; SEAcquisition.set_description("Sample the spin echo directly with the last EPI"); append_parameter(SEAcquisition,"SEAcquisition"); Blades=1; Blades.set_description("Number of long-axis PROPELLER blades"); append_parameter(Blades,"Blades"); Shots=1; Shots.set_description("Number of shots, multi-shot (segmented) EPI if Shots>1"); append_parameter(Shots,"Shots"); PulseDur=4.0; // start with large duration so that sequence can be loaded PulseDur.set_unit(ODIN_TIME_UNIT); PulseDur.set_description("Pulse duration of excitation and refocusing pulse"); append_parameter(PulseDur,"PulseDur"); RampSampling=false; RampSampling.set_description("Perform sampling during gradient ramps"); append_parameter(RampSampling,"RampSampling"); FatSaturation=true; FatSaturation.set_description("Saturation of fat resonance prior to excitation"); append_parameter(FatSaturation,"FatSaturation"); fMRITrigger=true; fMRITrigger.set_description("External triggering"); append_parameter(fMRITrigger,"fMRITrigger"); FWbVal=0.0; FWbVal.set_unit("s/mm^2"); FWbVal.set_description("b-Value of Weak flow weighting after excitation"); append_parameter(FWbVal,"FWbVal"); FieldMap=false; FieldMap.set_description("Fieldmap pre-scan for distortion correction"); append_parameter(FieldMap,"FieldMap"); fmapscan.init("fmapscan"); append_parameter(fmapscan.get_parblock(),"FieldMapPars"); TEs.resize(2*NumOfEchoes); TEs.set_description("Echo times"); append_parameter(TEs,"TEs"); } void method_seq_init() { Log odinlog(this,"method_seq_init"); if(NumOfEchoes<2) NumOfEchoes=2; ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float slicegap=geometryInfo->get_sliceDistance()-slicethick; // excitation pulse exc=SeqPulsarSinc("exc",slicethick,false,PulseDur,commonPars->get_FlipAngle()); exc.set_freqlist( systemInfo->get_gamma() * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); exc.set_pulse_type(excitation); // Slightly thicker refocusing slice for better SNR // Since the same spatial resolution is used for exc and refoc, the gradient strengths will be the same float extra_slicethick_refoc=STD_min(0.5*slicethick, 0.3*slicegap); // refocusing pulse refoc=SeqPulsarSinc("refoc",slicethick+extra_slicethick_refoc,false,PulseDur,180.0); refoc.set_freqlist( systemInfo->get_gamma() * refoc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); if(!commonPars->get_RFSpoiling()) refoc.set_phase(90.0); refoc.set_pulse_type(refocusing); // fat saturation pulse fatsat=SeqSat("fatsat",fat); //////////////// EPI-Readout: ////////////////////////////// // set equivalent resolution in read and phase direction float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); int pelines=int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5); commonPars->set_MatrixSize(phaseDirection, pelines, noedit); float pefov=geometryInfo->get_FOV(phaseDirection); if(Blades>1) { pelines=int(0.5*PII*commonPars->get_MatrixSize(readDirection)/Blades+0.5); pefov=geometryInfo->get_FOV(readDirection); // quadratic FOV commonPars->set_MatrixSize(phaseDirection,commonPars->get_MatrixSize(readDirection),noedit); // quadratic size } float os_read=1.25; // slight oversampling to allow off-center FOV if(Blades>1) os_read=2.0; ge_epi=SeqAcqEPI("ge_epi",commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), pelines, pefov, Shots, commonPars->get_ReductionFactor(), os_read, "",0,0,linear,RampSampling,1.0,commonPars->get_PartialFourier()); // Phase-correction template ge_epi_template=ge_epi; ge_epi_template.set_label("ge_epi_template"); ge_epi_template.set_template_type(phasecorr_template); // Full multi-shot EPI readout as GRAPPA training data ge_epi_grappa=ge_epi; ge_epi_grappa.set_label("ge_epi_grappa"); ge_epi_grappa.set_template_type(grappa_template); se_epi=ge_epi; se_epi_template=ge_epi_template; se_epi_grappa=ge_epi_grappa; // EPI pre-dephase gradient ge_deph=SeqAcqDeph("ge_deph",ge_epi,FID); se_deph=SeqAcqDeph("se_deph",se_epi,FID); deph_template=SeqAcqDeph("deph_template",ge_epi_template,FID); ge_deph_grappa=SeqAcqDeph("ge_deph_grappa",ge_epi_grappa,FID); se_deph_grappa=SeqAcqDeph("se_deph_grappa",se_epi_grappa,FID); // EPI post-rephase gradients ge_reph=SeqAcqDeph("ge_reph",ge_epi,rephase); se_reph=SeqAcqDeph("se_reph",se_epi,rephase); reph_template=SeqAcqDeph("reph_template",ge_epi_template,rephase); ge_reph_grappa=SeqAcqDeph("ge_reph_grappa",ge_epi_grappa,rephase); se_reph_grappa=SeqAcqDeph("se_reph_grappa",se_epi_grappa,rephase); // EPI rewinder after each echo fvector gradint(3); float rewind_strength=0.4*systemInfo->get_max_grad(); // OK for stimulation monitor gradint=ge_reph.get_gradintegral()+ge_deph.get_gradintegral(); // collapse rephase and dephase into one gradient pulse rewind=SeqGradTrapezParallel("rewind",gradint[0],gradint[1],gradint[2],rewind_strength); gradint=reph_template.get_gradintegral()+deph_template.get_gradintegral(); rewind_template=SeqGradTrapezParallel("rewind_template",gradint[0],gradint[1],gradint[2],rewind_strength); ODINLOG(odinlog,significantDebug) << "rewind/rewind_template.get_duration()=" << rewind.get_duration() << "/" << rewind_template.get_duration() << STD_endl; rewind_paddelay=SeqDelay("rewind_paddelay",rewind.get_duration()-rewind_template.get_duration()); /////////////////// Rotation of Blades //////////////////////////////////////////////// bladerot=SeqRotMatrixVector("bladerot"); if(Blades>1) { bladeangels.resize(Blades); for(int iblade=0; ibladeget_RFSpoiling()) { // recommended by Goerke et al., NMR Biomed. 18, 534-542 (2005) int plistsize=16; double plistincr=45.0; exc.set_phasespoiling(plistsize, plistincr); refoc.set_phasespoiling(plistsize, plistincr, 90.0); ge_epi.set_phasespoiling(plistsize, plistincr); ge_epi_template.set_phasespoiling(plistsize, plistincr); ge_epi_grappa.set_phasespoiling(plistsize, plistincr); se_epi.set_phasespoiling(plistsize, plistincr); se_epi_template.set_phasespoiling(plistsize, plistincr); se_epi_grappa.set_phasespoiling(plistsize, plistincr); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(refoc.get_phaselist_vector()); phaseiter.add_vector(ge_epi.get_phaselist_vector()); phaseiter.add_vector(ge_epi_template.get_phaselist_vector()); phaseiter.add_vector(ge_epi_grappa.get_phaselist_vector()); phaseiter.add_vector(se_epi.get_phaselist_vector()); phaseiter.add_vector(se_epi_template.get_phaselist_vector()); phaseiter.add_vector(se_epi_grappa.get_phaselist_vector()); } //////////////// Loops: ////////////////////////////// // loop to iterate over slices sliceloop=SeqObjLoop("sliceloop"); // loop to iterate over repetitions reploop=SeqObjLoop("reploop"); // loop to iterate over segments segloop=SeqObjLoop("segloop"); // loop to iterate over GRAPPA interleaves grappaloop=SeqObjLoop("grappaloop"); // loop to iterate over EPI modules echoloop=SeqObjLoop("echoloop"); // loop to iterate over dummy cycles dummyloop=SeqObjLoop("dummyloop"); // loop over zoom sats // zoomloop=SeqObjLoop("zoomloop"); // loop to iterate over PROPELLER blades bladeloop=SeqObjLoop("bladeloop"); //////////////// Timing Delays: ////////////////////////////// // TR delay trdelay=SeqDelay("trdelay"); //////////////// Spoiler Gradient: ////////////////////////////// float spoiler_strength=0.5*systemInfo->get_max_grad(); float spoiler_integral=4.0*fabs(ge_deph.get_gradintegral().sum()); float spoiler_dur=secureDivision(spoiler_integral,spoiler_strength); spoiler=SeqGradConstPulse("spoiler",sliceDirection,spoiler_strength,spoiler_dur); //////////////// Crusher Gradient: ////////////////////////////// float crusher_strength=0.3*systemInfo->get_max_grad(); // Moderate strength to avoid problems with stimulation float crusher_integral=2.0*spoiler_integral; crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, crusher_strength); crusherdelay=SeqDelay("crusherdelay",1.0); // Small delay to avoid gradient-induced stimulation //////////////// Flow Weighting: ////////////////////////////// // reset fwpart.clear(); if(FWbVal>0.0) { fwmid=SeqDelay("fwmid",1.0); // Small delay to avoid nerve stimulation fvector bVals(1); bVals[0]=1000.0*FWbVal; fw=SeqDiffWeight("fw", bVals, 0.8*systemInfo->get_max_grad(), fwmid, sliceDirection); // Combine slice rephaser and flow weighting float fwint=fw.get_grad1().get_gradintegral()[sliceDirection]+exc.get_reph_gradintegral()[sliceDirection]; fw1st=SeqGradTrapez("fw1st", fwint, sliceDirection, fw.get_grad1().get_gradduration()); // fw2nd=SeqGradTrapez("fw2nd", fw.get_grad2().get_gradintegral()[sliceDirection], sliceDirection, fw.get_grad2().get_gradduration()); fw2nd_reph=SeqGradTrapezParallel("fw2nd_reph",0.0,0.0,fw.get_grad2().get_gradintegral()[sliceDirection],fw1st.get_strength()); fwpart=fw1st+fwmid+fw2nd_reph; } else { fw2nd_reph=SeqGradTrapezParallel("fw2nd_reph",0.0,0.0,exc.get_reph_gradintegral()[sliceDirection],0.8*systemInfo->get_max_grad()); fwpart=fw2nd_reph; } //////////////// fMRI trigger: ////////////////////////////// trigger=SeqTrigger("fmri_trigger",1.0); //////////////// Field-map template: ////////////////////////////// if(FieldMap) { if(FatSaturation) fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0,fatsat); // pass fat saturation on to field-map scan else fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0); } //////////////// Build the sequence: ////////////////////////////// // add fat saturation to template and repetitions if(FatSaturation) preppart += fatsat; if(fMRITrigger) slicepart += trigger; // GE part ivector ge_iv(NumOfEchoes); int i; for(i=0; i1) { gepart. set_gradrotmatrixvector(bladerot); gepart_template.set_gradrotmatrixvector(bladerot); gepart_grappa. set_gradrotmatrixvector(bladerot); separt. set_gradrotmatrixvector(bladerot); separt_template.set_gradrotmatrixvector(bladerot); separt_grappa. set_gradrotmatrixvector(bladerot); } sedelay=SeqDelay("sedelay",0.0); imagingpart= preppart + exc + fwpart + gepart + refoc + spoiler + sedelay + separt + crusherdelay + crusher + crusherdelay; dummypart= preppart + exc + fwpart + gepart_dummy + refoc + spoiler + sedelay + separt_dummy + crusherdelay + crusher + crusherdelay; templatepart= preppart + exc + fwpart + gepart_template + refoc + spoiler + sedelay + separt_template + crusherdelay + crusher + crusherdelay; grappapart= preppart + exc + fwpart + gepart_grappa + refoc + spoiler + sedelay + separt_grappa + crusherdelay + crusher + crusherdelay; slicepart += sliceloop( imagingpart + trdelay )[exc][refoc]; slicepart_dummy = sliceloop( dummypart + trdelay )[exc][refoc]; slicepart_template = sliceloop( templatepart + trdelay )[exc][refoc]; slicepart_grappa = sliceloop( grappapart + trdelay )[exc][refoc]; if(commonPars->get_RFSpoiling()) { slicepart += phaseiter; slicepart_dummy += phaseiter; slicepart_template += phaseiter; slicepart_grappa += phaseiter; } if(FieldMap) scan += fmapscan + trdelay; scan += dummyloop( slicepart_dummy )[3]; // template scan for phase correction scan+= bladeloop( slicepart_template )[bladerot]; if(commonPars->get_ReductionFactor()>1) { // Fully sampled k-space scan+= grappaloop( bladeloop( segloop( slicepart_grappa )[ge_deph_grappa.get_epi_segment_vector()][ge_reph_grappa.get_epi_segment_vector()][se_deph_grappa.get_epi_segment_vector()][se_reph_grappa.get_epi_segment_vector()] )[bladerot] )[ge_deph_grappa.get_epi_reduction_vector()][ge_reph_grappa.get_epi_reduction_vector()][se_deph_grappa.get_epi_reduction_vector()][se_reph_grappa.get_epi_reduction_vector()]; } // actual scan loop scan+= reploop( bladeloop( segloop( slicepart )[ge_deph.get_epi_segment_vector()][se_deph.get_epi_segment_vector()][ge_reph.get_epi_segment_vector()][se_reph.get_epi_segment_vector()] )[bladerot] )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } void method_rels() { Log odinlog(this,"method_rels"); double TEexc= exc.get_duration() - exc.get_magnetic_center() + fwpart.get_duration(); ODINLOG(odinlog,significantDebug) << "TEexc=" << TEexc << STD_endl; // Fixed TE according to GE part double TEhalf = TEexc + gepart.get_duration() // + spoiler.get_duration() + refoc.get_magnetic_center(); commonPars->set_EchoTime(2.0*TEhalf); int nechoes_se=NumOfEchoes; TEs.resize(NumOfEchoes+nechoes_se); double TEdeph=ge_deph.get_duration(); double TEepi=ge_epi.get_duration()+rewind.get_duration(); double TEacq=ge_epi.get_acquisition_center(); ODINLOG(odinlog,significantDebug) << "TEdeph/TEepi/TEacq=" << TEdeph << "/" << TEepi << "/" << TEacq << STD_endl; // GE echo times int i; for(i=0; iget_EchoTime()) << STD_endl; } } if(SEAcquisition) { double tediff=commonPars->get_EchoTime()-TEs[2*NumOfEchoes-1]; sedelay=tediff; for(i=0; iget_RepetitionTime()set_RepetitionTime(slicedur); trdelay=(commonPars->get_RepetitionTime()-slicedur)/double(geometryInfo->get_nSlices()); } void method_pars_set() { // extra information for the automatic reconstruction ge_epi. set_reco_vector(slice,exc); ge_epi_template.set_reco_vector(slice,exc); ge_epi_grappa. set_reco_vector(slice,exc); se_epi. set_reco_vector(slice,exc); se_epi_template.set_reco_vector(slice,exc); se_epi_grappa. set_reco_vector(slice,exc); // Index for TEs ge_epi. set_reco_vector(userdef,gerewindvec); ge_epi_template.set_reco_vector(userdef,gerewindvec_template); ge_epi_grappa. set_reco_vector(userdef,gerewindvec_grappa); se_epi. set_reco_vector(userdef,serewindvec); se_epi_template.set_reco_vector(userdef,serewindvec_template); se_epi_grappa. set_reco_vector(userdef,serewindvec_grappa); recoInfo->set_DimValues(userdef,TEs); if(Blades>1) { ge_epi. set_reco_vector(cycle,bladerot); ge_epi_template.set_reco_vector(cycle,bladerot); ge_epi_grappa. set_reco_vector(cycle,bladerot); se_epi. set_reco_vector(cycle,bladerot); se_epi_template.set_reco_vector(cycle,bladerot); se_epi_grappa. set_reco_vector(cycle,bladerot); recoInfo->set_DimValues(cycle,bladeangels); } recoInfo->set_PostProc3D("usercoll | messer"); recoInfo->set_CmdLineOpts("-ff Hamming -fp 0.8"); } }; ///////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinrare.cpp0000644000175000017500000002650611363773557013733 00000000000000#include class METHOD_CLASS : public SeqMethod { private: SeqPulsar exc; SeqPulsarReph exc_reph; SeqPulsar refoc; SeqAcqRead acqread; SeqAcqRead acqread_templ; SeqAcqDeph readdeph; SeqGradPhaseEnc pe1,pe2; SeqGradPhaseEnc pe3d1,pe3d2; SeqGradConstPulse spoiler; SeqDelay echopad; SeqDelay excpad; SeqDelay relaxdelay; SeqObjList echopart; SeqObjList echopart_templ; SeqGradTrapezParallel postexc; SeqObjList scan; SeqObjList readout; SeqObjList readout_templ; SeqObjList pe1part; SeqObjList pe2part; SeqDelay pe1delay; SeqDelay pe2delay; SeqObjLoop echoloop; SeqObjLoop segloop; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop loop3d; SeqVector echoindex; // index vector for echoes JDXenum PhaseEncoding; JDXint NumOfSegments; JDXdouble PulseDur; JDXdouble refocFlipAngle; JDXdouble SpoilerStrength; JDXdouble SpoilerDuration; JDXbool TemplScan; public: METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("Segmented 2D/3D RARE (Turbo SE) Sequence. " "Phase correction is possible by using a prescan with phase-encoding gradients switched off. "); } unsigned int numof_testcases() const {return 3;} void method_pars_init() { PhaseEncoding.add_item("Linear",linearEncoding); PhaseEncoding.add_item("Reverse",reverseEncoding); PhaseEncoding.add_item("CenterOut",centerOutEncoding); PhaseEncoding.add_item("CenterIn",centerInEncoding); PhaseEncoding=centerOutEncoding; PhaseEncoding.set_description("Phase encoding order"); NumOfSegments=4; NumOfSegments.set_description("Number of excitation to acquire one slice/partition"); PulseDur=5.0; PulseDur.set_unit(ODIN_TIME_UNIT).set_description("Duration of excitation and refocusing pulse"); refocFlipAngle=180.0; refocFlipAngle.set_unit(ODIN_ANGLE_UNIT).set_description("Refocusing flip angle"); SpoilerStrength=50.0; SpoilerStrength.set_unit("%").set_description("Spoiler-gradient strength in percent of max gradient amplitude"); SpoilerDuration=1.0; SpoilerDuration.set_unit(ODIN_TIME_UNIT).set_description("Spoiler-gradient duration"); TemplScan=true; TemplScan.set_description("Acquire and use template scan for phase correction"); // alternative default settings for sequence test if(get_current_testcase()==1) { geometryInfo->set_Mode(voxel_3d); PulseDur=6.0; refocFlipAngle=120.0; SpoilerStrength=30.0; SpoilerDuration=2.0; } if(get_current_testcase()==2) { commonPars->set_ReductionFactor(3); TemplScan=false; NumOfSegments=1; } append_parameter(PhaseEncoding,"PhaseEncoding"); append_parameter(NumOfSegments,"NumOfSegments"); append_parameter(PulseDur,"PulseDur"); append_parameter(TemplScan,"TemplScan"); append_parameter(refocFlipAngle,"refocFlipAngle"); append_parameter(SpoilerStrength,"SpoilerStrength"); append_parameter(SpoilerDuration,"SpoilerDuration"); } ///////////////////////////////////////////////////////////////////////////////////////////////// void method_seq_init(){ Log odinlog(this,"method_seq_init"); float gamma=systemInfo->get_gamma(""); ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); if(geometryInfo->get_Mode()==voxel_3d) { slicethick=geometryInfo->get_FOV(sliceDirection); } float spatres=slicethick/4.0; // Excitation Pulse exc=SeqPulsarSinc("exc",slicethick,false,PulseDur,commonPars->get_FlipAngle(),spatres,256); if(geometryInfo->get_Mode()==slicepack) exc.set_freqlist (gamma * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); if(geometryInfo->get_Mode()==voxel_3d) exc.set_freqoffset(gamma * exc.get_strength() / (2.0*PII) * geometryInfo->get_offset(sliceDirection) ); exc.set_pulse_type(excitation); // rephasing lobe for excitation pulse exc_reph=SeqPulsarReph("exc_reph",exc); // Refocusing Pulse refoc=SeqPulsarSinc("refoc",slicethick,false,PulseDur,refocFlipAngle,spatres,256); refoc.set_phase(90.0); if(geometryInfo->get_Mode()==slicepack) refoc.set_freqlist (gamma * refoc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); if(geometryInfo->get_Mode()==voxel_3d) refoc.set_freqoffset(gamma * refoc.get_strength() / (2.0*PII) * geometryInfo->get_offset(sliceDirection) ); refoc.set_pulse_type(refocusing); ////////////////// Geometry: ///////////////////////////////// // calculate the resolution in the read Channel and set the number of phase encoding // steps so that we will obtain a uniform resolution in read and phase Channel: float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5),noedit); commonPars->set_MatrixSize(sliceDirection,int(secureDivision(geometryInfo->get_FOV(sliceDirection),resolution)+0.5),noedit); //////////////// Phase Encoding: ////////////////////////// pe1=SeqGradPhaseEnc("pe1",commonPars->get_MatrixSize(phaseDirection),geometryInfo->get_FOV(phaseDirection), phaseDirection,0.25*systemInfo->get_max_grad(), encodingScheme(int(PhaseEncoding)),interleavedSegmented,NumOfSegments, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, commonPars->get_PartialFourier()); pe2=pe1; pe2.set_label("pe2"); pe2.invert_strength(); // Echo indices for template correction unsigned int nechoes=((const SeqVector&)pe1).get_numof_iterations(); ODINLOG(odinlog,significantDebug) << "nechoes=" << nechoes << STD_endl; echoindex=SeqVector("echoindex",nechoes); //////////////// Phase Encoding (3D): ////////////////////////// if(geometryInfo->get_Mode()==voxel_3d) { pe3d1=SeqGradPhaseEnc("pe3d1",commonPars->get_MatrixSize(sliceDirection),geometryInfo->get_FOV(sliceDirection),pe1.get_constduration(), sliceDirection, linearEncoding, noReorder, 1, commonPars->get_ReductionFactor()); pe3d2=pe3d1; pe3d2.set_label("pe3d2"); pe3d2.invert_strength(); } //////////////// Readout: ////////////////////////////// acqread=SeqAcqRead("acqread",commonPars->get_AcqSweepWidth(),commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection),readDirection); acqread_templ=SeqAcqRead(acqread); acqread_templ.set_label("acqread_templ"); acqread_templ.set_template_type(phasecorr_template); readdeph=SeqAcqDeph("readdeph",acqread,spinEcho); //////////////// Spoiler: ////////////////////////////// float spoiler_strength_phys=(double)SpoilerStrength/100.0*systemInfo->get_max_grad(); spoiler=SeqGradConstPulse("spoiler",phaseDirection,spoiler_strength_phys,SpoilerDuration); //////////////// several padding delays //////////////////// excpad=SeqDelay("excpad"); echopad=SeqDelay("echopad"); relaxdelay=SeqDelay("relaxdelay"); pe1delay=SeqDelay("pe1delay"); pe2delay=SeqDelay("pe2delay"); //////////////// total sequence: ////////////////////////////// echopart=SeqObjList("echopart"); echopart_templ=SeqObjList("echopart_templ"); scan=SeqObjList("scan"); echoloop=SeqObjLoop("echoloop"); segloop=SeqObjLoop("segloop"); sliceloop=SeqObjLoop("sliceloop"); reploop=SeqObjLoop("reploop"); loop3d=SeqObjLoop("loop3d"); readout=SeqObjList("readout"); fvector gradint(3); gradint=0.0; gradint+=exc_reph.get_gradintegral(); gradint+=readdeph.get_gradintegral(); gradint+=spoiler.get_gradintegral(); postexc=SeqGradTrapezParallel("postexc",gradint[0],gradint[1],gradint[2],0.5*systemInfo->get_max_grad()); ODINLOG(odinlog,significantDebug) << "postexc. get_gradintegral()=" << postexc.get_gradintegral().printbody() << STD_endl; float spoiler_k_diff=systemInfo->get_gamma()*(spoiler.get_gradintegral()[1]-postexc.get_gradintegral()[1]); ODINLOG(odinlog,significantDebug) << "spoiler_k_diff=" << spoiler_k_diff << STD_endl; if(geometryInfo->get_Mode()==voxel_3d) { pe1part+=pe1/pe3d1; pe2part+=pe2/pe3d2; } else { pe1part+=pe1; pe2part+=pe2; } pe1delay=SeqDelay("pe1delay",pe1part.get_duration()); pe2delay=SeqDelay("pe2delay",pe2part.get_duration()); echopart_templ= refoc + spoiler + echopad + pe1delay + acqread_templ + pe2delay + echopad + spoiler; echopart = refoc + spoiler + echopad + pe1part + acqread + pe2part + echopad + spoiler; readout_templ = exc + postexc + excpad + echoloop(echopart_templ)[echoindex]; readout = exc + postexc + excpad + echoloop(echopart) [pe1][pe2][echoindex]; if(geometryInfo->get_Mode()==voxel_3d) { if(TemplScan) { scan+= readout_templ + relaxdelay; } scan+= reploop( segloop( loop3d( readout + relaxdelay )[pe3d1][pe3d2] )[pe1.get_reorder_vector()][pe2.get_reorder_vector()] )[commonPars->get_NumOfRepetitions()]; } else { if(TemplScan) { scan+= sliceloop( readout_templ + relaxdelay )[exc][refoc]; } scan+= reploop( segloop( sliceloop( readout + relaxdelay )[exc][refoc] )[pe1.get_reorder_vector()][pe2.get_reorder_vector()] )[commonPars->get_NumOfRepetitions()]; } set_sequence( scan ); } ///////////////////////////////////////////////////////////////////////////////////////////////// void method_rels(){ Log odinlog(this,"method_rels"); // CPMG timings double TE1=exc.get_duration()-exc.get_magnetic_center()+ postexc.get_duration()+ refoc.get_magnetic_center(); double TE2=(echopart.get_duration())/2.; ODINLOG(odinlog,significantDebug) << "TE1/TE2=" << TE1 << "/" << TE2 << STD_endl; if(TE2-TE1 < 0) echopad.set_duration(echopad.get_duration()-(TE2-TE1)); else excpad.set_duration(excpad.get_duration()+(TE2-TE1)); ODINLOG(odinlog,significantDebug) << "echopad=" << echopad.get_duration() << STD_endl; ODINLOG(odinlog,significantDebug) << "excpad=" << excpad.get_duration() << STD_endl; commonPars->set_EchoTime(echopart.get_duration(),noedit); // calculate relaxdelay to get the desired repetition time float scandur=readout.get_duration()*float(geometryInfo->get_nSlices()); if(scandur>commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(scandur); relaxdelay=(commonPars->get_RepetitionTime()-scandur)/float(geometryInfo->get_nSlices()); } ///////////////////////////////////////////////////////////////////////////////////////////////// void method_pars_set(){ // inform the readout about the used phase encoding and slice vector (for automatic reconstruction) acqread.set_reco_vector(line,pe1); acqread_templ.set_reco_vector(echo,echoindex); acqread.set_reco_vector(echo,echoindex); if(geometryInfo->get_Mode()==voxel_3d) { acqread.set_reco_vector(line3d,pe3d1); } acqread.set_reco_vector(slice,exc); acqread_templ.set_reco_vector(slice,exc); } }; ///////////////////////////////////////////////////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinpilot.cpp0000644000175000017500000002363011455553544014116 00000000000000////////////////////////////////////////////////////////////////////////////// // // A navigator sequence for the ODIN framework // ////////////////////////////////////////////////////////////////////////////// // includes for the sequence objects #include // The method itself is a class that is derived from // an abstract base class 'SeqMethod' that contains all // routines common to all methods: class METHOD_CLASS : public SeqMethod { public: // Constructor that takes the methods identifier (unique string) as its argument METHOD_CLASS(const STD_string& label); // virtual functions that are overwritten in this method to build the sequence, // calculate parameter relations, etc.: void method_pars_init(); void method_seq_init(); void method_rels(); void method_pars_set(); private: // Parameters for this method: JDXfloat T1Ernst; JDXint DummyCycles; JDXint NumSagSlices; JDXint NumCorSlices; JDXint NumAxiSlices; JDXfloat PilotSliceDist; // Sequence objects for this method: SeqPulsar exc; SeqDelay relaxdelay; SeqObjLoop peloop; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop dummyloop; SeqObjList scanpart; SeqObjList dummypart; SeqDelay dummypad; SeqGradEcho grech; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; SeqRotMatrixVector pilotrot; unsigned int nslices; ivector nslices_dir; dvector dirvec; Geometry area[n_orientations]; }; //////////////////////////////////////////////////////////////////////////////////// METHOD_CLASS::METHOD_CLASS (const STD_string& label) : SeqMethod(label) { // Put in here all stuff that will once be initialised and // never changed // Specify a short description of the method set_description("Navigator which acquires three orthogonal sets of slices." ); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_init() { // In this function the methods parameters will be initialised // Assign default values: commonPars->set_RepetitionTime(300.0); commonPars->set_AcqSweepWidth(25.0); commonPars->set_MatrixSize(readDirection,128); // set default values and a short a description (which // will appear as a tooltip in the UI) for each parameter T1Ernst=1300.0; T1Ernst.set_minmaxval(0.0,5000.0).set_description("For optimum SNR, the flip angle will be set to the Ernst angle using this T1"); DummyCycles=3; DummyCycles.set_description("Number of dummy shots before actual acquisition"); NumSagSlices=3; NumSagSlices.set_description("Number of sagittal slices in Pilot"); NumCorSlices=3; NumCorSlices.set_description("Number of coronal slices in Pilot"); NumAxiSlices=3; NumAxiSlices.set_description("Number of axial slices in Pilot"); PilotSliceDist=25.0; PilotSliceDist.set_description("Slice distance of Pilot"); // Make method specific parameters visible in the user interface append_parameter(T1Ernst,"T1Ernst"); append_parameter(DummyCycles,"DummyCycles"); append_parameter(NumSagSlices,"NumSagSlices"); append_parameter(NumCorSlices,"NumCorSlices"); append_parameter(NumAxiSlices,"NumAxiSlices"); append_parameter(PilotSliceDist,"PilotSliceDist"); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_seq_init() { Log odinlog(this,"method_seq_init"); // Put in here all stuff to create the layout of the sequence // number of slices in each direction nslices_dir.resize(n_orientations); nslices_dir[sagittal]=NumSagSlices; nslices_dir[coronal]=NumCorSlices; nslices_dir[axial]=NumAxiSlices; nslices=nslices_dir.sum(); geometryInfo->reset(); // Use default orientations ///////////////// Excitation Pulse: ///////////////////// // Get the slice thickness from the global geometry handler 'geometryInfo': float slicethick=4.0; // Create the sinc shaped excitation pulse. exc=SeqPulsarSinc("exc",slicethick,false,2.0,commonPars->get_FlipAngle()); // This is useful for simulating/visualization of the sequence exc.set_pulse_type(excitation); // Do not use maxDistEncoding exc.set_encoding_scheme(linearEncoding); // Pilot rotation and slice offset dvector offset(nslices); offset=0.0; pilotrot=SeqRotMatrixVector("pilotrot"); dirvec.resize(nslices); int ioffset=0; for(int idir=0; idirget_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5),noedit); //////////////// Delays: ////////////////////////////// // relaxation delay after each readout relaxdelay=SeqDelay("relaxdelay"); //////////////// Gradient Echo Module: ////////////////////////////// float os_factor=2.0; // avoid cut-off in read direction for off-center FOV // This is the gradient-recalled echo kernel of the sequence. // Calculations of read/phase gradient strengts and durations are // performed by this module itself so we just have to pass in the size and FOV // in each direction. This module has a tight timing scheme so that short TE is possible. grech=SeqGradEcho("grech", exc, commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), linearEncoding, noReorder, 1, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, false, commonPars->get_PartialFourier(),0.0,false,os_factor); grech.set_gradrotmatrixvector(pilotrot); // rotate grech //////////////// Crusher Gradient: ////////////////////////////// float crusher_strength=0.5*systemInfo->get_max_grad(); float crusher_integral=4.0*fabs(grech.get_gradintegral().sum()); crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, crusher_strength); crusherdelay=SeqDelay("crusherdelay",0.1); // Small delay to avoid gradient-induced stimulation //////////////// Loops: ////////////////////////////// // Construct a loop object to iterate through the phase encoding steps peloop=SeqObjLoop("peloop"); // Construct a loop object to perform repetitions of the experiment reploop=SeqObjLoop("reploop"); // Construct a loop object to perform dummy cylces dummyloop=SeqObjLoop("dummyloop"); //////////////// Constructing the Sequence: /////////////// // This sequence container will hold the objects for one readout: scanpart=SeqObjList("scanpart"); scanpart = grech + crusherdelay + crusher; // Contains kernel of one dummy cycle dummypart=SeqObjList("dummypart"); dummypad=SeqDelay("dummypad",scanpart.get_duration()-exc.get_duration()); // Padding delay for dummy cycle dummypart = exc + dummypad + relaxdelay; // Finally, build the whole sequence set_sequence( dummyloop( sliceloop( dummypart )[grech.get_exc_vector()][pilotrot] )[DummyCycles] + peloop( sliceloop( scanpart + relaxdelay // the sequence kernel )[grech.get_exc_vector()][pilotrot] )[grech.get_pe_vector()] ); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_rels() { // Put in here all stuff that has to be performed whenever one of the sequence parameters // has been changed by the user // calculate relaxdelay to get the desired repetition time float scandur=scanpart.get_duration()*float(nslices); if(scandur>commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(scandur); relaxdelay.set_duration( (commonPars->get_RepetitionTime()-scandur)/float(nslices) ); // calculate Ernst angle accordng to TR float flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), T1Ernst) ) ); commonPars->set_FlipAngle( flipangle, noedit ); exc.set_flipangle( flipangle ); // retrieve echo time from gradient echo module to display it in the user interface commonPars->set_EchoTime(grech.get_echo_time(), noedit ); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_set() { // Put in here all stuff that has to be performed after the parameters have been edited by the user // and before the sequence is played out // for odinreco grech.set_reco_vector(userdef,pilotrot,dirvec); // distinguish slices by their orientation recoInfo->set_Recipe("kspace | fft | offset | oversampling | usercoll | pilot("+ftos(PilotSliceDist)+") | store"); } //////////////////////////////////////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odingrech.cpp0000644000175000017500000002425411455553544014062 00000000000000////////////////////////////////////////////////////////////////////////////// // // A simple gradient echo sequence for the ODIN framework // ////////////////////////////////////////////////////////////////////////////// // includes for the sequence objects #include // The method itself is a class that is derived from // an abstract base class 'SeqMethod' that contains all // routines common to all methods: class METHOD_CLASS : public SeqMethod { public: // Constructor that takes the methods identifier (unique string) as its argument METHOD_CLASS(const STD_string& label); // virtual functions that are overwritten in this method to build the sequence, // calculate parameter relations, etc.: void method_pars_init(); void method_seq_init(); void method_rels(); void method_pars_set(); private: // Parameters for this method: JDXfloat T1Ernst; JDXint DummyCycles; JDXfloat PartialFourierRead; // Sequence objects for this method: SeqPulsar exc; SeqDelay relaxdelay; SeqObjLoop peloop; SeqObjLoop peloop3d; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop dummyloop; SeqObjList scanpart; SeqObjList slicepart; SeqObjList dummypart; SeqDelay dummypad; SeqGradEcho grech; SeqVecIter phaseiter; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; }; //////////////////////////////////////////////////////////////////////////////////// METHOD_CLASS::METHOD_CLASS (const STD_string& label) : SeqMethod(label) { // Put in here all stuff that will once be initialised and // never changed // Specify a short description of the method set_description("This is a simple spoiled gradient echo sequence where " "each excitation is used to scan one line " "in k-space via a gradient echo with the " "apropriate phase encoding. The flip angle is " "the Ernst angle for the given T1 (to obtain maximum SNR). " ); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_init() { // In this function the methods parameters will be initialised // Assign default values: commonPars->set_RepetitionTime(1000.0); commonPars->set_AcqSweepWidth(25.0); commonPars->set_MatrixSize(readDirection,128); // set default values and a short a description (which // will appear as a tooltip in the UI) for each parameter T1Ernst=1300.0; T1Ernst.set_minmaxval(0.0,5000.0).set_description("For optimum SNR, the flip angle will be set to the Ernst angle using this T1"); DummyCycles=3; DummyCycles.set_description("Number of dummy shots before actual acquisition"); PartialFourierRead=0.0; PartialFourierRead.set_description("The amount of partial Fourier undersampling in readout direction (0=no undersampling, 1=half fourier)"); // Make method specific parameters visible in the user interface append_parameter(T1Ernst,"T1Ernst"); append_parameter(DummyCycles,"DummyCycles"); append_parameter(PartialFourierRead,"PartialFourierRead"); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_seq_init() { // Put in here all stuff to create the layout of the sequence ///////////////// Excitation Pulse: ///////////////////// // Get the slice thickness from the global geometry handler 'geometryInfo': float slicethick=geometryInfo->get_sliceThickness(); if(geometryInfo->get_Mode()==voxel_3d) slicethick=0.9*geometryInfo->get_FOV(sliceDirection); float spatres=slicethick/4.0; // Create the sinc shaped excitation pulse. exc=SeqPulsarSinc("exc",slicethick,false,2.0,commonPars->get_FlipAngle(),spatres); // Set the frequency list of the excitation pulse so that we will excite all slices in the slicepack exc.set_freqlist( systemInfo->get_gamma("") * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); // This is useful for simulating/visualization of the sequence exc.set_pulse_type(excitation); // This loop object is used to loop over the slices sliceloop=SeqObjLoop("sliceloop"); ////////////////// Geometry: ///////////////////////////////// // calculate the resolution in the read Channel and set the number of phase encoding // steps so that we will obtain a isotropic resolution in read and phase Channel: float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution)+0.5),noedit); int size3d=1; if(geometryInfo->get_Mode()==voxel_3d) { size3d=int(secureDivision(geometryInfo->get_FOV(sliceDirection),resolution)+0.5); // isotropic resolution } commonPars->set_MatrixSize(sliceDirection,size3d,noedit); //////////////// Delays: ////////////////////////////// // relaxation delay after each readout relaxdelay=SeqDelay("relaxdelay"); //////////////// Gradient Echo Module: ////////////////////////////// // This is the gradient-recalled echo kernel of the sequence. // Calculations of read/phase gradient strengts and durations are // performed by this module itself so we just have to pass in the size and FOV // in each direction. This module has a tight timing scheme so that short TE is possible. if(geometryInfo->get_Mode()==voxel_3d) { // 3D mode grech=SeqGradEcho("grech", commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), commonPars->get_MatrixSize(sliceDirection), geometryInfo->get_FOV(sliceDirection), exc, commonPars->get_AcqSweepWidth(), commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, false, commonPars->get_PartialFourier(),PartialFourierRead); } else { // 2D mode grech=SeqGradEcho("grech", exc, commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), linearEncoding, noReorder, 1, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, false, commonPars->get_PartialFourier(),PartialFourierRead); } if(commonPars->get_RFSpoiling()) { exc.set_phasespoiling(); grech.set_phasespoiling(); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(grech.get_phaselist_vector()); } //////////////// Crusher Gradient: ////////////////////////////// float crusher_strength=0.5*systemInfo->get_max_grad(); float crusher_integral=4.0*fabs(grech.get_gradintegral().sum()); crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, crusher_strength); crusherdelay=SeqDelay("crusherdelay",0.1); // Small delay to avoid gradient-induced stimulation //////////////// Loops: ////////////////////////////// // Construct a loop object to iterate through the phase encoding steps peloop=SeqObjLoop("peloop"); // Construct a loop object to iterate through the 2nd phase encoding steps peloop3d=SeqObjLoop("peloop3d"); // Construct a loop object to perform repetitions of the experiment reploop=SeqObjLoop("reploop"); // Construct a loop object to perform dummy cylces dummyloop=SeqObjLoop("dummyloop"); //////////////// Constructing the Sequence: /////////////// // This sequence container will hold the objects for one readout: scanpart=SeqObjList("scanpart"); scanpart = grech + crusherdelay + crusher; if(commonPars->get_RFSpoiling()) scanpart+=phaseiter; // Contains kernel of one dummy cycle dummypart=SeqObjList("dummypart"); dummypad=SeqDelay("dummypad",scanpart.get_duration()-exc.get_duration()); // Padding delay for dummy cycle dummypart = exc + dummypad + relaxdelay; // This sequence container will hold the objects for one slicepack: slicepart=SeqObjList("slicepart"); if(geometryInfo->get_Mode()==voxel_3d) { slicepart = peloop3d( peloop( sliceloop( scanpart + relaxdelay // the sequence kernel )[grech.get_exc_vector()] )[grech.get_pe_vector()] )[grech.get_pe3d_vector()]; } else { slicepart = peloop( sliceloop( scanpart + relaxdelay // the sequence kernel )[grech.get_exc_vector()] )[grech.get_pe_vector()]; } // Finally, build the whole sequence set_sequence( dummyloop( sliceloop( dummypart )[grech.get_exc_vector()] )[DummyCycles] + reploop( slicepart )[commonPars->get_NumOfRepetitions()] ); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_rels() { // Put in here all stuff that has to be performed whenever one of the sequence parameters // has been changed by the user // calculate relaxdelay to get the desired repetition time float scandur=scanpart.get_duration()*float(geometryInfo->get_nSlices()); if(scandur>commonPars->get_RepetitionTime()) commonPars->set_RepetitionTime(scandur); relaxdelay.set_duration( (commonPars->get_RepetitionTime()-scandur)/float(geometryInfo->get_nSlices()) ); // calculate Ernst angle accordng to TR float flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), T1Ernst) ) ); commonPars->set_FlipAngle( flipangle, noedit ); exc.set_flipangle( flipangle ); // retrieve echo time from gradient echo module to display it in the user interface commonPars->set_EchoTime(grech.get_echo_time(), noedit ); } //////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::method_pars_set() { // Put in here all stuff that has to be performed after the parameters have been edited by the user // and before the sequence is played out } //////////////////////////////////////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinmdeft.cpp0000644000175000017500000001374411322062347014060 00000000000000#include #define DUMMY_SCANS 3 #define INTER_ACQ_DELAY 2.0 class METHOD_CLASS : public SeqMethod { public: METHOD_CLASS(const STD_string& label); // implementing virtual functions of SeqMethod void method_pars_init(); void method_seq_init(); void method_rels(); void method_pars_set(); private: SeqPulsar inv; SeqPulsar exc; SeqGradEcho grech; SeqDelay inv2exc; SeqDelay exc2inv; SeqDelay dummypad; SeqDelay interacq; SeqGradConstPulse spoiler; SeqObjLoop segloop; SeqObjLoop peloop; SeqObjLoop sliceloop; SeqObjLoop dummyloop; SeqObjList prep; SeqObjList kernel; SeqObjList readout; SeqObjList dummyreadout; SeqObjList scanseq; }; ///////////////////////////////////////////////////////////////////////////// METHOD_CLASS::METHOD_CLASS (const STD_string& label) : SeqMethod(label) { set_description("Multi-slice MDEFT sequence for high-contrast T1-weighted images (DG Norris, J Magn Reson Imag 11:445-451 (2000))."); } void METHOD_CLASS::method_pars_init() { // default values commonPars->set_RepetitionTime(1300.0); commonPars->set_MatrixSize(phaseDirection,128); commonPars->set_MatrixSize(readDirection,128,noedit); commonPars->set_EchoTime(0.0,noedit); } void METHOD_CLASS::method_seq_init() { Log odinlog(this,"method_seq_init"); ///////////////// Inversion Pulse: ///////////////////// inv=SeqPulsar("inv",false,false); inv.set_dim_mode(zeroDeeMode); inv.set_Tp(10.0); inv.resize(256); inv.set_shape("Wurst(2.96,26.48)"); // bandwidth ~ 1kHz inv.set_pulse_type(inversion); inv.refresh(); // because it's non-interactive ODINLOG(odinlog,normalDebug) << "Inversion Pulse done" << STD_endl; ///////////////// Excitation Pulses and rotation matrix of pilot: ///////////////////// exc=SeqPulsarSinc("exc",geometryInfo->get_sliceThickness(),false); exc.set_freqlist(systemInfo->get_gamma()*exc.get_strength()/(2.0*PII)*geometryInfo->get_sliceOffsetVector()); ////////////////// Geometry: ///////////////////////////////// // condition for reduced power multi-slice MDEFT unsigned int pesize=commonPars->get_MatrixSize(phaseDirection)/geometryInfo->get_nSlices(); commonPars->set_MatrixSize(phaseDirection,pesize*geometryInfo->get_nSlices()); ODINLOG(odinlog,normalDebug) << "MatrixSizePhase=" << commonPars->get_MatrixSize(phaseDirection) << STD_endl; // uniform resolution in read and phase direction // Does not work on Siemens as ADC can only have certain sizes if(systemInfo->get_platform()!=numaris_4) { float resolution=secureDivision( geometryInfo->get_FOV(phaseDirection) , commonPars->get_MatrixSize(phaseDirection) ); commonPars->set_MatrixSize(readDirection,int(secureDivision(geometryInfo->get_FOV(readDirection),resolution)+0.5),noedit); } ///////////////// Delays: ///////////////////// inv2exc=SeqDelay("inv2exc"); exc2inv=SeqDelay("exc2inv"); dummypad=SeqDelay("dummypad"); interacq=SeqDelay("interacq",INTER_ACQ_DELAY); ODINLOG(odinlog,normalDebug) << "Delays done" << STD_endl; ///////////////// Spoiler Gradient: ///////////////////// spoiler=SeqGradConstPulse("spoiler",readDirection,0.5*systemInfo->get_max_grad(),5.0); ODINLOG(odinlog,normalDebug) << "Spoiler Gradient done" << STD_endl; //////////////// Preparation: /////////////// prep=SeqObjList("prep"); prep= exc2inv + inv + spoiler + inv2exc ; ODINLOG(odinlog,normalDebug) << "Preparation done" << STD_endl; //////////////// Loops: /////////////// peloop=SeqObjLoop("peloop"); sliceloop=SeqObjLoop("sliceloop"); segloop=SeqObjLoop("segloop"); dummyloop=SeqObjLoop("dummyloop"); //////////////// Gradient Echo Module: ////////////////////////////// grech=SeqGradEcho("grech", exc, commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), linearEncoding, blockedSegmented, geometryInfo->get_nSlices(), commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, false, commonPars->get_PartialFourier()); grech.set_freq_reorder_scheme(rotateReorder); // rotate slice order ODINLOG(odinlog,normalDebug) << "kernel done" << STD_endl; //////////////// Constructing the Sequence: /////////////// kernel=SeqObjList("kernel"); readout=SeqObjList("readout"); dummyreadout=SeqObjList("dummyreadout"); scanseq=SeqObjList("scanseq"); kernel = grech; kernel += interacq; // Reuired to avoid SAR issue on Siemens // iterate over slices readout = sliceloop ( kernel ) [grech.get_exc_vector()][grech.get_pe_reorder_vector()]; dummyreadout = sliceloop( exc + dummypad )[exc]; // spoiler after each pack of slices readout += spoiler; scanseq = segloop ( peloop ( prep + readout ) [grech.get_pe_vector()] ) [grech.get_freq_reorder_vector()]; set_sequence( dummyloop( prep + dummyreadout )[DUMMY_SCANS] + scanseq ); ODINLOG(odinlog,normalDebug) << "set_sequence done" << STD_endl; } void METHOD_CLASS::method_rels() { Log odinlog(this,"method_rels"); //////////////// Timings for MDEFT condition: /////////////// float readoutduration=readout.get_duration(); float inv2exc_duration=( inv.get_duration() - inv.get_magnetic_center() ) + spoiler.get_duration() + 0.5*readoutduration; inv2exc.set_duration(0.5*commonPars->get_RepetitionTime()-inv2exc_duration); float exc2inv_duration= inv.get_magnetic_center() + 0.5*readoutduration; exc2inv.set_duration(0.5*commonPars->get_RepetitionTime()-exc2inv_duration); dummypad=secureDivision(readoutduration,geometryInfo->get_nSlices())-exc.get_duration(); commonPars->set_EchoTime(grech.get_echo_time(),noedit); } void METHOD_CLASS::method_pars_set() { } ///////////////////////////////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/Makefile.am0000644000175000017500000000152111455553544013440 00000000000000EXTRA_DIST = odindti.cpp odinepi.cpp odinfisp.cpp odingrech.cpp odinmdeft.cpp odinonep.cpp odinpilot.cpp odinprop.cpp odinquant.cpp odinrare.cpp odinrefg.cpp odinspir.cpp odinswi.cpp \ tj_messer.cpp tj_gesse.cpp \ mk_prop.cpp if ONLY_LIBS else seqdir = $(datadir)/odin/sequences seq_DATA = $(EXTRA_DIST) test: rm -rf seqtestfiles if test ! -f seqtestfiles.tar.gz ; then wget od1n.sourceforge.net/seqtestfiles.tar.gz ; fi tar -xvzf seqtestfiles.tar.gz ./seqtest.sh committest: if test ! -d seqtestfiles; then ./seqtest.sh; fi tar -cvzf seqtestfiles.tar.gz seqtestfiles scp seqtestfiles.tar.gz wodan,od1n@web.sourceforge.net:/home/groups/o/od/od1n/htdocs/ endif clean-local: if test -f ./seqtest.sh; then ./seqtest.sh clean; 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void method_pars_set(); unsigned int numof_testcases() const {return 4;} private: JDXenum Mode; JDXdouble ExpectedT1; JDXdouble ExpectedT2; JDXdouble MinEchoTime; JDXdouble MaxEchoTime; JDXint NumOfEchoes; JDXint NumOfDummyEchoes; JDXdoubleArr EchoTimes; JDXdouble B1PulseDur; SeqPulsar exc; SeqPulsar refoc; SeqPulsar inv; SeqAcqRead acqread; SeqDelay acqdummy; SeqAcqDeph readdeph; SeqObjLoop echoloop; SeqObjLoop dummyecholoop; SeqObjLoop peloop; SeqGradConstPulse spoiler1; SeqGradVectorPulse spoiler2; // objects for fieldmap scan SeqAcqEPI epi; SeqAcqDeph epideph; SeqVector echovec; // index vector for echoes SeqDelay excdelay; SeqDelay echodelay1; SeqDelay echodelay2; SeqDelay invdelay; SeqGradPhaseEnc pe1; SeqGradPhaseEnc pe2; SeqObjList echopart; SeqObjList grechpart; SeqObjList dummyechopart; SeqObjList kernel; SeqObjList slicepart; SeqDelay relaxdelay; SeqDelay dummype; SeqObjLoop sliceloop; SeqObjLoop acculoop; SeqObjLoop fliploop; SeqObjList postexc; SeqObjList postrefoc; SeqObjList postrefoctmpl; SeqObjList postinv; SeqObjList baselinepart; SeqGradEcho grech; fvector b1flips; }; ////////////////////////////////////////////////////////////////////////////////////////// METHOD_CLASS::METHOD_CLASS (const STD_string& label) : SeqMethod(label) { set_description("A method to measure proton density, T1, T2, and frequency offset. " "T1 maps and proton density maps are acquired using a Look-Locher sequence. " "T2 maps are acquired using a CPMG sequence whereby each echo train acquires one line in k-space for all TEs. " "Field maps are acquired using a spoiled gradient-echo sequence with different TEs. " "B1 maps are acquired as described in Dowell et al., Magn Reson Med 58 (2007). " "Maps are generated automatically by the reco method in this sequence module. "); } void METHOD_CLASS::method_pars_init() { Log odinlog(this,"method_pars_init"); Mode.add_item("T2_CPMG"); Mode.add_item("T1_LookLocker"); Mode.add_item("FIELD_MAP"); Mode.add_item("B1"); Mode.set_actual(get_current_testcase()); // alternative default settings for sequence test Mode.set_description("The quantitiy (and sequence) to measure."); ExpectedT1.set_minmaxval(10.0,10000.0); ExpectedT1=1300.0; ExpectedT1.set_description("The T1 which is expected. The TR and inversion-recovery timing will be optimized for this value."); ExpectedT1.set_unit(ODIN_TIME_UNIT); ExpectedT2.set_minmaxval(10.0,10000.0); ExpectedT2=90.0; ExpectedT2.set_description("The T2 which is expected. The CPMG timing will be optimized for this value."); ExpectedT2.set_unit(ODIN_TIME_UNIT); commonPars->set_MatrixSize(readDirection,128); commonPars->set_FlipAngle(90.0); NumOfEchoes=8; NumOfDummyEchoes=1; B1PulseDur=6.4; // use 30.0 for 7 Tesla; EchoTimes.resize(NumOfEchoes); append_parameter(Mode,"Mode"); append_parameter(ExpectedT1,"ExpectedT1"); append_parameter(ExpectedT2,"ExpectedT2"); append_parameter(MinEchoTime,"MinEchoTime",noedit); append_parameter(MaxEchoTime,"MaxEchoTime",noedit); append_parameter(NumOfEchoes,"NumOfEchoes"); append_parameter(NumOfDummyEchoes,"NumOfDummyEchoes"); append_parameter(EchoTimes,"EchoTimes"); append_parameter(B1PulseDur,"B1PulseDur"); } void METHOD_CLASS::method_seq_init() { Log odinlog(this,"method_seq_init"); if(NumOfEchoes<2) NumOfEchoes=2; // adjust echo timings if(Mode=="T2_CPMG") { double te=ExpectedT2*T2_CPMG_ECHO_FACTOR/NumOfEchoes; commonPars->set_EchoTime(te,noedit); MinEchoTime=te; MaxEchoTime=NumOfEchoes*te; } if(Mode=="T1_LookLocker") { double ti_step=ExpectedT1*T1_IR_FACTOR/(NumOfEchoes-1); commonPars->set_EchoTime(ti_step,noedit); MinEchoTime=ExpectedT1/50.0; MaxEchoTime=MinEchoTime+(NumOfEchoes-1)*ti_step; float trwait=4.0*ExpectedT1; if(commonPars->get_RepetitionTime()set_RepetitionTime(trwait); } if(Mode=="FIELD_MAP") { if(NumOfEchoes%2) NumOfEchoes++; // even number of echoes (echo pairs) in EPI module // get TE later from EPI module } ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float spatres=slicethick/4.0; float gamma=systemInfo->get_gamma(); // Sinc Excitation Pulse exc=SeqPulsarSinc("exc",slicethick,true,4.0,commonPars->get_FlipAngle(),spatres,256); exc.set_freqlist( gamma * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); exc.set_pulse_type(excitation); if(Mode=="T1_LookLocker") exc.set_rephased(false); if(Mode=="B1") { exc.set_rephased(false); b1flips.resize(5); b1flips[0]=110.0; b1flips[1]=145.0; b1flips[2]=180.0; b1flips[3]=215.0; b1flips[4]=250.0; exc.set_flipangles(b1flips); exc.set_pulsduration(B1PulseDur); } // 90-180-90 Refocusing Pulse refoc=SeqPulsarBP("refoc", 1.0, 180.0); refoc.set_composite_pulse("90(x) 180(y) 90(x)"); refoc.set_pulse_type(refocusing); // Inversion Pulse inv=SeqPulsar("inv",false,false); inv.set_dim_mode(zeroDeeMode); inv.set_Tp(10.0); inv.resize(256); inv.set_spat_resolution(0.0); inv.set_shape("Wurst(2.96,26.48)"); // bandwidth ~ 1kHz inv.set_trajectory("Const(0.0,1.0)"); inv.set_filter("Gauss"); inv.set_pulse_type(inversion); inv.refresh(); ////////////////// Resolution: ///////////////////////////////// // uniform resolution in read and phase direction float Resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),Resolution)+0.5),noedit); //////////////// Phase Encoding: ////////////////////////// // Phase encoding before acquisition pe1=SeqGradPhaseEnc("pe1",commonPars->get_MatrixSize(phaseDirection),geometryInfo->get_FOV(phaseDirection), phaseDirection,0.25*systemInfo->get_max_grad(), linearEncoding, noReorder, 1, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, commonPars->get_PartialFourier()); // Rephasing before the refocusing pulse for CPMG pe2=pe1; pe2.set_label("pe2"); pe2.invert_strength(); SeqObjList pe1dummy; pe1dummy+=pe1; dummype=SeqDelay("dummype",pe1dummy.get_duration()); //////////////// Readout: ////////////////////////////// float os_read=1.0; acqread=SeqAcqRead("acqread",commonPars->get_AcqSweepWidth(),commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), readDirection, os_read); dephaseMode dephmode=spinEcho; if(Mode=="T1_LookLocker" || Mode=="FIELD_MAP") dephmode=FID; readdeph=SeqAcqDeph("readdeph",acqread,dephmode); acqdummy=SeqDelay("acqdummy",acqread.get_duration()); //////////////// Gradient Echo Module: ////////////////////////////// grech=SeqGradEcho("grech", exc, commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), linearEncoding, noReorder, 1, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, false, commonPars->get_PartialFourier()); //////////////// EPI module: ////////////////////////////// epi=SeqAcqEPI("epi",commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection), geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection), geometryInfo->get_FOV(phaseDirection), commonPars->get_MatrixSize(phaseDirection), 1, os_read,"",0,0,linear,false,1.0,0.0,NumOfEchoes/2); epideph=SeqAcqDeph("epideph",epi,FID); //////////////// Timng Delays: ////////////////////////////// excdelay=SeqDelay("excdelay",systemInfo->get_min_duration(delayObj)); echodelay1=SeqDelay("echodelay1",systemInfo->get_min_duration(delayObj)); echodelay2=SeqDelay("echodelay2",systemInfo->get_min_duration(delayObj)); relaxdelay=SeqDelay("relaxdelay",0.0); invdelay=SeqDelay("invdelay"); //////////////// Echo Vector: ////////////////////////////// // an index vector is used which is responsible for assigning // the ADCs to the correct k-space data in the reconstruction echovec=SeqVector("echovec",NumOfEchoes); //////////////// Loops: ////////////////////////////// echoloop=SeqObjLoop("echoloop"); dummyecholoop=SeqObjLoop("dummyecholoop"); peloop=SeqObjLoop("peloop"); sliceloop=SeqObjLoop("sliceloop"); acculoop=SeqObjLoop("acculoop"); fliploop=SeqObjLoop("fliploop"); //////////////// Spoiler: ////////////////////////////// double SpoilerDuration=2.0; double SpoilerStrength=60.0; float spoiler_strength_phys=(double)SpoilerStrength/100.0*systemInfo->get_max_grad(); spoiler1=SeqGradConstPulse("spoiler1",phaseDirection,spoiler_strength_phys,SpoilerDuration); fvector spoilertrims(NumOfEchoes); spoilertrims.fill_linear(-1.0,1.0); spoiler2=SeqGradVectorPulse("spoiler2",readDirection,spoiler_strength_phys,spoilertrims,SpoilerDuration*double(NumOfEchoes)); //////////////// Building the sequence: ////////////////////////////// postexc=SeqObjList("postexc"); postrefoc=SeqObjList("postrefoc"); postrefoctmpl=SeqObjList("postrefoctmpl"); echopart=SeqObjList("echopart"); grechpart=SeqObjList("grechpart"); dummyechopart=SeqObjList("dummyechopart"); kernel=SeqObjList("kernel"); slicepart=SeqObjList("slicepart"); if(Mode=="T2_CPMG") { postexc=excdelay + readdeph ; postrefoc= spoiler1 + echodelay1 + pe1; postrefoctmpl=spoiler1 + echodelay1 + dummype; echopart= spoiler1 + refoc + postrefoc + acqread + pe2 + echodelay2 ; dummyechopart= spoiler1 + refoc + postrefoctmpl + acqdummy + dummype + echodelay2 ; if (NumOfDummyEchoes>1) { kernel= exc + postexc + dummyecholoop(dummyechopart)[NumOfDummyEchoes] + echoloop(echopart)[echovec]; } else { kernel= exc + postexc + echoloop(echopart)[echovec]; } slicepart= sliceloop( kernel + relaxdelay )[exc]; set_sequence( acculoop( peloop( slicepart )[pe1][pe2] )[commonPars->get_NumOfRepetitions()] ); } if(Mode=="T1_LookLocker") { grechpart= sliceloop( grech )[exc]; echopart= grechpart + spoiler2 + echodelay1; kernel= inv + spoiler1 + invdelay + echoloop( echopart )[spoiler2]; slicepart= kernel + relaxdelay; set_sequence( acculoop ( peloop( slicepart )[grech.get_pe_vector()] )[commonPars->get_NumOfRepetitions()] ); } if(Mode=="FIELD_MAP") { kernel= exc + epideph + epi; slicepart= sliceloop( kernel + relaxdelay )[exc]; set_sequence( acculoop ( peloop( slicepart )[epideph.get_epi_segment_vector()] )[commonPars->get_NumOfRepetitions()] ); } if(Mode=="B1") { slicepart= sliceloop( grech + spoiler1 + relaxdelay )[exc]; set_sequence( fliploop( acculoop ( peloop( slicepart )[grech.get_pe_vector()] )[commonPars->get_NumOfRepetitions()] )[exc.get_flipangle_vector()] ); } } void METHOD_CLASS::method_rels() { Log odinlog(this,"method_rels"); //////////////// Timings: ////////////////////////////// float exc2refoc_duration; float refoc2acq_duration; float acq_shift; float min_echo_time=0.0; float mindelaydur=systemInfo->get_min_duration(delayObj); echodelay1.set_duration(mindelaydur); echodelay2.set_duration(mindelaydur); excdelay.set_duration(mindelaydur); EchoTimes.resize(NumOfEchoes); if(Mode=="T2_CPMG") { //////////////// Duration from the middle of the excitation pulse /////////////////// //////////////// to the middle of the refocusing pulse: ///////////////////////////// exc2refoc_duration=( exc.get_duration() - exc.get_magnetic_center() ) + postexc.get_duration() + echoloop.get_preduration() + spoiler1.get_duration() + refoc.get_magnetic_center(); if(min_echo_time < exc2refoc_duration*2.0 ) min_echo_time=exc2refoc_duration*2.0; float echoloopdur=echoloop.get_preduration()+echopart.get_duration(); if(min_echo_time < echoloopdur) min_echo_time=echoloopdur; if(commonPars->get_EchoTime()set_EchoTime(min_echo_time); echodelay1.set_duration( ( commonPars->get_EchoTime() - echoloopdur )/2.0 ); echodelay2.set_duration( ( commonPars->get_EchoTime() - echoloopdur )/2.0 ); //////////////// Duration from the middle of the refocusing pulse /////////////////// //////////////// to the middle of the acquisition window: /////////////////////////// refoc2acq_duration=( refoc.get_duration() - refoc.get_magnetic_center() ) + postrefoc.get_duration() + acqread.get_acquisition_center(); echoloopdur=echoloop.get_preduration()+echopart.get_duration(); acq_shift=refoc2acq_duration-echoloopdur/2.0; echodelay1.set_duration( echodelay1.get_duration() - acq_shift ); echodelay2.set_duration( echodelay2.get_duration() + acq_shift ); excdelay=commonPars->get_EchoTime()/2.0-exc2refoc_duration; EchoTimes.fill_linear(commonPars->get_EchoTime(),NumOfEchoes*commonPars->get_EchoTime()); } if(Mode=="T1_LookLocker") { float inv2acq_duration=( inv.get_duration() - inv.get_magnetic_center() ) +spoiler1.get_duration() +grech.get_acquisition_center(); if(MinEchoTimeget_RepetitionTime()set_RepetitionTime(slicepackdur); else relaxdelay=secureDivision(commonPars->get_RepetitionTime()-slicepackdur,n_slices_to_consider); float flipangle=90.0; if(Mode=="FIELD_MAP") { // calculate Ernst angle according to TR flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), ExpectedT1) ) ); commonPars->set_FlipAngle( flipangle, noedit ); } else if(Mode=="T1_LookLocker") { flipangle=commonPars->get_FlipAngle(); float maxflip=15.0; if(flipangle>maxflip) flipangle=maxflip; commonPars->set_FlipAngle( flipangle, edit ); } else { commonPars->set_FlipAngle( flipangle, noedit ); } if(Mode!="B1") { exc.set_flipangle( flipangle ); } } void METHOD_CLASS::method_pars_set() { Log odinlog(this,"method_pars_set"); if(Mode=="T2_CPMG") { // inform the readout about the used phase encoding and slice vector (for automatic reconstruction) acqread.set_reco_vector(line,pe1).set_reco_vector(slice,exc); // store different echoes in te dimension with echo times attached acqread.set_reco_vector(userdef, echovec, EchoTimes); recoInfo->set_PostProc3D("usercoll | expfit(true) "); } if(Mode=="T1_LookLocker") { // store different echoes in te dimension with echo times attached grech.set_reco_vector(userdef, spoiler2, EchoTimes); recoInfo->set_PostProc3D("usercoll | t1fit "); } if(Mode=="FIELD_MAP") { // inform the readout about the used slice vector (for automatic reconstruction) epi.set_reco_vector(slice,exc); // epi.set_te_offset(exc.get_duration()-exc.get_magnetic_center()+epideph.get_duration()); recoInfo->set_PreProc3D("tecoll | fieldmap "); // calculate fieldmap before summing up channels! } if(Mode=="B1") { // store different echoes in te dimension with echo times attached grech.set_reco_vector(userdef, exc.get_flipangle_vector(), fvector2dvector(b1flips)); recoInfo->set_PostProc3D("usercoll | b1fit "); } } /////////////////////////////////////////////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinprop.cpp0000644000175000017500000006071511625224371013744 00000000000000#include class METHOD_CLASS : public SeqMethod { private: JDXint Blades; JDXbool ShortAxis; JDXfloat BladeOversampling; JDXbool TakeMinEchoTime; JDXenum TemplateScan; JDXbool RampSampling; JDXenum RampMode; JDXfloat RampSteepness; JDXbool FatSaturation; JDXfloat T1Ernst; JDXenum EPIMode; JDXint DummyCycles; JDXint NumOfGradEchoes; JDXint NumOfSamples; JDXdouble PulseDur; JDXbool fMRITrigger; JDXbool UpDownBlade; JDXbool FieldMap; JDXbool InvertPartialFourier; SeqPulsar exc; SeqPulsar refoc; SeqSat fatsat; SeqAcqEPI epiacq; SeqDelay epiacq_dummy; SeqAcqEPI epiacq_template; SeqAcqEPI epiacq_grappa; SeqAcqDeph deph; SeqAcqDeph deph_template; SeqAcqDeph deph_grappa; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop bladeloop; SeqObjLoop grappaloop; SeqObjLoop dummyloop; SeqDelay trdelay; SeqObjList scan; SeqObjList dummypart; SeqObjList templatepart; SeqObjList grappapart; SeqObjList imagingpart; SeqObjList slicepart; SeqObjList slicepart_dummy; SeqObjList slicepart_template; SeqObjList slicepart_grappa; SeqObjList preppart; SeqObjList bladepart; SeqDelay exc2acq; SeqDelay exc2refoc; SeqDelay refoc2acq; SeqGradConstPulse spoiler; SeqTrigger trigger; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; SeqFieldMap fmapscan; SeqVecIter phaseiter; SeqGradTrapez deph3d; SeqGradTrapez blip3d_read; SeqGradTrapez blip3d_phase; SeqGradTrapez blip3d_template_read; SeqGradTrapez blip3d_template_phase; SeqGradTrapez blip3d_grappa_read; SeqGradTrapez blip3d_grappa_phase; SeqGradVectorPulse blip3d_slice; SeqGradChanParallel blip3d; SeqGradChanParallel blip3d_template; SeqGradChanParallel blip3d_grappa; SeqObjLoop loop3d; SeqVector index3d; SeqVector epiindex; SeqObjList epiacq_part; SeqObjList epiacq_dummy_part; SeqObjList epiacq_template_part; SeqObjList epiacq_grappa_part; SeqRotMatrixVector bladerot; SeqMagnReset reset; dvector bladeangels; public: // This constructor creates an empty EPI sequence METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("EPI-based Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction (PROPELLER) sequence. See for example J. G. Pipe, Magn. Reson. Med. 42:963-969 (1999)"); } unsigned int numof_testcases() const {return 2;} void method_pars_init() { // In this function, parameters are initialized and default values are set commonPars->set_MatrixSize(readDirection,128); commonPars->set_MatrixSize(phaseDirection,128,noedit); commonPars->set_NumOfRepetitions(1); commonPars->set_RepetitionTime(1000.0); commonPars->set_AcqSweepWidth(100.0); Blades=8; Blades.set_description("Number of PROPELLER blades"); ShortAxis=false; ShortAxis.set_description("Readout direction along short axis of blades"); BladeOversampling=0.0; BladeOversampling.set_minmaxval(0.0,100.0); BladeOversampling.set_unit("%").set_description("Oversampling (overlap) in short direction of blade"); EPIMode.add_item("FIDMode"); EPIMode.add_item("SEMode"); EPIMode.set_actual("FIDMode"); EPIMode.set_description("Gradient-echo EPI (FIDMode) or spin-echo EPI (SEMode)"); TemplateScan.add_item("NoCorrection"); TemplateScan.add_item("PhaseCorrection"); TemplateScan.set_actual("PhaseCorrection"); TemplateScan.set_description("The type of template scan which is acquired beforehand"); RampSampling=false; RampSampling.set_description("Perform sampling during gradient ramps"); RampMode.add_item("linear",linear); RampMode.add_item("sinusoidal",sinusoidal); RampMode.add_item("half_sinusoidal",half_sinusoidal); RampMode.set_actual(linear); RampMode.set_description("The shape of the ramps of the read gradient"); RampSteepness=1.0; RampSteepness.set_description("Relative steepness (slew rate) of the EPI readout ramps"); FatSaturation=true; FatSaturation.set_description("Saturation of fat resonance prior to excitation"); T1Ernst=0.0; T1Ernst.set_minmaxval(0.0,5000.0).set_description("If non-zero, the flip angle will be set to the Ernst angle using this T1 for optimum SNR"); TakeMinEchoTime=true; TakeMinEchoTime.set_description("Use minimum possible TE"); DummyCycles=3; DummyCycles.set_description("Number of dummy shots before actual acquisition"); fMRITrigger=true; fMRITrigger.set_description("External triggering"); InvertPartialFourier=false; InvertPartialFourier.set_description("Invert position in phase encoding direction at which partial Fourier cut off is performed (i.e. beginning or end of readout)"); UpDownBlade=false; UpDownBlade.set_description("Sample each blade twice with opposite phase-encoding direction"); FieldMap=false; FieldMap.set_description("Fieldmap pre-scan for distortion correction"); PulseDur=4.0; // avoid initial high RF amplitude PulseDur.set_description("Pulse duration of excitation/refocusing pulse"); // register method parameters for user interface, parameter files, etc. append_parameter(Blades,"Blades"); append_parameter(ShortAxis,"ShortAxis"); append_parameter(EPIMode,"EPIMode"); append_parameter(TakeMinEchoTime,"TakeMinEchoTime"); append_parameter(DummyCycles,"DummyCycles"); append_parameter(TemplateScan,"TemplateScan"); append_parameter(RampSampling,"RampSampling"); append_parameter(FatSaturation,"FatSaturation"); append_parameter(T1Ernst,"T1Ernst"); append_parameter(FieldMap,"FieldMap"); fmapscan.init("fmapscan"); append_parameter(fmapscan.get_parblock(),"FieldMapPars"); append_parameter(UpDownBlade,"UpDownBlade"); append_parameter(PulseDur,"PulseDur"); append_parameter(fMRITrigger,"fMRITrigger"); append_parameter(InvertPartialFourier,"InvertPartialFourier"); if(systemInfo->get_platform()!=numaris_4) { append_parameter(BladeOversampling,"BladeOversampling"); append_parameter(RampMode,"RampMode"); append_parameter(RampSteepness,"RampSteepness"); append_parameter(NumOfGradEchoes,"NumOfGradEchoes",noedit); append_parameter(NumOfSamples,"NumOfSamples",noedit); } // alternative default settings for sequence test if(get_current_testcase()==1) { geometryInfo->set_Mode(voxel_3d); ShortAxis=false; BladeOversampling=0.0; TemplateScan.set_actual("NoCorrection"); } } void method_seq_init() { Log odinlog(this,"method_seq_init"); float gamma=systemInfo->get_gamma(); ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float slicegap=geometryInfo->get_sliceDistance()-slicethick; // Slightly thicker refocusing slice for better SNR // Since the same spatial resolution is used for exc and refoc, the gradient strengths will be the same float extra_slicethick_refoc=STD_min(0.5*slicethick, 0.3*slicegap); if(geometryInfo->get_Mode()==voxel_3d) { slicethick=0.8*geometryInfo->get_FOV(sliceDirection); extra_slicethick_refoc=0.2*slicethick; } float spatres=slicethick/4.0; // calculate Ernst angle accordng to TR float flipangle=commonPars->get_FlipAngle(); if(T1Ernst>0.0) { flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), T1Ernst) ) ); commonPars->set_FlipAngle( flipangle ); } // excitation pulse exc=SeqPulsarSinc("exc", slicethick, true,PulseDur,flipangle,spatres); exc.set_rephased(true, 0.8*systemInfo->get_max_grad()); // short rephaser exc.set_freqlist( gamma * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); exc.set_pulse_type(excitation); // refocusing pulse refoc=SeqPulsarSinc("refoc",slicethick+extra_slicethick_refoc,false,PulseDur,180.0,spatres); refoc.set_freqlist( gamma * refoc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); if(!commonPars->get_RFSpoiling()) refoc.set_phase(90.0); refoc.set_pulse_type(refocusing); // fat saturation module fatsat=SeqSat("fatsat",fat); //////////////// EPI-Readout: ////////////////////////////// // square FOV int sizeRadial=commonPars->get_MatrixSize(readDirection); commonPars->set_MatrixSize(phaseDirection,sizeRadial,noedit); int size3d=1; if(geometryInfo->get_Mode()==voxel_3d) { float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); size3d=int(secureDivision(geometryInfo->get_FOV(sliceDirection),resolution)+0.5); // isotropic resolution } commonPars->set_MatrixSize(sliceDirection,size3d,noedit); int readpts_blade=sizeRadial; int pelines_blade=sizeRadial; int bladewidth=sizeRadial; if(Blades>1) { float min_bladewidth=sizeRadial*tan(0.5*PII/Blades); // exact solution bladewidth=int( ( (1.0-0.01*BladeOversampling) * min_bladewidth + 0.01*BladeOversampling*sizeRadial ) +0.5 ); } if(ShortAxis) readpts_blade=bladewidth; else pelines_blade=bladewidth; float os_read=2.0; // For reduced undersampling artifacts float fov=geometryInfo->get_FOV(readDirection); // uniform FOV int epi_reduction=commonPars->get_ReductionFactor(); float epi_partfour=commonPars->get_PartialFourier(); if(geometryInfo->get_Mode()==voxel_3d) { epi_reduction=1; // 3D phase encoding gets the reduction epi_partfour=0.0; // 3D phase encoding gets the partial fourier } epiacq=SeqAcqEPI("epiacq",commonPars->get_AcqSweepWidth(), readpts_blade, fov, pelines_blade, fov, 1, epi_reduction, os_read, "", 0, 0, rampType(int(RampMode)), RampSampling, RampSteepness, epi_partfour, 0, InvertPartialFourier); // display sampling extents in read/phase direction NumOfGradEchoes=epiacq.get_numof_gradechoes(); NumOfSamples=epiacq.get_npts_read(); // Template scan fo EPI, begin with copy of actual EPI epiacq_template=epiacq; epiacq_template.set_label("epiacq_template"); // 1D phase correction if(TemplateScan=="PhaseCorrection") { epiacq_template.set_template_type(phasecorr_template); } // Full multi-shot EPI readout as GRAPPA training data epiacq_grappa=epiacq; epiacq_grappa.set_label("epiacq_grappa"); epiacq_grappa.set_template_type(grappa_template); // Delay instead of actual EPI readout for dummy scans epiacq_dummy=SeqDelay("epiacq_dummy",epiacq.get_duration()); // EPI pre-dephase gradient dephaseMode dephmode=FID; if (EPIMode=="SEMode") dephmode=spinEcho; deph=SeqAcqDeph("deph",epiacq,dephmode); deph_template=SeqAcqDeph("deph_template",epiacq_template,dephmode); deph_grappa=SeqAcqDeph("deph_grappa",epiacq_grappa,dephmode); //////////////// 3D encoding: ////////////////////////// if(geometryInfo->get_Mode()==voxel_3d) { // use SeqGradPhaseEnc as a template to calculate phase encoding SeqGradPhaseEnc pe3d("pe3d", commonPars->get_MatrixSize(sliceDirection), geometryInfo->get_FOV(sliceDirection), deph.get_gradduration(), sliceDirection, linearEncoding, noReorder, 1, commonPars->get_ReductionFactor(), DEFAULT_ACL_BANDS, commonPars->get_PartialFourier()); fvector gradints3d=pe3d.get_trims()*pe3d.get_constduration()*pe3d.get_strength(); ODINLOG(odinlog,normalDebug) << "gradints3d=" << gradints3d << STD_endl; const SeqVector& pe3dvec=pe3d; // access to vectorgrad ivector indexvec3d=pe3dvec.get_indexvec(); ODINLOG(odinlog,normalDebug) << "indexvec3d=" << indexvec3d << STD_endl; float strength3d=0.7*systemInfo->get_max_grad(); // dephaser before readout float dephintegral=0.0; if(gradints3d.size()) dephintegral=gradints3d[0]; deph3d=SeqGradTrapez("deph3d", dephintegral, strength3d, sliceDirection); deph/=deph3d; deph_template/=deph3d; deph_grappa/=deph3d; // rephasers inbetween readouts fvector rewind_integral=-epiacq.get_gradintegral(); fvector rewind_template_integral=-epiacq_template.get_gradintegral(); fvector rewind_grappa_integral=-epiacq_grappa.get_gradintegral(); blip3d_read= SeqGradTrapez("blip3d_read", rewind_integral[readDirection], strength3d, readDirection); blip3d_phase=SeqGradTrapez("blip3d_phase", rewind_integral[phaseDirection], strength3d, phaseDirection); blip3d_template_read= SeqGradTrapez("blip3d_template_read", rewind_template_integral[readDirection], strength3d, readDirection); blip3d_template_phase=SeqGradTrapez("blip3d_template_phase", rewind_template_integral[phaseDirection], strength3d, phaseDirection); blip3d_grappa_read= SeqGradTrapez("blip3d_grappa_read", rewind_grappa_integral[readDirection], strength3d, readDirection); blip3d_grappa_phase=SeqGradTrapez("blip3d_grappa_phase", rewind_grappa_integral[phaseDirection], strength3d, phaseDirection); // blip in slice direction fvector blipintegrals(gradints3d.size()); blipintegrals=0.0; for(unsigned int i=0; i<(gradints3d.size()-1); i++) blipintegrals[i]=gradints3d[i+1]-gradints3d[i]; // differences for blips ODINLOG(odinlog,normalDebug) << "blipintegrals=" << blipintegrals << STD_endl; float maxabsintegral=blipintegrals.maxabs(); float blipstrength_slice=sqrt(0.5*systemInfo->get_max_slew_rate()*maxabsintegral); // At least one half of the gradient as flat top float gradduration_slice=secureDivision(maxabsintegral, blipstrength_slice); blip3d_slice=SeqGradVectorPulse("blip3d_slice", sliceDirection, blipstrength_slice, blipintegrals/maxabsintegral, gradduration_slice); /* if(UpDownBlade) { deph3d.invert_strength(); blip3d_slice.invert_strength(); } */ blip3d=SeqGradChanParallel("blip3d"); blip3d_template=SeqGradChanParallel("blip3d_template"); blip3d_grappa=SeqGradChanParallel("blip3d_grappa"); blip3d += blip3d_read / blip3d_phase / blip3d_slice; blip3d_template += blip3d_template_read / blip3d_template_phase / blip3d_slice; blip3d_grappa += blip3d_grappa_read / blip3d_grappa_phase / blip3d_slice; index3d=SeqVector("index3d"); index3d.set_indexvec(indexvec3d); epiindex=SeqVector("epiindex",indexvec3d.size()); // to enumerate EPI readouts } /////////////////// Rotation of Blades //////////////////////////////////////////////// bladerot=SeqRotMatrixVector("bladerot"); bool full_cycle=UpDownBlade; //(geometryInfo->get_Mode()!=voxel_3d && UpDownBlade); int nangles=Blades; if(full_cycle) nangles=2*Blades; bladeangels.resize(nangles); for(int iangle=0; iangleget_RFSpoiling()) { // recommended by Goerke et al., NMR Biomed. 18, 534-542 (2005) int plistsize=16; double plistincr=45.0; exc.set_phasespoiling(plistsize, plistincr); refoc.set_phasespoiling(plistsize, plistincr, 90.0); epiacq.set_phasespoiling(plistsize, plistincr); epiacq_template.set_phasespoiling(plistsize, plistincr); epiacq_grappa.set_phasespoiling(plistsize, plistincr); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(refoc.get_phaselist_vector()); phaseiter.add_vector(epiacq.get_phaselist_vector()); phaseiter.add_vector(epiacq_template.get_phaselist_vector()); phaseiter.add_vector(epiacq_grappa.get_phaselist_vector()); } //////////////// Loops: ////////////////////////////// // loop to iterate over slices sliceloop=SeqObjLoop("sliceloop"); // loop to iterate over repetitions reploop=SeqObjLoop("reploop"); // loop to iterate over blades bladeloop=SeqObjLoop("bladeloop"); // loop to iterate over GRAPPA interleaves to obtain training data grappaloop=SeqObjLoop("grappaloop"); // loop to iterate over dummy scans dummyloop=SeqObjLoop("dummyloop"); // loop to iterate over 3rd dimension phase encoding loop3d=SeqObjLoop("loop3d"); //////////////// Timing Delays: ////////////////////////////// trdelay=SeqDelay("trdelay"); //////////////// Spoiler Gradient: ////////////////////////////// double spoiler_strength=0.5*systemInfo->get_max_grad(); double spoiler_integral=4.0*fabs(deph.get_gradintegral().sum()); double spoiler_dur=secureDivision(spoiler_integral,spoiler_strength); spoiler=SeqGradConstPulse("spoiler",sliceDirection,spoiler_strength,spoiler_dur); //////////////// Crusher Gradient: ////////////////////////////// float crusher_integral=2.0*spoiler_integral; crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, spoiler_strength); crusherdelay=SeqDelay("crusherdelay",0.1); // Small delay to avoid gradient-induced stimulation //////////////// trigger: ////////////////////////////// trigger=SeqTrigger("fmri_trigger",1.0); reset=SeqMagnReset("reset"); //////////////// Field-map template: ////////////////////////////// if(FieldMap) { if(FatSaturation) fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0,fatsat); // pass fat saturation on to field-map scan else fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0); } //////////////// Build the sequence: ////////////////////////////// preppart+=reset; epiacq_part=SeqObjList("epiacq_part"); epiacq_dummy_part=SeqObjList("epiacq_dummy_part"); epiacq_template_part=SeqObjList("epiacq_template_part"); epiacq_grappa_part=SeqObjList("epiacq_grappa_part"); if(geometryInfo->get_Mode()==voxel_3d) { epiacq_part += loop3d( epiacq + blip3d )[index3d][epiindex][blip3d_slice]; epiacq_dummy_part += loop3d( epiacq_dummy + blip3d )[index3d][epiindex][blip3d_slice]; epiacq_template_part += loop3d( epiacq_template + blip3d_template )[index3d][epiindex][blip3d_slice]; epiacq_grappa_part += loop3d( epiacq_grappa + blip3d_grappa )[index3d][epiindex][blip3d_slice]; } else { epiacq_part += epiacq; epiacq_dummy_part += epiacq_dummy; epiacq_template_part += epiacq_template; epiacq_grappa_part += epiacq_grappa; } // add fat saturation to template and repetitions if(FatSaturation) preppart += fatsat; if(fMRITrigger && (geometryInfo->get_Mode()!=voxel_3d) ) slicepart+= trigger; // trigger for each single blade if (EPIMode=="FIDMode") { dummypart= preppart + exc + deph + exc2acq + epiacq_dummy_part + crusherdelay + crusher; templatepart= preppart + exc + deph_template + exc2acq + epiacq_template_part + crusherdelay + crusher; grappapart= preppart + exc + deph_grappa + exc2acq + epiacq_grappa_part + crusherdelay + crusher; imagingpart= preppart + exc + deph + exc2acq + epiacq_part + crusherdelay + crusher; } if (EPIMode=="SEMode") { dummypart= preppart + exc + exc2refoc + deph + spoiler + refoc + spoiler + refoc2acq + epiacq_dummy_part + crusherdelay + crusher; templatepart= preppart + exc + exc2refoc + deph_template + spoiler + refoc + spoiler + refoc2acq + epiacq_template_part + crusherdelay + crusher; grappapart= preppart + exc + exc2refoc + deph_grappa + spoiler + refoc + spoiler + refoc2acq + epiacq_grappa_part + crusherdelay + crusher; imagingpart= preppart + exc + exc2refoc + deph + spoiler + refoc + spoiler + refoc2acq + epiacq_part + crusherdelay + crusher; } templatepart.set_gradrotmatrixvector(bladerot); grappapart. set_gradrotmatrixvector(bladerot); imagingpart. set_gradrotmatrixvector(bladerot); if (EPIMode=="FIDMode") { slicepart_dummy = sliceloop( dummypart + trdelay )[exc]; slicepart_template = sliceloop( templatepart + trdelay )[exc]; slicepart_grappa = sliceloop( grappapart + trdelay )[exc]; slicepart += sliceloop( imagingpart + trdelay )[exc]; } if (EPIMode=="SEMode") { slicepart_dummy = sliceloop( dummypart + trdelay )[exc][refoc]; slicepart_template = sliceloop( templatepart + trdelay )[exc][refoc]; slicepart_grappa = sliceloop( grappapart + trdelay )[exc][refoc]; slicepart += sliceloop( imagingpart + trdelay )[exc][refoc]; } if(commonPars->get_RFSpoiling()) { slicepart += phaseiter; slicepart_dummy += phaseiter; slicepart_template += phaseiter; slicepart_grappa += phaseiter; } if(FieldMap) scan += fmapscan + trdelay; if(DummyCycles>0) { scan+= dummyloop( slicepart_dummy )[DummyCycles]; } if(TemplateScan=="PhaseCorrection") { scan += bladeloop( slicepart_template )[bladerot]; } if(commonPars->get_ReductionFactor()>1) { // Fully sampled k-space scan+= grappaloop( bladeloop( slicepart_grappa )[bladerot] )[deph_grappa.get_epi_reduction_vector()]; } if(fMRITrigger && (geometryInfo->get_Mode()==voxel_3d) ) bladepart+= trigger; // trigger only for each full blade cycle bladepart+= bladeloop( slicepart )[bladerot]; scan+= reploop( bladepart )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } void method_rels() { ////////////////// TE Timings: //////////////////////////////// double acq_center=epiacq.get_acquisition_center(); if(geometryInfo->get_Mode()==voxel_3d) acq_center= (1.0-commonPars->get_PartialFourier())*0.5*epiacq_part.get_duration(); double min_echo_time=0.0; if (EPIMode=="FIDMode") { min_echo_time=(exc.get_duration()-exc.get_magnetic_center())+deph.get_duration()+acq_center; if(commonPars->get_EchoTime()set_EchoTime(min_echo_time); if(TakeMinEchoTime) commonPars->set_EchoTime(min_echo_time); exc2acq=commonPars->get_EchoTime()-min_echo_time; } if (EPIMode=="SEMode") { //////////////// Duration from the middle of the excitation pulse /////////////////// //////////////// to the middle of the refocusing pulse: ///////////////////////////// double TE1=( exc.get_duration() - exc.get_magnetic_center() ) + deph.get_duration() + spoiler.get_duration() + refoc.get_magnetic_center(); if(min_echo_time<(2.0*TE1)) min_echo_time=2.0*TE1; //////////////// Duration from the middle of the refocusing pulse /////////////////// //////////////// to the middle of the acquisition window: /////////////////////////// double TE2=(refoc.get_duration() - refoc.get_magnetic_center()) + spoiler.get_duration() + acq_center; if(min_echo_time<(2.0*TE2)) min_echo_time=2.0*TE2; if (commonPars->get_EchoTime()set_EchoTime(min_echo_time); if(TakeMinEchoTime) commonPars->set_EchoTime(min_echo_time); exc2refoc=commonPars->get_EchoTime()/2.0-TE1; refoc2acq=commonPars->get_EchoTime()/2.0-TE2; } ////////////////// TR Timings: //////////////////////////////// // reset before recalculating timings trdelay=0.0; float slicedur=slicepart.get_duration(); if(commonPars->get_RepetitionTime()set_RepetitionTime(slicedur); trdelay=(commonPars->get_RepetitionTime()-slicedur)/double(geometryInfo->get_nSlices()); } void method_pars_set() { // extra information for the automatic reconstruction epiacq.set_reco_vector(slice,exc); epiacq_template.set_reco_vector(slice,exc); epiacq_grappa.set_reco_vector(slice,exc); if(geometryInfo->get_Mode()==voxel_3d) { epiacq.set_reco_vector(line3d,index3d); epiacq_template.set_reco_vector(line3d,index3d); epiacq_grappa.set_reco_vector(line3d,index3d); epiacq.set_reco_vector(epi, epiindex); epiacq_template.set_reco_vector(epi, epiindex); epiacq_grappa.set_reco_vector(epi, epiindex); // For multi-frequency distortion correction int nepi=epiindex.get_vectorsize(); dvector offsettime(nepi); double epidur=epiacq.get_duration() + blip3d.get_duration(); for(int i=0; iset_DimValues(epi,offsettime); } epiacq.set_reco_vector(cycle,bladerot); epiacq_template.set_reco_vector(cycle,bladerot); epiacq_grappa.set_reco_vector(cycle,bladerot); recoInfo->set_DimValues(cycle,bladeangels); // if(geometryInfo->get_Mode()==voxel_3d && UpDownBlade) recoInfo->set_CmdLineOpts("-ip -sflip"); } }; ///////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/odinrefg.cpp0000644000175000017500000001717011322062347013701 00000000000000#include class METHOD_CLASS : public SeqMethod { public: METHOD_CLASS(const STD_string& label); ~METHOD_CLASS() {delete_objs();} void method_pars_init(); void method_seq_init(); void method_rels(); void method_pars_set(); unsigned int numof_testcases() const {return 2;} private: void delete_objs(); JDXint NumOfRefgPulses; JDXdouble RefgainStartingValue; JDXdouble MaxFlipangle; JDXdoubleArr AttenuationVals; JDXdouble PulseGain; JDXdouble TemplPulseDuration; JDXdouble PulseDuration; JDXint NumOfDummyScans; JDXint NumOfReadPoints; JDXbool TestMode; SeqPulsar* exc_pulsar; SeqPulsNdim** exc; unsigned int numof_pulses; SeqPulsarReph reph; SeqAcqEPI* acqepi; SeqAcqEPI* acqtemplate; SeqAcq* acq; SeqAcqDeph deph; SeqAcqDeph dephtmpl; SeqObjLoop dummyloop; SeqDelay dummyacqdelay; SeqDelay relaxdelay; SeqObjVector exc_vector; SeqObjList slicepart; SeqObjLoop excloop; SeqObjLoop acculoop; }; ////////////////////////////////////////////////////////////////////////////////////////// void METHOD_CLASS::delete_objs() { if(exc_pulsar) delete exc_pulsar; exc_pulsar=0; // Use pointer-to-pointer because delete[] for objects does not work correctly on GCC2.9 if(exc) { for(unsigned int i=0; iset_MatrixSize(readDirection,48); commonPars->set_AcqSweepWidth(100.0); TestMode=false; TemplPulseDuration=4.0; // alternative default settings for sequence test if(get_current_testcase()==1) { TestMode=true; } if(systemInfo->get_platform()!=numaris_4) { append_parameter(RefgainStartingValue,"RefgainStartingValue"); append_parameter(MaxFlipangle,"MaxFlipangle"); append_parameter(NumOfRefgPulses,"NumOfRefgPulses"); append_parameter(AttenuationVals,"AttenuationVals",noedit); append_parameter(PulseGain,"PulseGain",noedit); append_parameter(TemplPulseDuration,"TemplPulseDuration"); append_parameter(PulseDuration,"PulseDuration",noedit); append_parameter(NumOfDummyScans,"NumOfDummyScans"); append_parameter(NumOfReadPoints,"NumOfReadPoints",noedit); } append_parameter(TestMode,"TestMode"); } void METHOD_CLASS::method_seq_init() { delete_objs(); relaxdelay=SeqDelay("relaxdelay",commonPars->get_RepetitionTime()); float resolution=secureDivision(geometryInfo->get_FOV(readDirection),commonPars->get_MatrixSize(readDirection)); commonPars->set_MatrixSize(phaseDirection,int(secureDivision(geometryInfo->get_FOV(phaseDirection),resolution))); commonPars->set_MatrixSize(phaseDirection,(commonPars->get_MatrixSize(phaseDirection)/2)*2); acqepi=new SeqAcqEPI("acqepi",commonPars->get_AcqSweepWidth(), commonPars->get_MatrixSize(readDirection),geometryInfo->get_FOV(readDirection), commonPars->get_MatrixSize(phaseDirection),geometryInfo->get_FOV(phaseDirection), 1,1,1.0,systemInfo->get_main_nucleus()); // use sagittal slice for reference gain Geometry sag; // dummy to calculate correct rotation matrix sag.set_orientation(sagittal); acqepi->set_gradrotmatrix(sag.get_gradrotmatrix()); acqtemplate=new SeqAcqEPI(*acqepi); acqtemplate->set_label("acqtemplate"); acqtemplate->set_template_type(phasecorr_template); acqtemplate->set_gradrotmatrix(sag.get_gradrotmatrix()); deph=SeqAcqDeph("deph",*acqepi); deph.set_gradrotmatrix(sag.get_gradrotmatrix()); dephtmpl=SeqAcqDeph("dephtmpl",*acqtemplate); dephtmpl.set_gradrotmatrix(sag.get_gradrotmatrix()); NumOfReadPoints=acqepi->get_npts_read(); numof_pulses=NumOfRefgPulses; if(!TestMode) exc=new SeqPulsNdim*[numof_pulses]; if(!TestMode) systemInfo->set_reference_gain(RefgainStartingValue); AttenuationVals.resize(NumOfRefgPulses); // allocate template pulse exc_pulsar=new SeqPulsarSinc("exc",5.0,true,TemplPulseDuration); exc_pulsar->set_nucleus(systemInfo->get_main_nucleus()); exc_pulsar->set_gradrotmatrix(sag.get_gradrotmatrix()); PulseGain=exc_pulsar->get_pulse_gain(); PulseDuration=exc_pulsar->get_pulsduration(); reph=SeqPulsarReph("reph",*exc_pulsar); float angle; int i,index; if(TestMode) { fvector flips(NumOfRefgPulses); for (i=0;iset_flipangles(flips); } else { // linear flipangle for (i=0;iset_flipangle(angle); exc[index]=new SeqPulsNdim(*exc_pulsar); exc[index]->set_gradrotmatrix(sag.get_gradrotmatrix()); AttenuationVals(index)=exc[index]->get_power(); } } slicepart=SeqObjList("slicepart"); dummyloop=SeqObjLoop("dummyloop"); dummyacqdelay=SeqDelay("dummyacqdelay",acqepi->get_duration()); if(NumOfDummyScans>0) { if(TestMode) { slicepart += dummyloop( *exc_pulsar + dephtmpl + dummyacqdelay + relaxdelay + *exc_pulsar + deph + dummyacqdelay + relaxdelay) [NumOfDummyScans]; } else { slicepart += dummyloop( *(exc[NumOfRefgPulses-1]) + reph + dephtmpl + dummyacqdelay + relaxdelay + *(exc[NumOfRefgPulses-1]) + reph + deph + dummyacqdelay + relaxdelay) [NumOfDummyScans]; } } exc_vector=SeqObjVector("exc_vector"); excloop=SeqObjLoop("excloop"); acculoop=SeqObjLoop("acculoop"); if(!TestMode) { for (i=0;iget_flipangle_vector()] + excloop ( *exc_pulsar + deph + (*acqepi) + relaxdelay ) [exc_pulsar->get_flipangle_vector()]; } else { slicepart += excloop ( exc_vector + reph + dephtmpl + (*acqtemplate) + relaxdelay ) [exc_vector] + excloop ( exc_vector + reph + deph + (*acqepi) + relaxdelay ) [exc_vector]; } set_sequence( acculoop(slicepart)[commonPars->get_NumOfRepetitions()] ); } void METHOD_CLASS::method_rels() { } void METHOD_CLASS::method_pars_set() { if(TestMode) { acqepi->set_reco_vector(userdef,exc_pulsar->get_flipangle_vector()); acqtemplate->set_reco_vector(userdef,exc_pulsar->get_flipangle_vector()); } else { acqepi->set_reco_vector(userdef,exc_vector,AttenuationVals); acqtemplate->set_reco_vector(userdef,exc_vector,AttenuationVals); recoInfo->set_PostProc3D("usercoll | refgain("+ftos(PulseDuration)+","+ftos(PulseGain)+")"); } } // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/sequences/mk_prop.cpp0000644000175000017500000004036611455553544013571 00000000000000#include class METHOD_CLASS : public SeqMethod { private: JDXint Blades; JDXbool ShortAxis; JDXfloat BladeOversampling; JDXbool TakeMinEchoTime; JDXbool RampSampling; JDXenum RampMode; JDXfloat RampSteepness; JDXbool FatSaturation; JDXfloat T1Ernst; JDXint DummyCycles; JDXint NumOfGradEchoes; JDXint NumOfSamples; JDXdouble PulseDur; JDXbool fMRITrigger; JDXbool UpDownBlade; JDXbool FieldMap; JDXbool EPIRef; SeqPulsar exc; SeqSat fatsat; SeqAcqEPI epiacq; SeqDelay epiacq_dummy; SeqAcqEPI epiacq_template; SeqAcqDeph deph; SeqAcqDeph deph_template; SeqObjLoop sliceloop; SeqObjLoop reploop; SeqObjLoop bladeloop; SeqObjLoop dummyloop; SeqDelay trdelay; SeqObjList scan; SeqObjList dummypart; SeqObjList templatepart; SeqObjList imagingpart; SeqObjList slicepart; SeqObjList slicepart_dummy; SeqObjList slicepart_template; SeqObjList preppart; SeqDelay exc2acq; SeqTrigger trigger; SeqGradTrapezParallel crusher; SeqDelay crusherdelay; SeqFieldMap fmapscan; SeqVecIter phaseiter; SeqRotMatrixVector bladerot; SeqMagnReset reset; // stuff for EPIRef SeqAcqEPI epiacq_ref; SeqDelay epiacq_ref_dummy; SeqAcqEPI epiacq_ref_template; SeqAcqEPI epiacq_ref_grappa; SeqAcqDeph deph_ref; SeqAcqDeph deph_ref_template; SeqAcqDeph deph_ref_grappa; SeqObjLoop grappaloop_ref; SeqDelay trdelay_ref; SeqObjList templatepart_ref; SeqObjList grappapart_ref; SeqObjList imagingpart_ref; SeqObjList slicepart_grappa_ref; SeqObjList slicepart_template_ref; SeqDelay exc2acq_ref; dvector bladeangels; public: // This constructor creates an empty EPI sequence METHOD_CLASS(const STD_string& label) : SeqMethod(label) { set_description("2D-PROPELLER-EPI with EPI reference scan."); } void method_pars_init() { // In this function, parameters are initialized and default values are set commonPars->set_MatrixSize(readDirection,128); commonPars->set_MatrixSize(phaseDirection,128,noedit); commonPars->set_NumOfRepetitions(1); commonPars->set_RepetitionTime(1000.0); commonPars->set_AcqSweepWidth(100.0); Blades=8; Blades.set_description("Number of PROPELLER blades"); ShortAxis=false; ShortAxis.set_description("Readout direction along short axis of blades"); BladeOversampling=1.0; BladeOversampling.set_minmaxval(0.0,100.0); BladeOversampling.set_unit("%").set_description("Oversampling (overlap) in short direction of blade"); RampSampling=false; RampSampling.set_description("Perform sampling during gradient ramps"); RampMode.add_item("linear",linear); RampMode.add_item("sinusoidal",sinusoidal); RampMode.add_item("half_sinusoidal",half_sinusoidal); RampMode.set_actual(linear); RampMode.set_description("The shape of the ramps of the read gradient"); RampSteepness=1.0; RampSteepness.set_description("Relative steepness (slew rate) of the EPI readout ramps"); FatSaturation=true; FatSaturation.set_description("Saturation of fat resonance prior to excitation"); T1Ernst=1300.0; T1Ernst.set_minmaxval(0.0,5000.0).set_description("If non-zero, the flip angle will be set to the Ernst angle using this T1 for optimum SNR"); TakeMinEchoTime=true; TakeMinEchoTime.set_description("Use minimum possible TE"); DummyCycles=3; DummyCycles.set_description("Number of dummy shots before actual acquisition"); fMRITrigger=true; fMRITrigger.set_description("External triggering"); UpDownBlade=false; UpDownBlade.set_description("Sample each blade twice with opposite phase-encoding direction"); FieldMap=false; FieldMap.set_description("Fieldmap pre-scan for distortion correction"); PulseDur=2.0; // avoid initial high RF amplitude PulseDur.set_description("Pulse duration of excitation/refocusing pulse"); EPIRef=false; EPIRef.set_description("Interleaved EPI reference scan"); // register method parameters for user interface, parameter files, etc. append_parameter(Blades,"Blades"); append_parameter(ShortAxis,"ShortAxis"); append_parameter(TakeMinEchoTime,"TakeMinEchoTime"); append_parameter(DummyCycles,"DummyCycles"); append_parameter(RampSampling,"RampSampling"); append_parameter(FatSaturation,"FatSaturation"); append_parameter(T1Ernst,"T1Ernst"); append_parameter(FieldMap,"FieldMap"); fmapscan.init("fmapscan"); append_parameter(fmapscan.get_parblock(),"FieldMapPars"); append_parameter(PulseDur,"PulseDur"); append_parameter(fMRITrigger,"fMRITrigger"); append_parameter(UpDownBlade,"UpDownBlade"); append_parameter(EPIRef,"EPIRef"); if(systemInfo->get_platform()!=numaris_4) { append_parameter(BladeOversampling,"BladeOversampling"); append_parameter(RampMode,"RampMode"); append_parameter(RampSteepness,"RampSteepness"); append_parameter(NumOfGradEchoes,"NumOfGradEchoes",noedit); append_parameter(NumOfSamples,"NumOfSamples",noedit); } } void method_seq_init() { Log odinlog(this,"method_seq_init"); float gamma=systemInfo->get_gamma(); ///////////////// Pulses: ///////////////////// float slicethick=geometryInfo->get_sliceThickness(); float spatres=slicethick/4.0; // calculate Ernst angle accordng to TR float flipangle=commonPars->get_FlipAngle(); if(T1Ernst>0.0) { flipangle=180.0/PII * acos( exp ( -secureDivision ( commonPars->get_RepetitionTime(), T1Ernst) ) ); commonPars->set_FlipAngle( flipangle ); } // excitation pulse exc=SeqPulsarSinc("exc", slicethick, true,PulseDur,flipangle,spatres); exc.set_rephased(true, 0.8*systemInfo->get_max_grad()); // short rephaser exc.set_freqlist( gamma * exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); exc.set_pulse_type(excitation); // fat saturation module fatsat=SeqSat("fatsat",fat); //////////////// EPI-Readout: ////////////////////////////// // square FOV int sizeRadial=commonPars->get_MatrixSize(readDirection); commonPars->set_MatrixSize(phaseDirection,sizeRadial,noedit); commonPars->set_MatrixSize(sliceDirection,1,noedit); int readpts_blade=sizeRadial; int pelines_blade=sizeRadial; int bladewidth=sizeRadial; if(Blades>1) { float min_bladewidth=sizeRadial*tan(0.5*PII/Blades); // exact solution bladewidth=int( ( (1.0-0.01*BladeOversampling) * min_bladewidth + 0.01*BladeOversampling*sizeRadial ) +0.5 ); } if(ShortAxis) readpts_blade=bladewidth; else pelines_blade=bladewidth; float os_read=2.0; // For reduced undersampling artifacts float fov=geometryInfo->get_FOV(readDirection); // uniform FOV epiacq=SeqAcqEPI("epiacq",commonPars->get_AcqSweepWidth(), readpts_blade, fov, pelines_blade, fov, 1, 1, os_read, "", 0, 0, rampType(int(RampMode)), RampSampling, RampSteepness, 0.0); // display sampling extents in read/phase direction NumOfGradEchoes=epiacq.get_numof_gradechoes(); NumOfSamples=epiacq.get_npts_read(); // Template scan fo EPI, begin with copy of actual EPI epiacq_template=epiacq; epiacq_template.set_label("epiacq_template"); // 1D phase correction epiacq_template.set_template_type(phasecorr_template); // Delay instead of actual EPI readout for dummy scans epiacq_dummy=SeqDelay("epiacq_dummy",epiacq.get_duration()); // EPI pre-dephase gradient deph=SeqAcqDeph("deph",epiacq); deph_template=SeqAcqDeph("deph_template",epiacq_template); /////////////////// Rotation of Blades //////////////////////////////////////////////// bladerot=SeqRotMatrixVector("bladerot"); bool full_cycle=UpDownBlade; int nangles=Blades; if(full_cycle) nangles=2*Blades; bladeangels.resize(nangles); for(int iangle=0; iangleget_AcqSweepWidth(), sizeRadial, fov, sizeRadial, fov, 1, commonPars->get_ReductionFactor(), os_read, "", 0, 0, rampType(int(RampMode)), RampSampling, RampSteepness, commonPars->get_PartialFourier()); // Template scan fo EPI, begin with copy of actual EPI epiacq_ref_template=epiacq_ref; epiacq_ref_template.set_label("epiacq_ref_template"); // 1D phase correction epiacq_ref_template.set_template_type(phasecorr_template); // Full multi-shot EPI readout as GRAPPA training data epiacq_ref_grappa=epiacq_ref; epiacq_ref_grappa.set_label("epiacq_ref_grappa"); epiacq_ref_grappa.set_template_type(grappa_template); // Delay instead of actual EPI readout for dummy scans epiacq_ref_dummy=SeqDelay("epiacq_ref_dummy",epiacq_ref.get_duration()); // EPI pre-dephase gradient deph_ref=SeqAcqDeph("deph_ref",epiacq_ref); deph_ref_template=SeqAcqDeph("deph_ref_template",epiacq_ref_template); deph_ref_grappa=SeqAcqDeph("deph_ref_grappa",epiacq_ref_grappa); } /////////////////// RF Spoiling /////////////////////////////////////////////////////// if(commonPars->get_RFSpoiling()) { // recommended by Goerke et al., NMR Biomed. 18, 534-542 (2005) int plistsize=16; double plistincr=45.0; exc.set_phasespoiling(plistsize, plistincr); epiacq.set_phasespoiling(plistsize, plistincr); epiacq_template.set_phasespoiling(plistsize, plistincr); epiacq_ref.set_phasespoiling(plistsize, plistincr); epiacq_ref_template.set_phasespoiling(plistsize, plistincr); epiacq_ref_grappa.set_phasespoiling(plistsize, plistincr); phaseiter=SeqVecIter("phaseiter"); phaseiter.add_vector(exc.get_phaselist_vector()); phaseiter.add_vector(epiacq.get_phaselist_vector()); phaseiter.add_vector(epiacq_template.get_phaselist_vector()); phaseiter.add_vector(epiacq_ref.get_phaselist_vector()); phaseiter.add_vector(epiacq_ref_template.get_phaselist_vector()); phaseiter.add_vector(epiacq_ref_grappa.get_phaselist_vector()); } //////////////// Loops: ////////////////////////////// // loop to iterate over slices sliceloop=SeqObjLoop("sliceloop"); // loop to iterate over repetitions reploop=SeqObjLoop("reploop"); // loop to iterate over blades bladeloop=SeqObjLoop("bladeloop"); // loop to iterate over dummy scans dummyloop=SeqObjLoop("dummyloop"); grappaloop_ref=SeqObjLoop("grappaloop_ref"); //////////////// Timing Delays: ////////////////////////////// trdelay=SeqDelay("trdelay"); trdelay_ref=SeqDelay("trdelay_ref"); //////////////// Crusher Gradient: ////////////////////////////// double spoiler_strength=0.5*systemInfo->get_max_grad(); double spoiler_integral=4.0*fabs(deph.get_gradintegral().sum()); float crusher_integral=2.0*spoiler_integral; crusher=SeqGradTrapezParallel("crusher",crusher_integral,crusher_integral,crusher_integral, spoiler_strength); crusherdelay=SeqDelay("crusherdelay",0.1); // Small delay to avoid gradient-induced stimulation //////////////// trigger: ////////////////////////////// trigger=SeqTrigger("fmri_trigger",1.0); reset=SeqMagnReset("reset"); //////////////// Field-map template: ////////////////////////////// if(FieldMap) { if(FatSaturation) fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0,fatsat); // pass fat saturation on to field-map scan else fmapscan.build_seq(commonPars->get_AcqSweepWidth(),1.0); } //////////////// Build the sequence: ////////////////////////////// preppart+=reset; // add fat saturation to template and repetitions if(FatSaturation) preppart += fatsat; dummypart= preppart + exc + deph + exc2acq + epiacq_dummy + crusherdelay + crusher; templatepart= preppart + exc + deph_template + exc2acq + epiacq_template + crusherdelay + crusher; imagingpart= preppart + exc + deph + exc2acq + epiacq + crusherdelay + crusher; if(EPIRef) { templatepart_ref= preppart + exc + deph_ref_template + exc2acq_ref + epiacq_ref_template + crusherdelay + crusher; grappapart_ref= preppart + exc + deph_ref_grappa + exc2acq_ref + epiacq_ref_grappa + crusherdelay + crusher; imagingpart_ref= preppart + exc + deph_ref + exc2acq_ref + epiacq_ref + crusherdelay + crusher; } templatepart.set_gradrotmatrixvector(bladerot); imagingpart. set_gradrotmatrixvector(bladerot); if(fMRITrigger) slicepart+= trigger; // trigger for PROPELLER interleave slicepart_dummy = sliceloop( dummypart + trdelay )[exc]; slicepart_template = sliceloop( templatepart + trdelay )[exc]; slicepart += sliceloop( imagingpart + trdelay )[exc]; if(commonPars->get_RFSpoiling()) { slicepart += phaseiter; slicepart_dummy += phaseiter; slicepart_template += phaseiter; } if(EPIRef) { if(fMRITrigger) slicepart+= trigger; // trigger for EPIRef interleave slicepart_template_ref = sliceloop( templatepart_ref + trdelay_ref )[exc]; slicepart_grappa_ref = sliceloop( grappapart_ref + trdelay_ref )[exc]; slicepart += sliceloop( imagingpart_ref + trdelay_ref )[exc]; if(commonPars->get_RFSpoiling()) { slicepart += phaseiter; slicepart_template_ref += phaseiter; slicepart_grappa_ref += phaseiter; } } if(FieldMap) scan += fmapscan + trdelay; if(DummyCycles>0) { scan+= dummyloop( slicepart_dummy )[DummyCycles]; } scan += bladeloop( slicepart_template )[bladerot]; if(EPIRef) { scan += slicepart_template_ref; if(commonPars->get_ReductionFactor()>1) { // Fully sampled k-space scan+= grappaloop_ref( slicepart_grappa_ref )[deph_ref_grappa.get_epi_reduction_vector()]; } } scan+= reploop( bladeloop( slicepart )[bladerot] )[commonPars->get_NumOfRepetitions()]; set_sequence( scan ); } void method_rels() { ////////////////// TE Timings: //////////////////////////////// double exc_te=exc.get_duration()-exc.get_magnetic_center(); double min_echo_time_blade= exc_te + deph.get_duration()+epiacq.get_acquisition_center(); double min_echo_time_ref=0.0; if(EPIRef) { min_echo_time_ref=exc_te + deph_ref.get_duration()+epiacq_ref.get_acquisition_center(); } double min_echo_time=STD_max(min_echo_time_blade, min_echo_time_ref); if(commonPars->get_EchoTime()set_EchoTime(min_echo_time); if(TakeMinEchoTime) commonPars->set_EchoTime(min_echo_time); exc2acq= commonPars->get_EchoTime()-min_echo_time_blade; exc2acq_ref=commonPars->get_EchoTime()-min_echo_time_ref; ////////////////// TR Timings: //////////////////////////////// double slicedur =imagingpart.get_duration()*geometryInfo->get_nSlices(); double slicedur_ref=imagingpart_ref.get_duration()*geometryInfo->get_nSlices(); double mintr=STD_max(slicedur, slicedur_ref); if(commonPars->get_RepetitionTime()set_RepetitionTime(mintr); trdelay =secureDivision(commonPars->get_RepetitionTime()-slicedur, geometryInfo->get_nSlices()); trdelay_ref=secureDivision(commonPars->get_RepetitionTime()-slicedur_ref, geometryInfo->get_nSlices()); } void method_pars_set() { // extra information for the automatic reconstruction epiacq. set_default_reco_index(userdef,0).set_reco_vector(slice,exc); epiacq_template.set_default_reco_index(userdef,0).set_reco_vector(slice,exc); epiacq_ref. set_default_reco_index(userdef,1).set_reco_vector(slice,exc); epiacq_ref_template.set_default_reco_index(userdef,1).set_reco_vector(slice,exc); epiacq_ref_grappa. set_default_reco_index(userdef,1).set_reco_vector(slice,exc); epiacq.set_reco_vector(cycle,bladerot); epiacq_template.set_reco_vector(cycle,bladerot); recoInfo->set_DimValues(cycle,bladeangels); } }; ///////////////////////////////////////////////////// // entry point for the sequence module ODINMETHOD_ENTRY_POINT odin-1.8.5/install.win0000755000175000017500000001250311665172216011577 00000000000000#!/bin/sh # installation wrapper-script to compile and install ODIN # on Windows using an MSYS UNIX shell command="`basename $0`" usage="usage: $command [-d (debug mode)] [-n (no multi-threading)] [-j ] [-a ] " # parse options EXTRA_CONFIG_OPTS="--disable-unit-test" EXTRA_CXXFLAGS="-mthreads" EXTRA_LDFLAGS="-mthreads" MFLAGS="" ACMLDIR="" dist="yes" continue="yes" while [ $continue = "yes" ] ; do case "$1" in -d) EXTRA_CONFIG_OPTS="--enable-debug" ; dist="no" ; shift 1 ;; -n) EXTRA_CXXFLAGS="" ; EXTRA_LDFLAGS="" ; EXTRA_CONFIG_OPTS="--disable-threads $EXTRA_CONFIG_OPTS" ; shift 1 ;; -j) shift 1 ; MFLAGS="-j $1" ; shift 1 ;; -a) shift 1 ; ACMLDIR="$1" ; EXTRA_BUILD_LDFLAGS="-L${ACMLDIR} $EXTRA_BUILD_LDFLAGS" ; EXTRA_CONFIG_OPTS="--enable-acmlsupport $EXTRA_CONFIG_OPTS" ; shift 1 ;; *) continue="no" ;; esac done case $# in 2) MR_SOFTWARE_DIR="$1" INSTALLDIR="$2";; *) echo $usage; exit;; esac for checkpath in "$MR_SOFTWARE_DIR" "$INSTALLDIR" "$ACMLDIR" ; do if test ! -z $checkpath ; then if ! (echo $checkpath | grep -q "^.:/") ; then echo "ERROR: Please use the drive letter notation X:/somedir instead of $checkpath" ; exit -1; fi fi done # -O2 does not work withc GCC 3.4.5 EXTRA_CXXFLAGS="$EXTRA_CXXFLAGS -O1" EXTRA_BUILD_CXXFLAGS="-I${MR_SOFTWARE_DIR}/include $EXTRA_BUILD_CXXFLAGS" EXTRA_BUILD_LDFLAGS="-L${MR_SOFTWARE_DIR}/lib $EXTRA_BUILD_LDFLAGS" QTDIR_SLASH="`echo $QTDIR | sed 's/\\\\/\\//g'`" echo "EXTRA_CXXFLAGS=$EXTRA_CXXFLAGS" echo "EXTRA_LDFLAGS =$EXTRA_LDFLAGS" echo "EXTRA_BUILD_CXXFLAGS=$EXTRA_BUILD_CXXFLAGS" echo "EXTRA_BUILD_LDFLAGS =$EXTRA_BUILD_LDFLAGS" echo "EXTRA_CONFIG_OPTS =$EXTRA_CONFIG_OPTS" if [ ! -f Makefile ] ; then if ! CXXFLAGS="$EXTRA_CXXFLAGS" LDFLAGS="$EXTRA_LDFLAGS" ./configure \ --with-extra-build-cxxflags="$EXTRA_BUILD_CXXFLAGS" \ --with-extra-build-ldflags="$EXTRA_BUILD_LDFLAGS" \ --prefix=$INSTALLDIR \ --with-qt-dir="$QTDIR_SLASH" \ --enable-static --disable-shared \ $EXTRA_CONFIG_OPTS then echo "ERROR: MinGW configure failed" exit -1 fi fi if ! make $MFLAGS install ; then echo "ERROR: MinGW build failed" exit -1 fi if [ $dist = "yes" ] ; then # Modify doxygen file: Add dot path cat odin.doxygen | grep -v DOT_PATH > odin.doxygen.tmp mv odin.doxygen.tmp odin.doxygen echo "DOT_PATH = c:/Programme/ATT/Graphviz/bin" >> odin.doxygen # Add path for extra DLLs required during printing usage for manual export PATH="$PATH":"$MR_SOFTWARE_DIR/bin" if [ ! -d manual ] ; then echo -n "Creating Manual ..." if ! (cp /c/Programme/Doxygen/doxygen.exe . && make manual && mkdir -p $INSTALLDIR/share/doc/odin && cp -r manual $INSTALLDIR/share/doc/odin/) then echo "ERROR: Manual failed" exit -1 fi fi fi echo -n "Copying ODIN source code to $INSTALLDIR ..." if ! (make dist && mkdir -p $INSTALLDIR/src && cp odin-*.tar.gz $INSTALLDIR/src/) then echo "ERROR: Copy source failed" exit -1 fi echo "done" echo -n "Copying MR-Software stuff to $INSTALLDIR ..." for mrsoftbin in notepad2.exe ; do cp $MR_SOFTWARE_DIR/bin/$mrsoftbin $INSTALLDIR/bin done for mrsoftinclude in blitz ; do cp -r $MR_SOFTWARE_DIR/include/$mrsoftinclude $INSTALLDIR/include done for mrsoftlib in libniftiio.a libznz.a libz.a libgsl.a libgslcblas.a libblitz.a libofstd.a libdcmdata.a libdcmimgle.a ; do cp $MR_SOFTWARE_DIR/lib/$mrsoftlib $INSTALLDIR/lib done echo "done" echo -n "Copying MinGW stuff to $INSTALLDIR ..." MINGWDIR=$(dirname $(dirname $(which g++))) for subdir in bin include lib libexec mingw32 ; do cp -r $MINGWDIR/$subdir $INSTALLDIR/ done echo "done" echo -n "Copying MSYS stuff to $INSTALLDIR ..." mkdir -p $INSTALLDIR/msys for subdir in /bin /etc ; do cp -r $subdir $INSTALLDIR/msys done echo "done" echo -n "Setting up $INSTALLDIR/bin/shell.bat ..." echo 'set PATH=%1\bin;%PATH%' > $INSTALLDIR/bin/shell.bat echo 'set LD_LIBRARY_PATH=%1\lib;%LD_LIBRARY_PATH%' >> $INSTALLDIR/bin/shell.bat echo 'set LIBRARY_PATH=%1\lib;%LIBRARY_PATH%' >> $INSTALLDIR/bin/shell.bat echo 'set CPLUS_INCLUDE_PATH=%1\include;%CPLUS_INCLUDE_PATH%' >> $INSTALLDIR/bin/shell.bat echo 'set MANPATH=%1\man;%MANPATH%' >> $INSTALLDIR/bin/shell.bat echo 'start %1%\msys\bin\rxvt.exe -backspacekey  -sl 2500 -fg White -bg Black -sr -fn Courier-12 -tn msys -e /bin/sh --login -i' >> $INSTALLDIR/bin/shell.bat echo "done" echo -n "Creating dummy cygpath ..." echo "#!/bin/sh" > $INSTALLDIR/msys/bin/cygpath echo "eval echo \\\"\\\$\\{\$#\\}\\\"" >> $INSTALLDIR/msys/bin/cygpath echo "done" echo -n "Copying Qt stuff to $INSTALLDIR ..." for qtbin in QtCore4.dll QtGui4.dll ; do cp $QTDIR_SLASH/bin/$qtbin $INSTALLDIR/bin done echo "done" if test ! -z $ACMLDIR ; then echo -n "Copying AMD Core Math Lib to $INSTALLDIR ..." cp $ACMLDIR/libacml.a $INSTALLDIR/lib echo "done" fi if [ $dist = "yes" ] ; then echo -n "Creating NSIS distribution ..." rm -f $INSTALLDIR/bin/odintestsuite.exe # Remove obsolete stuff before distributing VERSION=`grep "VERSION=[0-9].[0-9].[0-9]" configure | sed s/\ *VERSION=//` cat odin.nsi | sed s/VERSION/$VERSION/ > $INSTALLDIR/odin.nsi OLDPWD=$PWD pushd $INSTALLDIR if ! /c/Programme/NSIS/makensis.exe odin.nsi then echo "ERROR: NSIS failed" fi mv odin-${VERSION}.exe $OLDPWD pushd $OLDPWD fi odin-1.8.5/coils/0000755000175000017500000000000011735135552010577 500000000000000odin-1.8.5/coils/radialInhomogen.coi0000644000175000017500000053226111322062355014314 00000000000000##TITLE=Coil 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If not, a copy # can be downloaded from http://www.gnu.org/licenses/gpl.html, or # obtained by writing to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. ]) # serial 56 LT_INIT # LT_PREREQ(VERSION) # ------------------ # Complain and exit if this libtool version is less that VERSION. m4_defun([LT_PREREQ], [m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1, [m4_default([$3], [m4_fatal([Libtool version $1 or higher is required], 63)])], [$2])]) # _LT_CHECK_BUILDDIR # ------------------ # Complain if the absolute build directory name contains unusual characters m4_defun([_LT_CHECK_BUILDDIR], [case `pwd` in *\ * | *\ *) AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;; esac ]) # LT_INIT([OPTIONS]) # ------------------ AC_DEFUN([LT_INIT], [AC_PREREQ([2.58])dnl We use AC_INCLUDES_DEFAULT AC_BEFORE([$0], [LT_LANG])dnl AC_BEFORE([$0], [LT_OUTPUT])dnl AC_BEFORE([$0], [LTDL_INIT])dnl m4_require([_LT_CHECK_BUILDDIR])dnl dnl Autoconf doesn't catch unexpanded LT_ macros by default: m4_pattern_forbid([^_?LT_[A-Z_]+$])dnl m4_pattern_allow([^(_LT_EOF|LT_DLGLOBAL|LT_DLLAZY_OR_NOW|LT_MULTI_MODULE)$])dnl dnl aclocal doesn't pull ltoptions.m4, ltsugar.m4, or ltversion.m4 dnl unless we require an AC_DEFUNed macro: AC_REQUIRE([LTOPTIONS_VERSION])dnl AC_REQUIRE([LTSUGAR_VERSION])dnl AC_REQUIRE([LTVERSION_VERSION])dnl AC_REQUIRE([LTOBSOLETE_VERSION])dnl m4_require([_LT_PROG_LTMAIN])dnl dnl Parse OPTIONS _LT_SET_OPTIONS([$0], [$1]) # This can be used to rebuild libtool when needed LIBTOOL_DEPS="$ltmain" # Always use our own libtool. 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then wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" AC_CACHE_CHECK([whether a statically linked program can dlopen itself], lt_cv_dlopen_self_static, [dnl _LT_TRY_DLOPEN_SELF( lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross) ]) fi CPPFLAGS="$save_CPPFLAGS" LDFLAGS="$save_LDFLAGS" LIBS="$save_LIBS" ;; esac case $lt_cv_dlopen_self in yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;; *) enable_dlopen_self=unknown ;; esac case $lt_cv_dlopen_self_static in yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;; *) enable_dlopen_self_static=unknown ;; esac fi _LT_DECL([dlopen_support], [enable_dlopen], [0], [Whether dlopen is supported]) _LT_DECL([dlopen_self], [enable_dlopen_self], [0], [Whether dlopen of programs is supported]) _LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0], [Whether dlopen of statically linked programs is supported]) ])# LT_SYS_DLOPEN_SELF # Old name: AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], []) # _LT_COMPILER_C_O([TAGNAME]) # --------------------------- # Check to see if options -c and -o are simultaneously supported by compiler. # This macro does not hard code the compiler like AC_PROG_CC_C_O. m4_defun([_LT_COMPILER_C_O], [m4_require([_LT_DECL_SED])dnl m4_require([_LT_FILEUTILS_DEFAULTS])dnl m4_require([_LT_TAG_COMPILER])dnl AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no $RM -r conftest 2>/dev/null mkdir conftest cd conftest mkdir out echo "$lt_simple_compile_test_code" > conftest.$ac_ext lt_compiler_flag="-o out/conftest2.$ac_objext" # Insert the option either (1) after the last *FLAGS variable, or # (2) before a word containing "conftest.", or (3) at the end. # Note that $ac_compile itself does not contain backslashes and begins # with a dollar sign (not a hyphen), so the echo should work correctly. lt_compile=`echo "$ac_compile" | $SED \ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; 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then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. 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newsos6) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[[89]] | openbsd2.[[89]].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. Preferred cross-host = GNU/Linux. version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; uts4*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH ;; *) dynamic_linker=no ;; esac AC_MSG_RESULT([$dynamic_linker]) test "$dynamic_linker" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" fi if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" fi _LT_DECL([], [variables_saved_for_relink], [1], [Variables whose values should be saved in libtool wrapper scripts and restored at link time]) _LT_DECL([], [need_lib_prefix], [0], [Do we need the "lib" prefix for modules?]) _LT_DECL([], [need_version], [0], [Do we need a version for libraries?]) _LT_DECL([], [version_type], [0], [Library versioning type]) _LT_DECL([], [runpath_var], [0], [Shared library runtime path variable]) _LT_DECL([], [shlibpath_var], [0],[Shared library path variable]) _LT_DECL([], [shlibpath_overrides_runpath], [0], [Is shlibpath searched before the hard-coded library search path?]) _LT_DECL([], [libname_spec], [1], [Format of library name prefix]) _LT_DECL([], [library_names_spec], [1], [[List of archive names. First name is the real one, the rest are links. The last name is the one that the linker finds with -lNAME]]) _LT_DECL([], [soname_spec], [1], [[The coded name of the library, if different from the real name]]) _LT_DECL([], [postinstall_cmds], [2], [Command to use after installation of a shared archive]) _LT_DECL([], [postuninstall_cmds], [2], [Command to use after uninstallation of a shared archive]) _LT_DECL([], [finish_cmds], [2], [Commands used to finish a libtool library installation in a directory]) _LT_DECL([], [finish_eval], [1], [[As "finish_cmds", except a single script fragment to be evaled but not shown]]) _LT_DECL([], [hardcode_into_libs], [0], [Whether we should hardcode library paths into libraries]) _LT_DECL([], [sys_lib_search_path_spec], [2], [Compile-time system search path for libraries]) _LT_DECL([], [sys_lib_dlsearch_path_spec], [2], [Run-time system search path for libraries]) ])# _LT_SYS_DYNAMIC_LINKER # _LT_PATH_TOOL_PREFIX(TOOL) # -------------------------- # find a file program which can recognize shared library AC_DEFUN([_LT_PATH_TOOL_PREFIX], [m4_require([_LT_DECL_EGREP])dnl AC_MSG_CHECKING([for $1]) AC_CACHE_VAL(lt_cv_path_MAGIC_CMD, [case $MAGIC_CMD in [[\\/*] | ?:[\\/]*]) lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. ;; *) lt_save_MAGIC_CMD="$MAGIC_CMD" lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR dnl $ac_dummy forces splitting on constant user-supplied paths. dnl POSIX.2 word splitting is done only on the output of word expansions, dnl not every word. This closes a longstanding sh security hole. ac_dummy="m4_if([$2], , $PATH, [$2])" for ac_dir in $ac_dummy; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/$1; then lt_cv_path_MAGIC_CMD="$ac_dir/$1" if test -n "$file_magic_test_file"; then case $deplibs_check_method in "file_magic "*) file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"` MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null | $EGREP "$file_magic_regex" > /dev/null; then : else cat <<_LT_EOF 1>&2 *** Warning: the command libtool uses to detect shared libraries, *** $file_magic_cmd, produces output that libtool cannot recognize. *** The result is that libtool may fail to recognize shared libraries *** as such. This will affect the creation of libtool libraries that *** depend on shared libraries, but programs linked with such libtool *** libraries will work regardless of this problem. Nevertheless, you *** may want to report the problem to your system manager and/or to *** bug-libtool@gnu.org _LT_EOF fi ;; esac fi break fi done IFS="$lt_save_ifs" MAGIC_CMD="$lt_save_MAGIC_CMD" ;; esac]) MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if test -n "$MAGIC_CMD"; then AC_MSG_RESULT($MAGIC_CMD) else AC_MSG_RESULT(no) fi _LT_DECL([], [MAGIC_CMD], [0], [Used to examine libraries when file_magic_cmd begins with "file"])dnl ])# _LT_PATH_TOOL_PREFIX # Old name: AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], []) # _LT_PATH_MAGIC # -------------- # find a file program which can recognize a shared library m4_defun([_LT_PATH_MAGIC], [_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH) if test -z "$lt_cv_path_MAGIC_CMD"; then if test -n "$ac_tool_prefix"; then _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH) else MAGIC_CMD=: fi fi ])# _LT_PATH_MAGIC # LT_PATH_LD # ---------- # find the pathname to the GNU or non-GNU linker AC_DEFUN([LT_PATH_LD], [AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_CANONICAL_BUILD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl AC_ARG_WITH([gnu-ld], [AS_HELP_STRING([--with-gnu-ld], [assume the C compiler uses GNU ld @<:@default=no@:>@])], [test "$withval" = no || with_gnu_ld=yes], [with_gnu_ld=no])dnl ac_prog=ld if test "$GCC" = yes; then # Check if gcc -print-prog-name=ld gives a path. AC_MSG_CHECKING([for ld used by $CC]) case $host in *-*-mingw*) # gcc leaves a trailing carriage return which upsets mingw ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;; *) ac_prog=`($CC -print-prog-name=ld) 2>&5` ;; esac case $ac_prog in # Accept absolute paths. [[\\/]]* | ?:[[\\/]]*) re_direlt='/[[^/]][[^/]]*/\.\./' # Canonicalize the pathname of ld ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` done test -z "$LD" && LD="$ac_prog" ;; "") # If it fails, then pretend we aren't using GCC. ac_prog=ld ;; *) # If it is relative, then search for the first ld in PATH. with_gnu_ld=unknown ;; esac elif test "$with_gnu_ld" = yes; then AC_MSG_CHECKING([for GNU ld]) else AC_MSG_CHECKING([for non-GNU ld]) fi AC_CACHE_VAL(lt_cv_path_LD, [if test -z "$LD"; then lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then lt_cv_path_LD="$ac_dir/$ac_prog" # Check to see if the program is GNU ld. 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See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'] lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[[3-9]]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac ]) file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown _LT_DECL([], [deplibs_check_method], [1], [Method to check whether dependent libraries are shared objects]) _LT_DECL([], [file_magic_cmd], [1], [Command to use when deplibs_check_method == "file_magic"]) ])# _LT_CHECK_MAGIC_METHOD # LT_PATH_NM # ---------- # find the pathname to a BSD- or MS-compatible name lister AC_DEFUN([LT_PATH_NM], [AC_REQUIRE([AC_PROG_CC])dnl AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM, [if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi]) if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :) AC_SUBST([DUMPBIN]) if test "$DUMPBIN" != ":"; then NM="$DUMPBIN" fi fi test -z "$NM" && NM=nm AC_SUBST([NM]) _LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface], [lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD) cat conftest.out >&AS_MESSAGE_LOG_FD if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest*]) ])# LT_PATH_NM # Old names: AU_ALIAS([AM_PROG_NM], [LT_PATH_NM]) AU_ALIAS([AC_PROG_NM], [LT_PATH_NM]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_PROG_NM], []) dnl AC_DEFUN([AC_PROG_NM], []) # LT_LIB_M # -------- # check for math library AC_DEFUN([LT_LIB_M], [AC_REQUIRE([AC_CANONICAL_HOST])dnl LIBM= case $host in *-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*) # These system don't have libm, or don't need it ;; *-ncr-sysv4.3*) AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw") AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm") ;; *) AC_CHECK_LIB(m, cos, LIBM="-lm") ;; esac AC_SUBST([LIBM]) ])# LT_LIB_M # Old name: AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_CHECK_LIBM], []) # _LT_COMPILER_NO_RTTI([TAGNAME]) # ------------------------------- m4_defun([_LT_COMPILER_NO_RTTI], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], lt_cv_prog_compiler_rtti_exceptions, [-fno-rtti -fno-exceptions], [], [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) fi _LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1], [Compiler flag to turn off builtin functions]) ])# _LT_COMPILER_NO_RTTI # _LT_CMD_GLOBAL_SYMBOLS # ---------------------- m4_defun([_LT_CMD_GLOBAL_SYMBOLS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([LT_PATH_NM])dnl AC_REQUIRE([LT_PATH_LD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_TAG_COMPILER])dnl # Check for command to grab the raw symbol name followed by C symbol from nm. AC_MSG_CHECKING([command to parse $NM output from $compiler object]) AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe], [ # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[[BCDEGRST]]' # Regexp to match symbols that can be accessed directly from C. sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[[BCDT]]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[[ABCDGISTW]]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[[ABCDEGRST]]' fi ;; irix* | nonstopux*) symcode='[[BCDEGRST]]' ;; osf*) symcode='[[BCDEGQRST]]' ;; solaris*) symcode='[[BDRT]]' ;; sco3.2v5*) symcode='[[DT]]' ;; sysv4.2uw2*) symcode='[[DT]]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[[ABDT]]' ;; sysv4) symcode='[[DFNSTU]]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[[ABCDGIRSTW]]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK ['"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx]" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if AC_TRY_EVAL(ac_compile); then # Now try to grab the symbols. nlist=conftest.nm if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[[]] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD fi else echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done ]) if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then AC_MSG_RESULT(failed) else AC_MSG_RESULT(ok) fi _LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], [Take the output of nm and produce a listing of raw symbols and C names]) _LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], [Transform the output of nm in a proper C declaration]) _LT_DECL([global_symbol_to_c_name_address], [lt_cv_sys_global_symbol_to_c_name_address], [1], [Transform the output of nm in a C name address pair]) _LT_DECL([global_symbol_to_c_name_address_lib_prefix], [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], [Transform the output of nm in a C name address pair when lib prefix is needed]) ]) # _LT_CMD_GLOBAL_SYMBOLS # _LT_COMPILER_PIC([TAGNAME]) # --------------------------- m4_defun([_LT_COMPILER_PIC], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_wl, $1)= _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)= AC_MSG_CHECKING([for $compiler option to produce PIC]) m4_if([$1], [CXX], [ # C++ specific cases for pic, static, wl, etc. if test "$GXX" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; *djgpp*) # DJGPP does not support shared libraries at all _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else case $host_os in aix[[4-9]]*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; chorus*) case $cc_basename in cxch68*) # Green Hills C++ Compiler # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" ;; esac ;; dgux*) case $cc_basename in ec++*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; ghcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; freebsd* | dragonfly*) # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' if test "$host_cpu" != ia64; then _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' fi ;; aCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac ;; *) ;; esac ;; interix*) # This is c89, which is MS Visual C++ (no shared libs) # Anyone wants to do a port? ;; irix5* | irix6* | nonstopux*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' # CC pic flag -KPIC is the default. ;; *) ;; esac ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in KCC*) # KAI C++ Compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; ecpc* ) # old Intel C++ for x86_64 which still supported -KPIC. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; icpc* ) # Intel C++, used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; pgCC* | pgcpp*) # Portland Group C++ compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; cxx*) # Compaq C++ # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xlc* | xlC*) # IBM XL 8.0 on PPC _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C++ 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; esac ;; esac ;; lynxos*) ;; m88k*) ;; mvs*) case $cc_basename in cxx*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' ;; *) ;; esac ;; netbsd* | netbsdelf*-gnu) ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) case $cc_basename in KCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' ;; RCC*) # Rational C++ 2.4.1 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; cxx*) # Digital/Compaq C++ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; *) ;; esac ;; psos*) ;; solaris*) case $cc_basename in CC*) # Sun C++ 4.2, 5.x and Centerline C++ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; gcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' ;; *) ;; esac ;; sunos4*) case $cc_basename in CC*) # Sun C++ 4.x _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; lcc*) # Lucid _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; esac ;; tandem*) case $cc_basename in NCC*) # NonStop-UX NCC 3.20 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; *) ;; esac ;; vxworks*) ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ], [ if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; msdosdjgpp*) # Just because we use GCC doesn't mean we suddenly get shared libraries # on systems that don't support them. _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no enable_shared=no ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else # PORTME Check for flag to pass linker flags through the system compiler. case $host_os in aix*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; hpux9* | hpux10* | hpux11*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but # not for PA HP-UX. case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac # Is there a better lt_prog_compiler_static that works with the bundled CC? _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' ;; irix5* | irix6* | nonstopux*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC (with -KPIC) is the default. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in # old Intel for x86_64 which still supported -KPIC. ecc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; 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netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; newsos6) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no _LT_TAGVAR(hardcode_direct_absolute, $1)=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' else case $host_os in openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*) _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' ;; esac fi else _LT_TAGVAR(ld_shlibs, $1)=no fi ;; os2*) _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; 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do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir' fi _LT_TAGVAR(archive_cmds_need_lc, $1)='no' _LT_TAGVAR(hardcode_libdir_separator, $1)=: ;; solaris*) _LT_TAGVAR(no_undefined_flag, $1)=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; 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AC_MSG_CHECKING([whether -lc should be explicitly linked in]) $RM conftest* echo "$lt_simple_compile_test_code" > conftest.$ac_ext if AC_TRY_EVAL(ac_compile) 2>conftest.err; then soname=conftest lib=conftest libobjs=conftest.$ac_objext deplibs= wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1) compiler_flags=-v linker_flags=-v verstring= output_objdir=. libname=conftest lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1) _LT_TAGVAR(allow_undefined_flag, $1)= if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) then _LT_TAGVAR(archive_cmds_need_lc, $1)=no else _LT_TAGVAR(archive_cmds_need_lc, $1)=yes fi _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag else cat conftest.err 1>&5 fi $RM conftest* AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)]) ;; esac fi ;; esac _LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0], [Whether or not to add -lc for building shared libraries]) _LT_TAGDECL([allow_libtool_libs_with_static_runtimes], [enable_shared_with_static_runtimes], [0], [Whether or not to disallow shared libs when runtime libs are static]) _LT_TAGDECL([], [export_dynamic_flag_spec], [1], [Compiler flag to allow reflexive dlopens]) _LT_TAGDECL([], [whole_archive_flag_spec], [1], [Compiler flag to generate shared objects directly from archives]) _LT_TAGDECL([], [compiler_needs_object], [1], [Whether the compiler copes with passing no objects directly]) _LT_TAGDECL([], [old_archive_from_new_cmds], [2], [Create an old-style archive from a shared archive]) _LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2], [Create a temporary old-style archive to link instead of a shared archive]) _LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive]) _LT_TAGDECL([], [archive_expsym_cmds], [2]) _LT_TAGDECL([], [module_cmds], [2], [Commands used to build a loadable module if different from building a shared archive.]) _LT_TAGDECL([], [module_expsym_cmds], [2]) _LT_TAGDECL([], [with_gnu_ld], [1], [Whether we are building with GNU ld or not]) _LT_TAGDECL([], [allow_undefined_flag], [1], [Flag that allows shared libraries with undefined symbols to be built]) _LT_TAGDECL([], [no_undefined_flag], [1], [Flag that enforces no undefined symbols]) _LT_TAGDECL([], [hardcode_libdir_flag_spec], [1], [Flag to hardcode $libdir into a binary during linking. 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In particular, it aims at rapid prototyping of MRI sequences. The sequences can be programmed using a high-level, object oriented, C++ programming interface. It provides advanced sequence analysis tools, such as interactive plotting of k-space trajectories, a user interface for a fast compile-link-test cycle and a powerful MRI simulator which supports different virtual samples. For fast and flexible image reconstruction, ODIN contains a highly customizable, multi-threaded data-processing framework. In addition, ODIN features useful command-line utilities for converting, manipulating and viewing medical image data in various formats (DICOM, NIfTI, binary data, ...). For installation instructions, please see the file 'INSTALL' file. For up-to-date documentation, please take a look at http://od1n.sourceforge.net/documentation.html http://od1n.sourceforge.net/manual/html/index.html The subdirectory 'platforms' contains a short description (HOWTO.txt) how to set up ODIN to work together with the different scanners. 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1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc. # This is free software; see the source for copying conditions. There is NO # warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # GNU Libtool is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # As a special exception to the GNU General Public License, # if you distribute this file as part of a program or library that # is built using GNU Libtool, you may include this file under the # same distribution terms that you use for the rest of that program. # # GNU Libtool is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with GNU Libtool; see the file COPYING. If not, a copy # can be downloaded from http://www.gnu.org/licenses/gpl.html, # or obtained by writing to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # Usage: $progname [OPTION]... [MODE-ARG]... # # Provide generalized library-building support services. # # --config show all configuration variables # --debug enable verbose shell tracing # -n, --dry-run display commands without modifying any files # --features display basic configuration information and exit # --mode=MODE use operation mode MODE # --preserve-dup-deps don't remove duplicate dependency libraries # --quiet, --silent don't print informational messages # --tag=TAG use configuration variables from tag TAG # -v, --verbose print informational messages (default) # --version print version information # -h, --help print short or long help message # # MODE must be one of the following: # # clean remove files from the build directory # compile compile a source file into a libtool object # execute automatically set library path, then run a program # finish complete the installation of libtool libraries # install install libraries or executables # link create a library or an executable # uninstall remove libraries from an installed directory # # MODE-ARGS vary depending on the MODE. # Try `$progname --help --mode=MODE' for a more detailed description of MODE. # # When reporting a bug, please describe a test case to reproduce it and # include the following information: # # host-triplet: $host # shell: $SHELL # compiler: $LTCC # compiler flags: $LTCFLAGS # linker: $LD (gnu? $with_gnu_ld) # $progname: (GNU libtool) 2.2.6b Debian-2.2.6b-2 # automake: $automake_version # autoconf: $autoconf_version # # Report bugs to . PROGRAM=ltmain.sh PACKAGE=libtool VERSION="2.2.6b Debian-2.2.6b-2" TIMESTAMP="" package_revision=1.3017 # Be Bourne compatible if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # NLS nuisances: We save the old values to restore during execute mode. # Only set LANG and LC_ALL to C if already set. # These must not be set unconditionally because not all systems understand # e.g. LANG=C (notably SCO). lt_user_locale= lt_safe_locale= for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${$lt_var+set}\" = set; then save_$lt_var=\$$lt_var $lt_var=C export $lt_var lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\" lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\" fi" done $lt_unset CDPATH : ${CP="cp -f"} : ${ECHO="echo"} : ${EGREP="/bin/grep -E"} : ${FGREP="/bin/grep -F"} : ${GREP="/bin/grep"} : ${LN_S="ln -s"} : ${MAKE="make"} : ${MKDIR="mkdir"} : ${MV="mv -f"} : ${RM="rm -f"} : ${SED="/bin/sed"} : ${SHELL="${CONFIG_SHELL-/bin/sh}"} : ${Xsed="$SED -e 1s/^X//"} # Global variables: EXIT_SUCCESS=0 EXIT_FAILURE=1 EXIT_MISMATCH=63 # $? = 63 is used to indicate version mismatch to missing. EXIT_SKIP=77 # $? = 77 is used to indicate a skipped test to automake. exit_status=$EXIT_SUCCESS # Make sure IFS has a sensible default lt_nl=' ' IFS=" $lt_nl" dirname="s,/[^/]*$,," basename="s,^.*/,," # func_dirname_and_basename file append nondir_replacement # perform func_basename and func_dirname in a single function # call: # dirname: Compute the dirname of FILE. If nonempty, # add APPEND to the result, otherwise set result # to NONDIR_REPLACEMENT. # value returned in "$func_dirname_result" # basename: Compute filename of FILE. # value retuned in "$func_basename_result" # Implementation must be kept synchronized with func_dirname # and func_basename. For efficiency, we do not delegate to # those functions but instead duplicate the functionality here. func_dirname_and_basename () { # Extract subdirectory from the argument. func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` if test "X$func_dirname_result" = "X${1}"; then func_dirname_result="${3}" else func_dirname_result="$func_dirname_result${2}" fi func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` } # Generated shell functions inserted here. # Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh # is ksh but when the shell is invoked as "sh" and the current value of # the _XPG environment variable is not equal to 1 (one), the special # positional parameter $0, within a function call, is the name of the # function. progpath="$0" # The name of this program: # In the unlikely event $progname began with a '-', it would play havoc with # func_echo (imagine progname=-n), so we prepend ./ in that case: func_dirname_and_basename "$progpath" progname=$func_basename_result case $progname in -*) progname=./$progname ;; esac # Make sure we have an absolute path for reexecution: case $progpath in [\\/]*|[A-Za-z]:\\*) ;; *[\\/]*) progdir=$func_dirname_result progdir=`cd "$progdir" && pwd` progpath="$progdir/$progname" ;; *) save_IFS="$IFS" IFS=: for progdir in $PATH; do IFS="$save_IFS" test -x "$progdir/$progname" && break done IFS="$save_IFS" test -n "$progdir" || progdir=`pwd` progpath="$progdir/$progname" ;; esac # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed="${SED}"' -e 1s/^X//' sed_quote_subst='s/\([`"$\\]\)/\\\1/g' # Same as above, but do not quote variable references. double_quote_subst='s/\(["`\\]\)/\\\1/g' # Re-`\' parameter expansions in output of double_quote_subst that were # `\'-ed in input to the same. If an odd number of `\' preceded a '$' # in input to double_quote_subst, that '$' was protected from expansion. # Since each input `\' is now two `\'s, look for any number of runs of # four `\'s followed by two `\'s and then a '$'. `\' that '$'. bs='\\' bs2='\\\\' bs4='\\\\\\\\' dollar='\$' sed_double_backslash="\ s/$bs4/&\\ /g s/^$bs2$dollar/$bs&/ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g s/\n//g" # Standard options: opt_dry_run=false opt_help=false opt_quiet=false opt_verbose=false opt_warning=: # func_echo arg... # Echo program name prefixed message, along with the current mode # name if it has been set yet. func_echo () { $ECHO "$progname${mode+: }$mode: $*" } # func_verbose arg... # Echo program name prefixed message in verbose mode only. func_verbose () { $opt_verbose && func_echo ${1+"$@"} # A bug in bash halts the script if the last line of a function # fails when set -e is in force, so we need another command to # work around that: : } # func_error arg... # Echo program name prefixed message to standard error. func_error () { $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2 } # func_warning arg... # Echo program name prefixed warning message to standard error. func_warning () { $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2 # bash bug again: : } # func_fatal_error arg... # Echo program name prefixed message to standard error, and exit. func_fatal_error () { func_error ${1+"$@"} exit $EXIT_FAILURE } # func_fatal_help arg... # Echo program name prefixed message to standard error, followed by # a help hint, and exit. func_fatal_help () { func_error ${1+"$@"} func_fatal_error "$help" } help="Try \`$progname --help' for more information." ## default # func_grep expression filename # Check whether EXPRESSION matches any line of FILENAME, without output. func_grep () { $GREP "$1" "$2" >/dev/null 2>&1 } # func_mkdir_p directory-path # Make sure the entire path to DIRECTORY-PATH is available. func_mkdir_p () { my_directory_path="$1" my_dir_list= if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then # Protect directory names starting with `-' case $my_directory_path in -*) my_directory_path="./$my_directory_path" ;; esac # While some portion of DIR does not yet exist... while test ! -d "$my_directory_path"; do # ...make a list in topmost first order. 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Don't # stop in that case! $MKDIR "$my_dir" 2>/dev/null || : done IFS="$save_mkdir_p_IFS" # Bail out if we (or some other process) failed to create a directory. test -d "$my_directory_path" || \ func_fatal_error "Failed to create \`$1'" fi } # func_mktempdir [string] # Make a temporary directory that won't clash with other running # libtool processes, and avoids race conditions if possible. If # given, STRING is the basename for that directory. func_mktempdir () { my_template="${TMPDIR-/tmp}/${1-$progname}" if test "$opt_dry_run" = ":"; then # Return a directory name, but don't create it in dry-run mode my_tmpdir="${my_template}-$$" else # If mktemp works, use that first and foremost my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null` if test ! -d "$my_tmpdir"; then # Failing that, at least try and use $RANDOM to avoid a race my_tmpdir="${my_template}-${RANDOM-0}$$" save_mktempdir_umask=`umask` umask 0077 $MKDIR "$my_tmpdir" umask $save_mktempdir_umask fi # If we're not in dry-run mode, bomb out on failure test -d "$my_tmpdir" || \ func_fatal_error "cannot create temporary directory \`$my_tmpdir'" fi $ECHO "X$my_tmpdir" | $Xsed } # func_quote_for_eval arg # Aesthetically quote ARG to be evaled later. # This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT # is double-quoted, suitable for a subsequent eval, whereas # FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters # which are still active within double quotes backslashified. func_quote_for_eval () { case $1 in *[\\\`\"\$]*) func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;; *) func_quote_for_eval_unquoted_result="$1" ;; esac case $func_quote_for_eval_unquoted_result in # Double-quote args containing shell metacharacters to delay # word splitting, command substitution and and variable # expansion for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\"" ;; *) func_quote_for_eval_result="$func_quote_for_eval_unquoted_result" esac } # func_quote_for_expand arg # Aesthetically quote ARG to be evaled later; same as above, # but do not quote variable references. func_quote_for_expand () { case $1 in *[\\\`\"]*) my_arg=`$ECHO "X$1" | $Xsed \ -e "$double_quote_subst" -e "$sed_double_backslash"` ;; *) my_arg="$1" ;; esac case $my_arg in # Double-quote args containing shell metacharacters to delay # word splitting and command substitution for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") my_arg="\"$my_arg\"" ;; esac func_quote_for_expand_result="$my_arg" } # func_show_eval cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. func_show_eval () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$my_cmd" my_status=$? if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_show_eval_locale cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. Use the saved locale for evaluation. func_show_eval_locale () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$lt_user_locale $my_cmd" my_status=$? eval "$lt_safe_locale" if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_version # Echo version message to standard output and exit. func_version () { $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / { s/^# // s/^# *$// s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/ p }' < "$progpath" exit $? } # func_usage # Echo short help message to standard output and exit. func_usage () { $SED -n '/^# Usage:/,/# -h/ { s/^# // s/^# *$// s/\$progname/'$progname'/ p }' < "$progpath" $ECHO $ECHO "run \`$progname --help | more' for full usage" exit $? } # func_help # Echo long help message to standard output and exit. func_help () { $SED -n '/^# Usage:/,/# Report bugs to/ { s/^# // s/^# *$// s*\$progname*'$progname'* s*\$host*'"$host"'* s*\$SHELL*'"$SHELL"'* s*\$LTCC*'"$LTCC"'* s*\$LTCFLAGS*'"$LTCFLAGS"'* s*\$LD*'"$LD"'* s/\$with_gnu_ld/'"$with_gnu_ld"'/ s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/ s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/ p }' < "$progpath" exit $? } # func_missing_arg argname # Echo program name prefixed message to standard error and set global # exit_cmd. func_missing_arg () { func_error "missing argument for $1" exit_cmd=exit } exit_cmd=: # Check that we have a working $ECHO. if test "X$1" = X--no-reexec; then # Discard the --no-reexec flag, and continue. shift elif test "X$1" = X--fallback-echo; then # Avoid inline document here, it may be left over : elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then # Yippee, $ECHO works! : else # Restart under the correct shell, and then maybe $ECHO will work. exec $SHELL "$progpath" --no-reexec ${1+"$@"} fi if test "X$1" = X--fallback-echo; then # used as fallback echo shift cat </dev/null 2>&1; then taglist="$taglist $tagname" # Evaluate the configuration. Be careful to quote the path # and the sed script, to avoid splitting on whitespace, but # also don't use non-portable quotes within backquotes within # quotes we have to do it in 2 steps: extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"` eval "$extractedcf" else func_error "ignoring unknown tag $tagname" fi ;; esac } # Parse options once, thoroughly. This comes as soon as possible in # the script to make things like `libtool --version' happen quickly. { # Shorthand for --mode=foo, only valid as the first argument case $1 in clean|clea|cle|cl) shift; set dummy --mode clean ${1+"$@"}; shift ;; compile|compil|compi|comp|com|co|c) shift; set dummy --mode compile ${1+"$@"}; shift ;; execute|execut|execu|exec|exe|ex|e) shift; set dummy --mode execute ${1+"$@"}; shift ;; finish|finis|fini|fin|fi|f) shift; set dummy --mode finish ${1+"$@"}; shift ;; install|instal|insta|inst|ins|in|i) shift; set dummy --mode install ${1+"$@"}; shift ;; link|lin|li|l) shift; set dummy --mode link ${1+"$@"}; shift ;; uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) shift; set dummy --mode uninstall ${1+"$@"}; shift ;; esac # Parse non-mode specific arguments: while test "$#" -gt 0; do opt="$1" shift case $opt in --config) func_config ;; --debug) preserve_args="$preserve_args $opt" func_echo "enabling shell trace mode" opt_debug='set -x' $opt_debug ;; -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break execute_dlfiles="$execute_dlfiles $1" shift ;; --dry-run | -n) opt_dry_run=: ;; --features) func_features ;; --finish) mode="finish" ;; --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break case $1 in # Valid mode arguments: clean) ;; compile) ;; execute) ;; finish) ;; install) ;; link) ;; relink) ;; uninstall) ;; # Catch anything else as an error *) func_error "invalid argument for $opt" exit_cmd=exit break ;; esac mode="$1" shift ;; --preserve-dup-deps) opt_duplicate_deps=: ;; --quiet|--silent) preserve_args="$preserve_args $opt" opt_silent=: ;; --verbose| -v) preserve_args="$preserve_args $opt" opt_silent=false ;; --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break preserve_args="$preserve_args $opt $1" func_enable_tag "$1" # tagname is set here shift ;; # Separate optargs to long options: -dlopen=*|--mode=*|--tag=*) func_opt_split "$opt" set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"} shift ;; -\?|-h) func_usage ;; --help) opt_help=: ;; --version) func_version ;; -*) func_fatal_help "unrecognized option \`$opt'" ;; *) nonopt="$opt" break ;; esac done case $host in *cygwin* | *mingw* | *pw32* | *cegcc*) # don't eliminate duplications in $postdeps and $predeps opt_duplicate_compiler_generated_deps=: ;; *) opt_duplicate_compiler_generated_deps=$opt_duplicate_deps ;; esac # Having warned about all mis-specified options, bail out if # anything was wrong. $exit_cmd $EXIT_FAILURE } # func_check_version_match # Ensure that we are using m4 macros, and libtool script from the same # release of libtool. func_check_version_match () { if test "$package_revision" != "$macro_revision"; then if test "$VERSION" != "$macro_version"; then if test -z "$macro_version"; then cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from an older release. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from $PACKAGE $macro_version. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF fi else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision, $progname: but the definition of this LT_INIT comes from revision $macro_revision. $progname: You should recreate aclocal.m4 with macros from revision $package_revision $progname: of $PACKAGE $VERSION and run autoconf again. _LT_EOF fi exit $EXIT_MISMATCH fi } ## ----------- ## ## Main. ## ## ----------- ## $opt_help || { # Sanity checks first: func_check_version_match if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then func_fatal_configuration "not configured to build any kind of library" fi test -z "$mode" && func_fatal_error "error: you must specify a MODE." # Darwin sucks eval std_shrext=\"$shrext_cmds\" # Only execute mode is allowed to have -dlopen flags. if test -n "$execute_dlfiles" && test "$mode" != execute; then func_error "unrecognized option \`-dlopen'" $ECHO "$help" 1>&2 exit $EXIT_FAILURE fi # Change the help message to a mode-specific one. generic_help="$help" help="Try \`$progname --help --mode=$mode' for more information." } # func_lalib_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_lalib_p () { test -f "$1" && $SED -e 4q "$1" 2>/dev/null \ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1 } # func_lalib_unsafe_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function implements the same check as func_lalib_p without # resorting to external programs. To this end, it redirects stdin and # closes it afterwards, without saving the original file descriptor. # As a safety measure, use it only where a negative result would be # fatal anyway. Works if `file' does not exist. func_lalib_unsafe_p () { lalib_p=no if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then for lalib_p_l in 1 2 3 4 do read lalib_p_line case "$lalib_p_line" in \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;; esac done exec 0<&5 5<&- fi test "$lalib_p" = yes } # func_ltwrapper_script_p file # True iff FILE is a libtool wrapper script # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_script_p () { func_lalib_p "$1" } # func_ltwrapper_executable_p file # True iff FILE is a libtool wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_executable_p () { func_ltwrapper_exec_suffix= case $1 in *.exe) ;; *) func_ltwrapper_exec_suffix=.exe ;; esac $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1 } # func_ltwrapper_scriptname file # Assumes file is an ltwrapper_executable # uses $file to determine the appropriate filename for a # temporary ltwrapper_script. func_ltwrapper_scriptname () { func_ltwrapper_scriptname_result="" if func_ltwrapper_executable_p "$1"; then func_dirname_and_basename "$1" "" "." func_stripname '' '.exe' "$func_basename_result" func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" fi } # func_ltwrapper_p file # True iff FILE is a libtool wrapper script or wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_p () { func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1" } # func_execute_cmds commands fail_cmd # Execute tilde-delimited COMMANDS. # If FAIL_CMD is given, eval that upon failure. # FAIL_CMD may read-access the current command in variable CMD! func_execute_cmds () { $opt_debug save_ifs=$IFS; IFS='~' for cmd in $1; do IFS=$save_ifs eval cmd=\"$cmd\" func_show_eval "$cmd" "${2-:}" done IFS=$save_ifs } # func_source file # Source FILE, adding directory component if necessary. # Note that it is not necessary on cygwin/mingw to append a dot to # FILE even if both FILE and FILE.exe exist: automatic-append-.exe # behavior happens only for exec(3), not for open(2)! Also, sourcing # `FILE.' does not work on cygwin managed mounts. func_source () { $opt_debug case $1 in */* | *\\*) . "$1" ;; *) . "./$1" ;; esac } # func_infer_tag arg # Infer tagged configuration to use if any are available and # if one wasn't chosen via the "--tag" command line option. # Only attempt this if the compiler in the base compile # command doesn't match the default compiler. # arg is usually of the form 'gcc ...' func_infer_tag () { $opt_debug if test -n "$available_tags" && test -z "$tagname"; then CC_quoted= for arg in $CC; do func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case $@ in # Blanks in the command may have been stripped by the calling shell, # but not from the CC environment variable when configure was run. " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;; # Blanks at the start of $base_compile will cause this to fail # if we don't check for them as well. *) for z in $available_tags; do if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then # Evaluate the configuration. eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`" CC_quoted= for arg in $CC; do # Double-quote args containing other shell metacharacters. func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case "$@ " in " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) # The compiler in the base compile command matches # the one in the tagged configuration. # Assume this is the tagged configuration we want. tagname=$z break ;; esac fi done # If $tagname still isn't set, then no tagged configuration # was found and let the user know that the "--tag" command # line option must be used. if test -z "$tagname"; then func_echo "unable to infer tagged configuration" func_fatal_error "specify a tag with \`--tag'" # else # func_verbose "using $tagname tagged configuration" fi ;; esac fi } # func_write_libtool_object output_name pic_name nonpic_name # Create a libtool object file (analogous to a ".la" file), # but don't create it if we're doing a dry run. func_write_libtool_object () { write_libobj=${1} if test "$build_libtool_libs" = yes; then write_lobj=\'${2}\' else write_lobj=none fi if test "$build_old_libs" = yes; then write_oldobj=\'${3}\' else write_oldobj=none fi $opt_dry_run || { cat >${write_libobj}T <?"'"'"' &()|`$[]' \ && func_warning "libobj name \`$libobj' may not contain shell special characters." func_dirname_and_basename "$obj" "/" "" objname="$func_basename_result" xdir="$func_dirname_result" lobj=${xdir}$objdir/$objname test -z "$base_compile" && \ func_fatal_help "you must specify a compilation command" # Delete any leftover library objects. if test "$build_old_libs" = yes; then removelist="$obj $lobj $libobj ${libobj}T" else removelist="$lobj $libobj ${libobj}T" fi # On Cygwin there's no "real" PIC flag so we must build both object types case $host_os in cygwin* | mingw* | pw32* | os2* | cegcc*) pic_mode=default ;; esac if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then # non-PIC code in shared libraries is not supported pic_mode=default fi # Calculate the filename of the output object if compiler does # not support -o with -c if test "$compiler_c_o" = no; then output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext} lockfile="$output_obj.lock" else output_obj= need_locks=no lockfile= fi # Lock this critical section if it is needed # We use this script file to make the link, it avoids creating a new file if test "$need_locks" = yes; then until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done elif test "$need_locks" = warn; then if test -f "$lockfile"; then $ECHO "\ *** ERROR, $lockfile exists and contains: `cat $lockfile 2>/dev/null` This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi removelist="$removelist $output_obj" $ECHO "$srcfile" > "$lockfile" fi $opt_dry_run || $RM $removelist removelist="$removelist $lockfile" trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 if test -n "$fix_srcfile_path"; then eval srcfile=\"$fix_srcfile_path\" fi func_quote_for_eval "$srcfile" qsrcfile=$func_quote_for_eval_result # Only build a PIC object if we are building libtool libraries. if test "$build_libtool_libs" = yes; then # Without this assignment, base_compile gets emptied. fbsd_hideous_sh_bug=$base_compile if test "$pic_mode" != no; then command="$base_compile $qsrcfile $pic_flag" else # Don't build PIC code command="$base_compile $qsrcfile" fi func_mkdir_p "$xdir$objdir" if test -z "$output_obj"; then # Place PIC objects in $objdir command="$command -o $lobj" fi func_show_eval_locale "$command" \ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed, then go on to compile the next one if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then func_show_eval '$MV "$output_obj" "$lobj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi # Allow error messages only from the first compilation. if test "$suppress_opt" = yes; then suppress_output=' >/dev/null 2>&1' fi fi # Only build a position-dependent object if we build old libraries. if test "$build_old_libs" = yes; then if test "$pic_mode" != yes; then # Don't build PIC code command="$base_compile $qsrcfile$pie_flag" else command="$base_compile $qsrcfile $pic_flag" fi if test "$compiler_c_o" = yes; then command="$command -o $obj" fi # Suppress compiler output if we already did a PIC compilation. command="$command$suppress_output" func_show_eval_locale "$command" \ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then func_show_eval '$MV "$output_obj" "$obj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi fi $opt_dry_run || { func_write_libtool_object "$libobj" "$objdir/$objname" "$objname" # Unlock the critical section if it was locked if test "$need_locks" != no; then removelist=$lockfile $RM "$lockfile" fi } exit $EXIT_SUCCESS } $opt_help || { test "$mode" = compile && func_mode_compile ${1+"$@"} } func_mode_help () { # We need to display help for each of the modes. case $mode in "") # Generic help is extracted from the usage comments # at the start of this file. func_help ;; clean) $ECHO \ "Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE... Remove files from the build directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, object or program, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; compile) $ECHO \ "Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE Compile a source file into a libtool library object. This mode accepts the following additional options: -o OUTPUT-FILE set the output file name to OUTPUT-FILE -no-suppress do not suppress compiler output for multiple passes -prefer-pic try to building PIC objects only -prefer-non-pic try to building non-PIC objects only -shared do not build a \`.o' file suitable for static linking -static only build a \`.o' file suitable for static linking COMPILE-COMMAND is a command to be used in creating a \`standard' object file from the given SOURCEFILE. The output file name is determined by removing the directory component from SOURCEFILE, then substituting the C source code suffix \`.c' with the library object suffix, \`.lo'." ;; execute) $ECHO \ "Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]... Automatically set library path, then run a program. This mode accepts the following additional options: -dlopen FILE add the directory containing FILE to the library path This mode sets the library path environment variable according to \`-dlopen' flags. If any of the ARGS are libtool executable wrappers, then they are translated into their corresponding uninstalled binary, and any of their required library directories are added to the library path. Then, COMMAND is executed, with ARGS as arguments." ;; finish) $ECHO \ "Usage: $progname [OPTION]... --mode=finish [LIBDIR]... Complete the installation of libtool libraries. Each LIBDIR is a directory that contains libtool libraries. The commands that this mode executes may require superuser privileges. Use the \`--dry-run' option if you just want to see what would be executed." ;; install) $ECHO \ "Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND... Install executables or libraries. INSTALL-COMMAND is the installation command. The first component should be either the \`install' or \`cp' program. The following components of INSTALL-COMMAND are treated specially: -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation The rest of the components are interpreted as arguments to that command (only BSD-compatible install options are recognized)." ;; link) $ECHO \ "Usage: $progname [OPTION]... --mode=link LINK-COMMAND... Link object files or libraries together to form another library, or to create an executable program. LINK-COMMAND is a command using the C compiler that you would use to create a program from several object files. The following components of LINK-COMMAND are treated specially: -all-static do not do any dynamic linking at all -avoid-version do not add a version suffix if possible -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3) -export-symbols SYMFILE try to export only the symbols listed in SYMFILE -export-symbols-regex REGEX try to export only the symbols matching REGEX -LLIBDIR search LIBDIR for required installed libraries -lNAME OUTPUT-FILE requires the installed library libNAME -module build a library that can dlopened -no-fast-install disable the fast-install mode -no-install link a not-installable executable -no-undefined declare that a library does not refer to external symbols -o OUTPUT-FILE create OUTPUT-FILE from the specified objects -objectlist FILE Use a list of object files found in FILE to specify objects -precious-files-regex REGEX don't remove output files matching REGEX -release RELEASE specify package release information -rpath LIBDIR the created library will eventually be installed in LIBDIR -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries -shared only do dynamic linking of libtool libraries -shrext SUFFIX override the standard shared library file extension -static do not do any dynamic linking of uninstalled libtool libraries -static-libtool-libs do not do any dynamic linking of libtool libraries -version-info CURRENT[:REVISION[:AGE]] specify library version info [each variable defaults to 0] -weak LIBNAME declare that the target provides the LIBNAME interface All other options (arguments beginning with \`-') are ignored. Every other argument is treated as a filename. Files ending in \`.la' are treated as uninstalled libtool libraries, other files are standard or library object files. If the OUTPUT-FILE ends in \`.la', then a libtool library is created, only library objects (\`.lo' files) may be specified, and \`-rpath' is required, except when creating a convenience library. If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created using \`ar' and \`ranlib', or on Windows using \`lib'. If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file is created, otherwise an executable program is created." ;; uninstall) $ECHO \ "Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE... Remove libraries from an installation directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; *) func_fatal_help "invalid operation mode \`$mode'" ;; esac $ECHO $ECHO "Try \`$progname --help' for more information about other modes." exit $? } # Now that we've collected a possible --mode arg, show help if necessary $opt_help && func_mode_help # func_mode_execute arg... func_mode_execute () { $opt_debug # The first argument is the command name. cmd="$nonopt" test -z "$cmd" && \ func_fatal_help "you must specify a COMMAND" # Handle -dlopen flags immediately. for file in $execute_dlfiles; do test -f "$file" \ || func_fatal_help "\`$file' is not a file" dir= case $file in *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$lib' is not a valid libtool archive" # Read the libtool library. dlname= library_names= func_source "$file" # Skip this library if it cannot be dlopened. if test -z "$dlname"; then # Warn if it was a shared library. test -n "$library_names" && \ func_warning "\`$file' was not linked with \`-export-dynamic'" continue fi func_dirname "$file" "" "." dir="$func_dirname_result" if test -f "$dir/$objdir/$dlname"; then dir="$dir/$objdir" else if test ! -f "$dir/$dlname"; then func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" fi fi ;; *.lo) # Just add the directory containing the .lo file. func_dirname "$file" "" "." dir="$func_dirname_result" ;; *) func_warning "\`-dlopen' is ignored for non-libtool libraries and objects" continue ;; esac # Get the absolute pathname. absdir=`cd "$dir" && pwd` test -n "$absdir" && dir="$absdir" # Now add the directory to shlibpath_var. if eval "test -z \"\$$shlibpath_var\""; then eval "$shlibpath_var=\"\$dir\"" else eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\"" fi done # This variable tells wrapper scripts just to set shlibpath_var # rather than running their programs. libtool_execute_magic="$magic" # Check if any of the arguments is a wrapper script. args= for file do case $file in -*) ;; *) # Do a test to see if this is really a libtool program. if func_ltwrapper_script_p "$file"; then func_source "$file" # Transform arg to wrapped name. file="$progdir/$program" elif func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" func_source "$func_ltwrapper_scriptname_result" # Transform arg to wrapped name. file="$progdir/$program" fi ;; esac # Quote arguments (to preserve shell metacharacters). func_quote_for_eval "$file" args="$args $func_quote_for_eval_result" done if test "X$opt_dry_run" = Xfalse; then if test -n "$shlibpath_var"; then # Export the shlibpath_var. eval "export $shlibpath_var" fi # Restore saved environment variables for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${save_$lt_var+set}\" = set; then $lt_var=\$save_$lt_var; export $lt_var else $lt_unset $lt_var fi" done # Now prepare to actually exec the command. exec_cmd="\$cmd$args" else # Display what would be done. if test -n "$shlibpath_var"; then eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" $ECHO "export $shlibpath_var" fi $ECHO "$cmd$args" exit $EXIT_SUCCESS fi } test "$mode" = execute && func_mode_execute ${1+"$@"} # func_mode_finish arg... func_mode_finish () { $opt_debug libdirs="$nonopt" admincmds= if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then for dir do libdirs="$libdirs $dir" done for libdir in $libdirs; do if test -n "$finish_cmds"; then # Do each command in the finish commands. func_execute_cmds "$finish_cmds" 'admincmds="$admincmds '"$cmd"'"' fi if test -n "$finish_eval"; then # Do the single finish_eval. eval cmds=\"$finish_eval\" $opt_dry_run || eval "$cmds" || admincmds="$admincmds $cmds" fi done fi # Exit here if they wanted silent mode. $opt_silent && exit $EXIT_SUCCESS $ECHO "X----------------------------------------------------------------------" | $Xsed $ECHO "Libraries have been installed in:" for libdir in $libdirs; do $ECHO " $libdir" done $ECHO $ECHO "If you ever happen to want to link against installed libraries" $ECHO "in a given directory, LIBDIR, you must either use libtool, and" $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'" $ECHO "flag during linking and do at least one of the following:" if test -n "$shlibpath_var"; then $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable" $ECHO " during execution" fi if test -n "$runpath_var"; then $ECHO " - add LIBDIR to the \`$runpath_var' environment variable" $ECHO " during linking" fi if test -n "$hardcode_libdir_flag_spec"; then libdir=LIBDIR eval flag=\"$hardcode_libdir_flag_spec\" $ECHO " - use the \`$flag' linker flag" fi if test -n "$admincmds"; then $ECHO " - have your system administrator run these commands:$admincmds" fi if test -f /etc/ld.so.conf; then $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" fi $ECHO $ECHO "See any operating system documentation about shared libraries for" case $host in solaris2.[6789]|solaris2.1[0-9]) $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual" $ECHO "pages." ;; *) $ECHO "more information, such as the ld(1) and ld.so(8) manual pages." ;; esac $ECHO "X----------------------------------------------------------------------" | $Xsed exit $EXIT_SUCCESS } test "$mode" = finish && func_mode_finish ${1+"$@"} # func_mode_install arg... func_mode_install () { $opt_debug # There may be an optional sh(1) argument at the beginning of # install_prog (especially on Windows NT). if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || # Allow the use of GNU shtool's install command. $ECHO "X$nonopt" | $GREP shtool >/dev/null; then # Aesthetically quote it. func_quote_for_eval "$nonopt" install_prog="$func_quote_for_eval_result " arg=$1 shift else install_prog= arg=$nonopt fi # The real first argument should be the name of the installation program. # Aesthetically quote it. func_quote_for_eval "$arg" install_prog="$install_prog$func_quote_for_eval_result" # We need to accept at least all the BSD install flags. dest= files= opts= prev= install_type= isdir=no stripme= for arg do if test -n "$dest"; then files="$files $dest" dest=$arg continue fi case $arg in -d) isdir=yes ;; -f) case " $install_prog " in *[\\\ /]cp\ *) ;; *) prev=$arg ;; esac ;; -g | -m | -o) prev=$arg ;; -s) stripme=" -s" continue ;; -*) ;; *) # If the previous option needed an argument, then skip it. if test -n "$prev"; then prev= else dest=$arg continue fi ;; esac # Aesthetically quote the argument. func_quote_for_eval "$arg" install_prog="$install_prog $func_quote_for_eval_result" done test -z "$install_prog" && \ func_fatal_help "you must specify an install program" test -n "$prev" && \ func_fatal_help "the \`$prev' option requires an argument" if test -z "$files"; then if test -z "$dest"; then func_fatal_help "no file or destination specified" else func_fatal_help "you must specify a destination" fi fi # Strip any trailing slash from the destination. func_stripname '' '/' "$dest" dest=$func_stripname_result # Check to see that the destination is a directory. test -d "$dest" && isdir=yes if test "$isdir" = yes; then destdir="$dest" destname= else func_dirname_and_basename "$dest" "" "." destdir="$func_dirname_result" destname="$func_basename_result" # Not a directory, so check to see that there is only one file specified. set dummy $files; shift test "$#" -gt 1 && \ func_fatal_help "\`$dest' is not a directory" fi case $destdir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) for file in $files; do case $file in *.lo) ;; *) func_fatal_help "\`$destdir' must be an absolute directory name" ;; esac done ;; esac # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" staticlibs= future_libdirs= current_libdirs= for file in $files; do # Do each installation. case $file in *.$libext) # Do the static libraries later. staticlibs="$staticlibs $file" ;; *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$file' is not a valid libtool archive" library_names= old_library= relink_command= func_source "$file" # Add the libdir to current_libdirs if it is the destination. if test "X$destdir" = "X$libdir"; then case "$current_libdirs " in *" $libdir "*) ;; *) current_libdirs="$current_libdirs $libdir" ;; esac else # Note the libdir as a future libdir. case "$future_libdirs " in *" $libdir "*) ;; *) future_libdirs="$future_libdirs $libdir" ;; esac fi func_dirname "$file" "/" "" dir="$func_dirname_result" dir="$dir$objdir" if test -n "$relink_command"; then # Determine the prefix the user has applied to our future dir. inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"` # Don't allow the user to place us outside of our expected # location b/c this prevents finding dependent libraries that # are installed to the same prefix. # At present, this check doesn't affect windows .dll's that # are installed into $libdir/../bin (currently, that works fine) # but it's something to keep an eye on. test "$inst_prefix_dir" = "$destdir" && \ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir" if test -n "$inst_prefix_dir"; then # Stick the inst_prefix_dir data into the link command. relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` else relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"` fi func_warning "relinking \`$file'" func_show_eval "$relink_command" \ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"' fi # See the names of the shared library. set dummy $library_names; shift if test -n "$1"; then realname="$1" shift srcname="$realname" test -n "$relink_command" && srcname="$realname"T # Install the shared library and build the symlinks. func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \ 'exit $?' tstripme="$stripme" case $host_os in cygwin* | mingw* | pw32* | cegcc*) case $realname in *.dll.a) tstripme="" ;; esac ;; esac if test -n "$tstripme" && test -n "$striplib"; then func_show_eval "$striplib $destdir/$realname" 'exit $?' fi if test "$#" -gt 0; then # Delete the old symlinks, and create new ones. # Try `ln -sf' first, because the `ln' binary might depend on # the symlink we replace! Solaris /bin/ln does not understand -f, # so we also need to try rm && ln -s. for linkname do test "$linkname" != "$realname" \ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })" done fi # Do each command in the postinstall commands. lib="$destdir/$realname" func_execute_cmds "$postinstall_cmds" 'exit $?' fi # Install the pseudo-library for information purposes. func_basename "$file" name="$func_basename_result" instname="$dir/$name"i func_show_eval "$install_prog $instname $destdir/$name" 'exit $?' # Maybe install the static library, too. test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library" ;; *.lo) # Install (i.e. copy) a libtool object. # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # Deduce the name of the destination old-style object file. case $destfile in *.lo) func_lo2o "$destfile" staticdest=$func_lo2o_result ;; *.$objext) staticdest="$destfile" destfile= ;; *) func_fatal_help "cannot copy a libtool object to \`$destfile'" ;; esac # Install the libtool object if requested. test -n "$destfile" && \ func_show_eval "$install_prog $file $destfile" 'exit $?' # Install the old object if enabled. if test "$build_old_libs" = yes; then # Deduce the name of the old-style object file. func_lo2o "$file" staticobj=$func_lo2o_result func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?' fi exit $EXIT_SUCCESS ;; *) # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # If the file is missing, and there is a .exe on the end, strip it # because it is most likely a libtool script we actually want to # install stripped_ext="" case $file in *.exe) if test ! -f "$file"; then func_stripname '' '.exe' "$file" file=$func_stripname_result stripped_ext=".exe" fi ;; esac # Do a test to see if this is really a libtool program. case $host in *cygwin* | *mingw*) if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" wrapper=$func_ltwrapper_scriptname_result else func_stripname '' '.exe' "$file" wrapper=$func_stripname_result fi ;; *) wrapper=$file ;; esac if func_ltwrapper_script_p "$wrapper"; then notinst_deplibs= relink_command= func_source "$wrapper" # Check the variables that should have been set. test -z "$generated_by_libtool_version" && \ func_fatal_error "invalid libtool wrapper script \`$wrapper'" finalize=yes for lib in $notinst_deplibs; do # Check to see that each library is installed. libdir= if test -f "$lib"; then func_source "$lib" fi libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test if test -n "$libdir" && test ! -f "$libfile"; then func_warning "\`$lib' has not been installed in \`$libdir'" finalize=no fi done relink_command= func_source "$wrapper" outputname= if test "$fast_install" = no && test -n "$relink_command"; then $opt_dry_run || { if test "$finalize" = yes; then tmpdir=`func_mktempdir` func_basename "$file$stripped_ext" file="$func_basename_result" outputname="$tmpdir/$file" # Replace the output file specification. relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'` $opt_silent || { func_quote_for_expand "$relink_command" eval "func_echo $func_quote_for_expand_result" } if eval "$relink_command"; then : else func_error "error: relink \`$file' with the above command before installing it" $opt_dry_run || ${RM}r "$tmpdir" continue fi file="$outputname" else func_warning "cannot relink \`$file'" fi } else # Install the binary that we compiled earlier. file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"` fi fi # remove .exe since cygwin /usr/bin/install will append another # one anyway case $install_prog,$host in */usr/bin/install*,*cygwin*) case $file:$destfile in *.exe:*.exe) # this is ok ;; *.exe:*) destfile=$destfile.exe ;; *:*.exe) func_stripname '' '.exe' "$destfile" destfile=$func_stripname_result ;; esac ;; esac func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?' $opt_dry_run || if test -n "$outputname"; then ${RM}r "$tmpdir" fi ;; esac done for file in $staticlibs; do func_basename "$file" name="$func_basename_result" # Set up the ranlib parameters. oldlib="$destdir/$name" func_show_eval "$install_prog \$file \$oldlib" 'exit $?' if test -n "$stripme" && test -n "$old_striplib"; then func_show_eval "$old_striplib $oldlib" 'exit $?' fi # Do each command in the postinstall commands. func_execute_cmds "$old_postinstall_cmds" 'exit $?' done test -n "$future_libdirs" && \ func_warning "remember to run \`$progname --finish$future_libdirs'" if test -n "$current_libdirs"; then # Maybe just do a dry run. $opt_dry_run && current_libdirs=" -n$current_libdirs" exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs' else exit $EXIT_SUCCESS fi } test "$mode" = install && func_mode_install ${1+"$@"} # func_generate_dlsyms outputname originator pic_p # Extract symbols from dlprefiles and create ${outputname}S.o with # a dlpreopen symbol table. func_generate_dlsyms () { $opt_debug my_outputname="$1" my_originator="$2" my_pic_p="${3-no}" my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'` my_dlsyms= if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then if test -n "$NM" && test -n "$global_symbol_pipe"; then my_dlsyms="${my_outputname}S.c" else func_error "not configured to extract global symbols from dlpreopened files" fi fi if test -n "$my_dlsyms"; then case $my_dlsyms in "") ;; *.c) # Discover the nlist of each of the dlfiles. nlist="$output_objdir/${my_outputname}.nm" func_show_eval "$RM $nlist ${nlist}S ${nlist}T" # Parse the name list into a source file. func_verbose "creating $output_objdir/$my_dlsyms" $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\ /* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */ /* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */ #ifdef __cplusplus extern \"C\" { #endif /* External symbol declarations for the compiler. */\ " if test "$dlself" = yes; then func_verbose "generating symbol list for \`$output'" $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist" # Add our own program objects to the symbol list. progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` for progfile in $progfiles; do func_verbose "extracting global C symbols from \`$progfile'" $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'" done if test -n "$exclude_expsyms"; then $opt_dry_run || { eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi if test -n "$export_symbols_regex"; then $opt_dry_run || { eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi # Prepare the list of exported symbols if test -z "$export_symbols"; then export_symbols="$output_objdir/$outputname.exp" $opt_dry_run || { $RM $export_symbols eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"' ;; esac } else $opt_dry_run || { eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"' eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' case $host in *cygwin | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' ;; esac } fi fi for dlprefile in $dlprefiles; do func_verbose "extracting global C symbols from \`$dlprefile'" func_basename "$dlprefile" name="$func_basename_result" $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'" } done $opt_dry_run || { # Make sure we have at least an empty file. test -f "$nlist" || : > "$nlist" if test -n "$exclude_expsyms"; then $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T $MV "$nlist"T "$nlist" fi # Try sorting and uniquifying the output. if $GREP -v "^: " < "$nlist" | if sort -k 3 /dev/null 2>&1; then sort -k 3 else sort +2 fi | uniq > "$nlist"S; then : else $GREP -v "^: " < "$nlist" > "$nlist"S fi if test -f "$nlist"S; then eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' else $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms" fi $ECHO >> "$output_objdir/$my_dlsyms" "\ /* The mapping between symbol names and symbols. */ typedef struct { const char *name; void *address; } lt_dlsymlist; " case $host in *cygwin* | *mingw* | *cegcc* ) $ECHO >> "$output_objdir/$my_dlsyms" "\ /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */" lt_dlsym_const= ;; *osf5*) echo >> "$output_objdir/$my_dlsyms" "\ /* This system does not cope well with relocations in const data */" lt_dlsym_const= ;; *) lt_dlsym_const=const ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ extern $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[]; $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[] = {\ { \"$my_originator\", (void *) 0 }," case $need_lib_prefix in no) eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; *) eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt_${my_prefix}_LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif\ " } # !$opt_dry_run pic_flag_for_symtable= case "$compile_command " in *" -static "*) ;; *) case $host in # compiling the symbol table file with pic_flag works around # a FreeBSD bug that causes programs to crash when -lm is # linked before any other PIC object. But we must not use # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; *-*-hpux*) pic_flag_for_symtable=" $pic_flag" ;; *) if test "X$my_pic_p" != Xno; then pic_flag_for_symtable=" $pic_flag" fi ;; esac ;; esac symtab_cflags= for arg in $LTCFLAGS; do case $arg in -pie | -fpie | -fPIE) ;; *) symtab_cflags="$symtab_cflags $arg" ;; esac done # Now compile the dynamic symbol file. func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?' # Clean up the generated files. func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"' # Transform the symbol file into the correct name. symfileobj="$output_objdir/${my_outputname}S.$objext" case $host in *cygwin* | *mingw* | *cegcc* ) if test -f "$output_objdir/$my_outputname.def"; then compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` else compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` fi ;; *) compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` ;; esac ;; *) func_fatal_error "unknown suffix for \`$my_dlsyms'" ;; esac else # We keep going just in case the user didn't refer to # lt_preloaded_symbols. The linker will fail if global_symbol_pipe # really was required. # Nullify the symbol file. compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"` fi } # func_win32_libid arg # return the library type of file 'arg' # # Need a lot of goo to handle *both* DLLs and import libs # Has to be a shell function in order to 'eat' the argument # that is supplied when $file_magic_command is called. func_win32_libid () { $opt_debug win32_libid_type="unknown" win32_fileres=`file -L $1 2>/dev/null` case $win32_fileres in *ar\ archive\ import\ library*) # definitely import win32_libid_type="x86 archive import" ;; *ar\ archive*) # could be an import, or static if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then win32_nmres=`eval $NM -f posix -A $1 | $SED -n -e ' 1,100{ / I /{ s,.*,import, p q } }'` case $win32_nmres in import*) win32_libid_type="x86 archive import";; *) win32_libid_type="x86 archive static";; esac fi ;; *DLL*) win32_libid_type="x86 DLL" ;; *executable*) # but shell scripts are "executable" too... case $win32_fileres in *MS\ Windows\ PE\ Intel*) win32_libid_type="x86 DLL" ;; esac ;; esac $ECHO "$win32_libid_type" } # func_extract_an_archive dir oldlib func_extract_an_archive () { $opt_debug f_ex_an_ar_dir="$1"; shift f_ex_an_ar_oldlib="$1" func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?' if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then : else func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" fi } # func_extract_archives gentop oldlib ... func_extract_archives () { $opt_debug my_gentop="$1"; shift my_oldlibs=${1+"$@"} my_oldobjs="" my_xlib="" my_xabs="" my_xdir="" for my_xlib in $my_oldlibs; do # Extract the objects. case $my_xlib in [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;; *) my_xabs=`pwd`"/$my_xlib" ;; esac func_basename "$my_xlib" my_xlib="$func_basename_result" my_xlib_u=$my_xlib while :; do case " $extracted_archives " in *" $my_xlib_u "*) func_arith $extracted_serial + 1 extracted_serial=$func_arith_result my_xlib_u=lt$extracted_serial-$my_xlib ;; *) break ;; esac done extracted_archives="$extracted_archives $my_xlib_u" my_xdir="$my_gentop/$my_xlib_u" func_mkdir_p "$my_xdir" case $host in *-darwin*) func_verbose "Extracting $my_xabs" # Do not bother doing anything if just a dry run $opt_dry_run || { darwin_orig_dir=`pwd` cd $my_xdir || exit $? darwin_archive=$my_xabs darwin_curdir=`pwd` darwin_base_archive=`basename "$darwin_archive"` darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true` if test -n "$darwin_arches"; then darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'` darwin_arch= func_verbose "$darwin_base_archive has multiple architectures $darwin_arches" for darwin_arch in $darwin_arches ; do func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}" $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}" cd "unfat-$$/${darwin_base_archive}-${darwin_arch}" func_extract_an_archive "`pwd`" "${darwin_base_archive}" cd "$darwin_curdir" $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" done # $darwin_arches ## Okay now we've a bunch of thin objects, gotta fatten them up :) darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u` darwin_file= darwin_files= for darwin_file in $darwin_filelist; do darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP` $LIPO -create -output "$darwin_file" $darwin_files done # $darwin_filelist $RM -rf unfat-$$ cd "$darwin_orig_dir" else cd $darwin_orig_dir func_extract_an_archive "$my_xdir" "$my_xabs" fi # $darwin_arches } # !$opt_dry_run ;; *) func_extract_an_archive "$my_xdir" "$my_xabs" ;; esac my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP` done func_extract_archives_result="$my_oldobjs" } # func_emit_wrapper_part1 [arg=no] # # Emit the first part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part1 () { func_emit_wrapper_part1_arg1=no if test -n "$1" ; then func_emit_wrapper_part1_arg1=$1 fi $ECHO "\ #! $SHELL # $output - temporary wrapper script for $objdir/$outputname # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # The $output program cannot be directly executed until all the libtool # libraries that it depends on are installed. # # This wrapper script should never be moved out of the build directory. # If it is, it will not operate correctly. # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed='${SED} -e 1s/^X//' sed_quote_subst='$sed_quote_subst' # Be Bourne compatible if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST else case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # The HP-UX ksh and POSIX shell print the target directory to stdout # if CDPATH is set. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH relink_command=\"$relink_command\" # This environment variable determines our operation mode. if test \"\$libtool_install_magic\" = \"$magic\"; then # install mode needs the following variables: generated_by_libtool_version='$macro_version' notinst_deplibs='$notinst_deplibs' else # When we are sourced in execute mode, \$file and \$ECHO are already set. if test \"\$libtool_execute_magic\" != \"$magic\"; then ECHO=\"$qecho\" file=\"\$0\" # Make sure echo works. if test \"X\$1\" = X--no-reexec; then # Discard the --no-reexec flag, and continue. shift elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then # Yippee, \$ECHO works! : else # Restart under the correct shell, and then maybe \$ECHO will work. exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"} fi fi\ " $ECHO "\ # Find the directory that this script lives in. thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\` test \"x\$thisdir\" = \"x\$file\" && thisdir=. # Follow symbolic links until we get to the real thisdir. file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\` while test -n \"\$file\"; do destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\` # If there was a directory component, then change thisdir. if test \"x\$destdir\" != \"x\$file\"; then case \"\$destdir\" in [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; *) thisdir=\"\$thisdir/\$destdir\" ;; esac fi file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\` file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\` done " } # end: func_emit_wrapper_part1 # func_emit_wrapper_part2 [arg=no] # # Emit the second part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part2 () { func_emit_wrapper_part2_arg1=no if test -n "$1" ; then func_emit_wrapper_part2_arg1=$1 fi $ECHO "\ # Usually 'no', except on cygwin/mingw when embedded into # the cwrapper. WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1 if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then # special case for '.' if test \"\$thisdir\" = \".\"; then thisdir=\`pwd\` fi # remove .libs from thisdir case \"\$thisdir\" in *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;; $objdir ) thisdir=. ;; esac fi # Try to get the absolute directory name. absdir=\`cd \"\$thisdir\" && pwd\` test -n \"\$absdir\" && thisdir=\"\$absdir\" " if test "$fast_install" = yes; then $ECHO "\ program=lt-'$outputname'$exeext progdir=\"\$thisdir/$objdir\" if test ! -f \"\$progdir/\$program\" || { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ test \"X\$file\" != \"X\$progdir/\$program\"; }; then file=\"\$\$-\$program\" if test ! -d \"\$progdir\"; then $MKDIR \"\$progdir\" else $RM \"\$progdir/\$file\" fi" $ECHO "\ # relink executable if necessary if test -n \"\$relink_command\"; then if relink_command_output=\`eval \$relink_command 2>&1\`; then : else $ECHO \"\$relink_command_output\" >&2 $RM \"\$progdir/\$file\" exit 1 fi fi $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || { $RM \"\$progdir/\$program\"; $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } $RM \"\$progdir/\$file\" fi" else $ECHO "\ program='$outputname' progdir=\"\$thisdir/$objdir\" " fi $ECHO "\ if test -f \"\$progdir/\$program\"; then" # Export our shlibpath_var if we have one. if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then $ECHO "\ # Add our own library path to $shlibpath_var $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" # Some systems cannot cope with colon-terminated $shlibpath_var # The second colon is a workaround for a bug in BeOS R4 sed $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\` export $shlibpath_var " fi # fixup the dll searchpath if we need to. if test -n "$dllsearchpath"; then $ECHO "\ # Add the dll search path components to the executable PATH PATH=$dllsearchpath:\$PATH " fi $ECHO "\ if test \"\$libtool_execute_magic\" != \"$magic\"; then # Run the actual program with our arguments. " case $host in # Backslashes separate directories on plain windows *-*-mingw | *-*-os2* | *-cegcc*) $ECHO "\ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} " ;; *) $ECHO "\ exec \"\$progdir/\$program\" \${1+\"\$@\"} " ;; esac $ECHO "\ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 exit 1 fi else # The program doesn't exist. \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 exit 1 fi fi\ " } # end: func_emit_wrapper_part2 # func_emit_wrapper [arg=no] # # Emit a libtool wrapper script on stdout. # Don't directly open a file because we may want to # incorporate the script contents within a cygwin/mingw # wrapper executable. Must ONLY be called from within # func_mode_link because it depends on a number of variables # set therein. # # ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR # variable will take. If 'yes', then the emitted script # will assume that the directory in which it is stored is # the $objdir directory. This is a cygwin/mingw-specific # behavior. func_emit_wrapper () { func_emit_wrapper_arg1=no if test -n "$1" ; then func_emit_wrapper_arg1=$1 fi # split this up so that func_emit_cwrapperexe_src # can call each part independently. func_emit_wrapper_part1 "${func_emit_wrapper_arg1}" func_emit_wrapper_part2 "${func_emit_wrapper_arg1}" } # func_to_host_path arg # # Convert paths to host format when used with build tools. # Intended for use with "native" mingw (where libtool itself # is running under the msys shell), or in the following cross- # build environments: # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # where wine is equipped with the `winepath' executable. # In the native mingw case, the (msys) shell automatically # converts paths for any non-msys applications it launches, # but that facility isn't available from inside the cwrapper. # Similar accommodations are necessary for $host mingw and # $build cygwin. Calling this function does no harm for other # $host/$build combinations not listed above. # # ARG is the path (on $build) that should be converted to # the proper representation for $host. The result is stored # in $func_to_host_path_result. func_to_host_path () { func_to_host_path_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' case $build in *mingw* ) # actually, msys # awkward: cmd appends spaces to result lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_path_tmp1=`( cmd //c echo "$1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_path_tmp1=`cygpath -w "$1"` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # Unfortunately, winepath does not exit with a non-zero # error code, so we are forced to check the contents of # stdout. On the other hand, if the command is not # found, the shell will set an exit code of 127 and print # *an error message* to stdout. So we must check for both # error code of zero AND non-empty stdout, which explains # the odd construction: func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null` if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` else # Allow warning below. func_to_host_path_result="" fi ;; esac if test -z "$func_to_host_path_result" ; then func_error "Could not determine host path corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback: func_to_host_path_result="$1" fi ;; esac fi } # end: func_to_host_path # func_to_host_pathlist arg # # Convert pathlists to host format when used with build tools. # See func_to_host_path(), above. This function supports the # following $build/$host combinations (but does no harm for # combinations not listed here): # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # # Path separators are also converted from $build format to # $host format. If ARG begins or ends with a path separator # character, it is preserved (but converted to $host format) # on output. # # ARG is a pathlist (on $build) that should be converted to # the proper representation on $host. The result is stored # in $func_to_host_pathlist_result. func_to_host_pathlist () { func_to_host_pathlist_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' # Remove leading and trailing path separator characters from # ARG. msys behavior is inconsistent here, cygpath turns them # into '.;' and ';.', and winepath ignores them completely. func_to_host_pathlist_tmp2="$1" # Once set for this call, this variable should not be # reassigned. It is used in tha fallback case. func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e 's|^:*||' -e 's|:*$||'` case $build in *mingw* ) # Actually, msys. # Awkward: cmd appends spaces to result. lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # unfortunately, winepath doesn't convert pathlists func_to_host_pathlist_result="" func_to_host_pathlist_oldIFS=$IFS IFS=: for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do IFS=$func_to_host_pathlist_oldIFS if test -n "$func_to_host_pathlist_f" ; then func_to_host_path "$func_to_host_pathlist_f" if test -n "$func_to_host_path_result" ; then if test -z "$func_to_host_pathlist_result" ; then func_to_host_pathlist_result="$func_to_host_path_result" else func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result" fi fi fi IFS=: done IFS=$func_to_host_pathlist_oldIFS ;; esac if test -z "$func_to_host_pathlist_result" ; then func_error "Could not determine the host path(s) corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback. This may break if $1 contains DOS-style drive # specifications. The fix is not to complicate the expression # below, but for the user to provide a working wine installation # with winepath so that path translation in the cross-to-mingw # case works properly. lt_replace_pathsep_nix_to_dos="s|:|;|g" func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_replace_pathsep_nix_to_dos"` fi # Now, add the leading and trailing path separators back case "$1" in :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result" ;; esac case "$1" in *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;" ;; esac ;; esac fi } # end: func_to_host_pathlist # func_emit_cwrapperexe_src # emit the source code for a wrapper executable on stdout # Must ONLY be called from within func_mode_link because # it depends on a number of variable set therein. func_emit_cwrapperexe_src () { cat < #include #ifdef _MSC_VER # include # include # include # define setmode _setmode #else # include # include # ifdef __CYGWIN__ # include # define HAVE_SETENV # ifdef __STRICT_ANSI__ char *realpath (const char *, char *); int putenv (char *); int setenv (const char *, const char *, int); # endif # endif #endif #include #include #include #include #include #include #include #include #if defined(PATH_MAX) # define LT_PATHMAX PATH_MAX #elif defined(MAXPATHLEN) # define LT_PATHMAX MAXPATHLEN #else # define LT_PATHMAX 1024 #endif #ifndef S_IXOTH # define S_IXOTH 0 #endif #ifndef S_IXGRP # define S_IXGRP 0 #endif #ifdef _MSC_VER # define S_IXUSR _S_IEXEC # define stat _stat # ifndef _INTPTR_T_DEFINED # define intptr_t int # endif #endif #ifndef DIR_SEPARATOR # define DIR_SEPARATOR '/' # define PATH_SEPARATOR ':' #endif #if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \ defined (__OS2__) # define HAVE_DOS_BASED_FILE_SYSTEM # define FOPEN_WB "wb" # ifndef DIR_SEPARATOR_2 # define DIR_SEPARATOR_2 '\\' # endif # ifndef PATH_SEPARATOR_2 # define PATH_SEPARATOR_2 ';' # endif #endif #ifndef DIR_SEPARATOR_2 # define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR) #else /* DIR_SEPARATOR_2 */ # define IS_DIR_SEPARATOR(ch) \ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2)) #endif /* DIR_SEPARATOR_2 */ #ifndef PATH_SEPARATOR_2 # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR) #else /* PATH_SEPARATOR_2 */ # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2) #endif /* PATH_SEPARATOR_2 */ #ifdef __CYGWIN__ # define FOPEN_WB "wb" #endif #ifndef FOPEN_WB # define FOPEN_WB "w" #endif #ifndef _O_BINARY # define _O_BINARY 0 #endif #define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type))) #define XFREE(stale) do { \ if (stale) { free ((void *) stale); stale = 0; } \ } while (0) #undef LTWRAPPER_DEBUGPRINTF #if defined DEBUGWRAPPER # define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args static void ltwrapper_debugprintf (const char *fmt, ...) { va_list args; va_start (args, fmt); (void) vfprintf (stderr, fmt, args); va_end (args); } #else # define LTWRAPPER_DEBUGPRINTF(args) #endif const char *program_name = NULL; void *xmalloc (size_t num); char *xstrdup (const char *string); const char *base_name (const char *name); char *find_executable (const char *wrapper); char *chase_symlinks (const char *pathspec); int make_executable (const char *path); int check_executable (const char *path); char *strendzap (char *str, const char *pat); void lt_fatal (const char *message, ...); void lt_setenv (const char *name, const char *value); char *lt_extend_str (const char *orig_value, const char *add, int to_end); void lt_opt_process_env_set (const char *arg); void lt_opt_process_env_prepend (const char *arg); void lt_opt_process_env_append (const char *arg); int lt_split_name_value (const char *arg, char** name, char** value); void lt_update_exe_path (const char *name, const char *value); void lt_update_lib_path (const char *name, const char *value); static const char *script_text_part1 = EOF func_emit_wrapper_part1 yes | $SED -e 's/\([\\"]\)/\\\1/g' \ -e 's/^/ "/' -e 's/$/\\n"/' echo ";" cat <"))); for (i = 0; i < newargc; i++) { LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : ""))); } EOF case $host_os in mingw*) cat <<"EOF" /* execv doesn't actually work on mingw as expected on unix */ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz); if (rval == -1) { /* failed to start process */ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno)); return 127; } return rval; EOF ;; *) cat <<"EOF" execv (lt_argv_zero, newargz); return rval; /* =127, but avoids unused variable warning */ EOF ;; esac cat <<"EOF" } void * xmalloc (size_t num) { void *p = (void *) malloc (num); if (!p) lt_fatal ("Memory exhausted"); return p; } char * xstrdup (const char *string) { return string ? strcpy ((char *) xmalloc (strlen (string) + 1), string) : NULL; } const char * base_name (const char *name) { const char *base; #if defined (HAVE_DOS_BASED_FILE_SYSTEM) /* Skip over the disk name in MSDOS pathnames. */ if (isalpha ((unsigned char) name[0]) && name[1] == ':') name += 2; #endif for (base = name; *name; name++) if (IS_DIR_SEPARATOR (*name)) base = name + 1; return base; } int check_executable (const char *path) { struct stat st; LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if ((stat (path, &st) >= 0) && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH))) return 1; else return 0; } int make_executable (const char *path) { int rval = 0; struct stat st; LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if (stat (path, &st) >= 0) { rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR); } return rval; } /* Searches for the full path of the wrapper. Returns newly allocated full path name if found, NULL otherwise Does not chase symlinks, even on platforms that support them. */ char * find_executable (const char *wrapper) { int has_slash = 0; const char *p; const char *p_next; /* static buffer for getcwd */ char tmp[LT_PATHMAX + 1]; int tmp_len; char *concat_name; LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n", wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!")); if ((wrapper == NULL) || (*wrapper == '\0')) return NULL; /* Absolute path? */ #if defined (HAVE_DOS_BASED_FILE_SYSTEM) if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':') { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } else { #endif if (IS_DIR_SEPARATOR (wrapper[0])) { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } #if defined (HAVE_DOS_BASED_FILE_SYSTEM) } #endif for (p = wrapper; *p; p++) if (*p == '/') { has_slash = 1; break; } if (!has_slash) { /* no slashes; search PATH */ const char *path = getenv ("PATH"); if (path != NULL) { for (p = path; *p; p = p_next) { const char *q; size_t p_len; for (q = p; *q; q++) if (IS_PATH_SEPARATOR (*q)) break; p_len = q - p; p_next = (*q == '\0' ? q : q + 1); if (p_len == 0) { /* empty path: current directory */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); } else { concat_name = XMALLOC (char, p_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, p, p_len); concat_name[p_len] = '/'; strcpy (concat_name + p_len + 1, wrapper); } if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } } /* not found in PATH; assume curdir */ } /* Relative path | not found in path: prepend cwd */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); return NULL; } char * chase_symlinks (const char *pathspec) { #ifndef S_ISLNK return xstrdup (pathspec); #else char buf[LT_PATHMAX]; struct stat s; char *tmp_pathspec = xstrdup (pathspec); char *p; int has_symlinks = 0; while (strlen (tmp_pathspec) && !has_symlinks) { LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n", tmp_pathspec)); if (lstat (tmp_pathspec, &s) == 0) { if (S_ISLNK (s.st_mode) != 0) { has_symlinks = 1; break; } /* search backwards for last DIR_SEPARATOR */ p = tmp_pathspec + strlen (tmp_pathspec) - 1; while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) p--; if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) { /* no more DIR_SEPARATORS left */ break; } *p = '\0'; } else { char *errstr = strerror (errno); lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr); } } XFREE (tmp_pathspec); if (!has_symlinks) { return xstrdup (pathspec); } tmp_pathspec = realpath (pathspec, buf); if (tmp_pathspec == 0) { lt_fatal ("Could not follow symlinks for %s", pathspec); } return xstrdup (tmp_pathspec); #endif } char * strendzap (char *str, const char *pat) { size_t len, patlen; assert (str != NULL); assert (pat != NULL); len = strlen (str); patlen = strlen (pat); if (patlen <= len) { str += len - patlen; if (strcmp (str, pat) == 0) *str = '\0'; } return str; } static void lt_error_core (int exit_status, const char *mode, const char *message, va_list ap) { fprintf (stderr, "%s: %s: ", program_name, mode); vfprintf (stderr, message, ap); fprintf (stderr, ".\n"); if (exit_status >= 0) exit (exit_status); } void lt_fatal (const char *message, ...) { va_list ap; va_start (ap, message); lt_error_core (EXIT_FAILURE, "FATAL", message, ap); va_end (ap); } void lt_setenv (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n", (name ? name : ""), (value ? value : ""))); { #ifdef HAVE_SETENV /* always make a copy, for consistency with !HAVE_SETENV */ char *str = xstrdup (value); setenv (name, str, 1); #else int len = strlen (name) + 1 + strlen (value) + 1; char *str = XMALLOC (char, len); sprintf (str, "%s=%s", name, value); if (putenv (str) != EXIT_SUCCESS) { XFREE (str); } #endif } } char * lt_extend_str (const char *orig_value, const char *add, int to_end) { char *new_value; if (orig_value && *orig_value) { int orig_value_len = strlen (orig_value); int add_len = strlen (add); new_value = XMALLOC (char, add_len + orig_value_len + 1); if (to_end) { strcpy (new_value, orig_value); strcpy (new_value + orig_value_len, add); } else { strcpy (new_value, add); strcpy (new_value + add_len, orig_value); } } else { new_value = xstrdup (add); } return new_value; } int lt_split_name_value (const char *arg, char** name, char** value) { const char *p; int len; if (!arg || !*arg) return 1; p = strchr (arg, (int)'='); if (!p) return 1; *value = xstrdup (++p); len = strlen (arg) - strlen (*value); *name = XMALLOC (char, len); strncpy (*name, arg, len-1); (*name)[len - 1] = '\0'; return 0; } void lt_opt_process_env_set (const char *arg) { char *name = NULL; char *value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg); } lt_setenv (name, value); XFREE (name); XFREE (value); } void lt_opt_process_env_prepend (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg); } new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_opt_process_env_append (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg); } new_value = lt_extend_str (getenv (name), value, 1); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_update_exe_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); /* some systems can't cope with a ':'-terminated path #' */ int len = strlen (new_value); while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1])) { new_value[len-1] = '\0'; } lt_setenv (name, new_value); XFREE (new_value); } } void lt_update_lib_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); } } EOF } # end: func_emit_cwrapperexe_src # func_mode_link arg... func_mode_link () { $opt_debug case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) # It is impossible to link a dll without this setting, and # we shouldn't force the makefile maintainer to figure out # which system we are compiling for in order to pass an extra # flag for every libtool invocation. # allow_undefined=no # FIXME: Unfortunately, there are problems with the above when trying # to make a dll which has undefined symbols, in which case not # even a static library is built. For now, we need to specify # -no-undefined on the libtool link line when we can be certain # that all symbols are satisfied, otherwise we get a static library. allow_undefined=yes ;; *) allow_undefined=yes ;; esac libtool_args=$nonopt base_compile="$nonopt $@" compile_command=$nonopt finalize_command=$nonopt compile_rpath= finalize_rpath= compile_shlibpath= finalize_shlibpath= convenience= old_convenience= deplibs= old_deplibs= compiler_flags= linker_flags= dllsearchpath= lib_search_path=`pwd` inst_prefix_dir= new_inherited_linker_flags= avoid_version=no dlfiles= dlprefiles= dlself=no export_dynamic=no export_symbols= export_symbols_regex= generated= libobjs= ltlibs= module=no no_install=no objs= non_pic_objects= precious_files_regex= prefer_static_libs=no preload=no prev= prevarg= release= rpath= xrpath= perm_rpath= temp_rpath= thread_safe=no vinfo= vinfo_number=no weak_libs= single_module="${wl}-single_module" func_infer_tag $base_compile # We need to know -static, to get the right output filenames. for arg do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no break ;; -all-static | -static | -static-libtool-libs) case $arg in -all-static) if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then func_warning "complete static linking is impossible in this configuration" fi if test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; -static) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=built ;; -static-libtool-libs) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; esac build_libtool_libs=no build_old_libs=yes break ;; esac done # See if our shared archives depend on static archives. test -n "$old_archive_from_new_cmds" && build_old_libs=yes # Go through the arguments, transforming them on the way. while test "$#" -gt 0; do arg="$1" shift func_quote_for_eval "$arg" qarg=$func_quote_for_eval_unquoted_result func_append libtool_args " $func_quote_for_eval_result" # If the previous option needs an argument, assign it. if test -n "$prev"; then case $prev in output) func_append compile_command " @OUTPUT@" func_append finalize_command " @OUTPUT@" ;; esac case $prev in dlfiles|dlprefiles) if test "$preload" = no; then # Add the symbol object into the linking commands. func_append compile_command " @SYMFILE@" func_append finalize_command " @SYMFILE@" preload=yes fi case $arg in *.la | *.lo) ;; # We handle these cases below. force) if test "$dlself" = no; then dlself=needless export_dynamic=yes fi prev= continue ;; self) if test "$prev" = dlprefiles; then dlself=yes elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then dlself=yes else dlself=needless export_dynamic=yes fi prev= continue ;; *) if test "$prev" = dlfiles; then dlfiles="$dlfiles $arg" else dlprefiles="$dlprefiles $arg" fi prev= continue ;; esac ;; expsyms) export_symbols="$arg" test -f "$arg" \ || func_fatal_error "symbol file \`$arg' does not exist" prev= continue ;; expsyms_regex) export_symbols_regex="$arg" prev= continue ;; framework) case $host in *-*-darwin*) case "$deplibs " in *" $qarg.ltframework "*) ;; *) deplibs="$deplibs $qarg.ltframework" # this is fixed later ;; esac ;; esac prev= continue ;; inst_prefix) inst_prefix_dir="$arg" prev= continue ;; objectlist) if test -f "$arg"; then save_arg=$arg moreargs= for fil in `cat "$save_arg"` do # moreargs="$moreargs $fil" arg=$fil # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi done else func_fatal_error "link input file \`$arg' does not exist" fi arg=$save_arg prev= continue ;; precious_regex) precious_files_regex="$arg" prev= continue ;; release) release="-$arg" prev= continue ;; rpath | xrpath) # We need an absolute path. case $arg in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac if test "$prev" = rpath; then case "$rpath " in *" $arg "*) ;; *) rpath="$rpath $arg" ;; esac else case "$xrpath " in *" $arg "*) ;; *) xrpath="$xrpath $arg" ;; esac fi prev= continue ;; shrext) shrext_cmds="$arg" prev= continue ;; weak) weak_libs="$weak_libs $arg" prev= continue ;; xcclinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xcompiler) compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xlinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $wl$qarg" prev= func_append compile_command " $wl$qarg" func_append finalize_command " $wl$qarg" continue ;; *) eval "$prev=\"\$arg\"" prev= continue ;; esac fi # test -n "$prev" prevarg="$arg" case $arg in -all-static) if test -n "$link_static_flag"; then # See comment for -static flag below, for more details. func_append compile_command " $link_static_flag" func_append finalize_command " $link_static_flag" fi continue ;; -allow-undefined) # FIXME: remove this flag sometime in the future. func_fatal_error "\`-allow-undefined' must not be used because it is the default" ;; -avoid-version) avoid_version=yes continue ;; -dlopen) prev=dlfiles continue ;; -dlpreopen) prev=dlprefiles continue ;; -export-dynamic) export_dynamic=yes continue ;; -export-symbols | -export-symbols-regex) if test -n "$export_symbols" || test -n "$export_symbols_regex"; then func_fatal_error "more than one -exported-symbols argument is not allowed" fi if test "X$arg" = "X-export-symbols"; then prev=expsyms else prev=expsyms_regex fi continue ;; -framework) prev=framework continue ;; -inst-prefix-dir) prev=inst_prefix continue ;; # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:* # so, if we see these flags be careful not to treat them like -L -L[A-Z][A-Z]*:*) case $with_gcc/$host in no/*-*-irix* | /*-*-irix*) func_append compile_command " $arg" func_append finalize_command " $arg" ;; esac continue ;; -L*) func_stripname '-L' '' "$arg" dir=$func_stripname_result if test -z "$dir"; then if test "$#" -gt 0; then func_fatal_error "require no space between \`-L' and \`$1'" else func_fatal_error "need path for \`-L' option" fi fi # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) absdir=`cd "$dir" && pwd` test -z "$absdir" && \ func_fatal_error "cannot determine absolute directory name of \`$dir'" dir="$absdir" ;; esac case "$deplibs " in *" -L$dir "*) ;; *) deplibs="$deplibs -L$dir" lib_search_path="$lib_search_path $dir" ;; esac case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$dir:"*) ;; ::) dllsearchpath=$dir;; *) dllsearchpath="$dllsearchpath:$dir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) dllsearchpath="$dllsearchpath:$testbindir";; esac ;; esac continue ;; -l*) if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*) # These systems don't actually have a C or math library (as such) continue ;; *-*-os2*) # These systems don't actually have a C library (as such) test "X$arg" = "X-lc" && continue ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. test "X$arg" = "X-lc" && continue ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C and math libraries are in the System framework deplibs="$deplibs System.ltframework" continue ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype test "X$arg" = "X-lc" && continue ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work test "X$arg" = "X-lc" && continue ;; esac elif test "X$arg" = "X-lc_r"; then case $host in *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc_r directly, use -pthread flag. continue ;; esac fi deplibs="$deplibs $arg" continue ;; -module) module=yes continue ;; # Tru64 UNIX uses -model [arg] to determine the layout of C++ # classes, name mangling, and exception handling. # Darwin uses the -arch flag to determine output architecture. -model|-arch|-isysroot) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" prev=xcompiler continue ;; -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" case "$new_inherited_linker_flags " in *" $arg "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;; esac continue ;; -multi_module) single_module="${wl}-multi_module" continue ;; -no-fast-install) fast_install=no continue ;; -no-install) case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*) # The PATH hackery in wrapper scripts is required on Windows # and Darwin in order for the loader to find any dlls it needs. func_warning "\`-no-install' is ignored for $host" func_warning "assuming \`-no-fast-install' instead" fast_install=no ;; *) no_install=yes ;; esac continue ;; -no-undefined) allow_undefined=no continue ;; -objectlist) prev=objectlist continue ;; -o) prev=output ;; -precious-files-regex) prev=precious_regex continue ;; -release) prev=release continue ;; -rpath) prev=rpath continue ;; -R) prev=xrpath continue ;; -R*) func_stripname '-R' '' "$arg" dir=$func_stripname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac continue ;; -shared) # The effects of -shared are defined in a previous loop. continue ;; -shrext) prev=shrext continue ;; -static | -static-libtool-libs) # The effects of -static are defined in a previous loop. # We used to do the same as -all-static on platforms that # didn't have a PIC flag, but the assumption that the effects # would be equivalent was wrong. It would break on at least # Digital Unix and AIX. continue ;; -thread-safe) thread_safe=yes continue ;; -version-info) prev=vinfo continue ;; -version-number) prev=vinfo vinfo_number=yes continue ;; -weak) prev=weak continue ;; -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Wl,*) func_stripname '-Wl,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $wl$func_quote_for_eval_result" linker_flags="$linker_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Xcompiler) prev=xcompiler continue ;; -Xlinker) prev=xlinker continue ;; -XCClinker) prev=xcclinker continue ;; # -msg_* for osf cc -msg_*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; # -64, -mips[0-9] enable 64-bit mode on the SGI compiler # -r[0-9][0-9]* specifies the processor on the SGI compiler # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler # +DA*, +DD* enable 64-bit mode on the HP compiler # -q* pass through compiler args for the IBM compiler # -m*, -t[45]*, -txscale* pass through architecture-specific # compiler args for GCC # -F/path gives path to uninstalled frameworks, gcc on darwin # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC # @file GCC response files -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" func_append compile_command " $arg" func_append finalize_command " $arg" compiler_flags="$compiler_flags $arg" continue ;; # Some other compiler flag. -* | +*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; *.$objext) # A standard object. objs="$objs $arg" ;; *.lo) # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi ;; *.$libext) # An archive. deplibs="$deplibs $arg" old_deplibs="$old_deplibs $arg" continue ;; *.la) # A libtool-controlled library. if test "$prev" = dlfiles; then # This library was specified with -dlopen. dlfiles="$dlfiles $arg" prev= elif test "$prev" = dlprefiles; then # The library was specified with -dlpreopen. dlprefiles="$dlprefiles $arg" prev= else deplibs="$deplibs $arg" fi continue ;; # Some other compiler argument. *) # Unknown arguments in both finalize_command and compile_command need # to be aesthetically quoted because they are evaled later. func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; esac # arg # Now actually substitute the argument into the commands. if test -n "$arg"; then func_append compile_command " $arg" func_append finalize_command " $arg" fi done # argument parsing loop test -n "$prev" && \ func_fatal_help "the \`$prevarg' option requires an argument" if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then eval arg=\"$export_dynamic_flag_spec\" func_append compile_command " $arg" func_append finalize_command " $arg" fi oldlibs= # calculate the name of the file, without its directory func_basename "$output" outputname="$func_basename_result" libobjs_save="$libobjs" if test -n "$shlibpath_var"; then # get the directories listed in $shlibpath_var eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\` else shlib_search_path= fi eval sys_lib_search_path=\"$sys_lib_search_path_spec\" eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\" func_dirname "$output" "/" "" output_objdir="$func_dirname_result$objdir" # Create the object directory. func_mkdir_p "$output_objdir" # Determine the type of output case $output in "") func_fatal_help "you must specify an output file" ;; *.$libext) linkmode=oldlib ;; *.lo | *.$objext) linkmode=obj ;; *.la) linkmode=lib ;; *) linkmode=prog ;; # Anything else should be a program. esac specialdeplibs= libs= # Find all interdependent deplibs by searching for libraries # that are linked more than once (e.g. -la -lb -la) for deplib in $deplibs; do if $opt_duplicate_deps ; then case "$libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi libs="$libs $deplib" done if test "$linkmode" = lib; then libs="$predeps $libs $compiler_lib_search_path $postdeps" # Compute libraries that are listed more than once in $predeps # $postdeps and mark them as special (i.e., whose duplicates are # not to be eliminated). pre_post_deps= if $opt_duplicate_compiler_generated_deps; then for pre_post_dep in $predeps $postdeps; do case "$pre_post_deps " in *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;; esac pre_post_deps="$pre_post_deps $pre_post_dep" done fi pre_post_deps= fi deplibs= newdependency_libs= newlib_search_path= need_relink=no # whether we're linking any uninstalled libtool libraries notinst_deplibs= # not-installed libtool libraries notinst_path= # paths that contain not-installed libtool libraries case $linkmode in lib) passes="conv dlpreopen link" for file in $dlfiles $dlprefiles; do case $file in *.la) ;; *) func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file" ;; esac done ;; prog) compile_deplibs= finalize_deplibs= alldeplibs=no newdlfiles= newdlprefiles= passes="conv scan dlopen dlpreopen link" ;; *) passes="conv" ;; esac for pass in $passes; do # The preopen pass in lib mode reverses $deplibs; put it back here # so that -L comes before libs that need it for instance... if test "$linkmode,$pass" = "lib,link"; then ## FIXME: Find the place where the list is rebuilt in the wrong ## order, and fix it there properly tmp_deplibs= for deplib in $deplibs; do tmp_deplibs="$deplib $tmp_deplibs" done deplibs="$tmp_deplibs" fi if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan"; then libs="$deplibs" deplibs= fi if test "$linkmode" = prog; then case $pass in dlopen) libs="$dlfiles" ;; dlpreopen) libs="$dlprefiles" ;; link) libs="$deplibs %DEPLIBS%" test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs" ;; esac fi if test "$linkmode,$pass" = "lib,dlpreopen"; then # Collect and forward deplibs of preopened libtool libs for lib in $dlprefiles; do # Ignore non-libtool-libs dependency_libs= case $lib in *.la) func_source "$lib" ;; esac # Collect preopened libtool deplibs, except any this library # has declared as weak libs for deplib in $dependency_libs; do deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"` case " $weak_libs " in *" $deplib_base "*) ;; *) deplibs="$deplibs $deplib" ;; esac done done libs="$dlprefiles" fi if test "$pass" = dlopen; then # Collect dlpreopened libraries save_deplibs="$deplibs" deplibs= fi for deplib in $libs; do lib= found=no case $deplib in -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else compiler_flags="$compiler_flags $deplib" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -l*) if test "$linkmode" != lib && test "$linkmode" != prog; then func_warning "\`-l' is ignored for archives/objects" continue fi func_stripname '-l' '' "$deplib" name=$func_stripname_result if test "$linkmode" = lib; then searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path" else searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path" fi for searchdir in $searchdirs; do for search_ext in .la $std_shrext .so .a; do # Search the libtool library lib="$searchdir/lib${name}${search_ext}" if test -f "$lib"; then if test "$search_ext" = ".la"; then found=yes else found=no fi break 2 fi done done if test "$found" != yes; then # deplib doesn't seem to be a libtool library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue else # deplib is a libtool library # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib, # We need to do some special things here, and not later. if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $deplib "*) if func_lalib_p "$lib"; then library_names= old_library= func_source "$lib" for l in $old_library $library_names; do ll="$l" done if test "X$ll" = "X$old_library" ; then # only static version available found=no func_dirname "$lib" "" "." ladir="$func_dirname_result" lib=$ladir/$old_library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue fi fi ;; *) ;; esac fi fi ;; # -l *.ltframework) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -L*) case $linkmode in lib) deplibs="$deplib $deplibs" test "$pass" = conv && continue newdependency_libs="$deplib $newdependency_libs" func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; prog) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi if test "$pass" = scan; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; *) func_warning "\`-L' is ignored for archives/objects" ;; esac # linkmode continue ;; # -L -R*) if test "$pass" = link; then func_stripname '-R' '' "$deplib" dir=$func_stripname_result # Make sure the xrpath contains only unique directories. case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac fi deplibs="$deplib $deplibs" continue ;; *.la) lib="$deplib" ;; *.$libext) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi case $linkmode in lib) # Linking convenience modules into shared libraries is allowed, # but linking other static libraries is non-portable. case " $dlpreconveniencelibs " in *" $deplib "*) ;; *) valid_a_lib=no case $deplibs_check_method in match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \ | $EGREP "$match_pattern_regex" > /dev/null; then valid_a_lib=yes fi ;; pass_all) valid_a_lib=yes ;; esac if test "$valid_a_lib" != yes; then $ECHO $ECHO "*** Warning: Trying to link with static lib archive $deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because the file extensions .$libext of this argument makes me believe" $ECHO "*** that it is just a static archive that I should not use here." else $ECHO $ECHO "*** Warning: Linking the shared library $output against the" $ECHO "*** static library $deplib is not portable!" deplibs="$deplib $deplibs" fi ;; esac continue ;; prog) if test "$pass" != link; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi continue ;; esac # linkmode ;; # *.$libext *.lo | *.$objext) if test "$pass" = conv; then deplibs="$deplib $deplibs" elif test "$linkmode" = prog; then if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlopen support or we're linking statically, # we need to preload. newdlprefiles="$newdlprefiles $deplib" compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else newdlfiles="$newdlfiles $deplib" fi fi continue ;; %DEPLIBS%) alldeplibs=yes continue ;; esac # case $deplib if test "$found" = yes || test -f "$lib"; then : else func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'" fi # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$lib" \ || func_fatal_error "\`$lib' is not a valid libtool archive" func_dirname "$lib" "" "." ladir="$func_dirname_result" dlname= dlopen= dlpreopen= libdir= library_names= old_library= inherited_linker_flags= # If the library was installed with an old release of libtool, # it will not redefine variables installed, or shouldnotlink installed=yes shouldnotlink=no avoidtemprpath= # Read the .la file func_source "$lib" # Convert "-framework foo" to "foo.ltframework" if test -n "$inherited_linker_flags"; then tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'` for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do case " $new_inherited_linker_flags " in *" $tmp_inherited_linker_flag "*) ;; *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";; esac done fi dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan" || { test "$linkmode" != prog && test "$linkmode" != lib; }; then test -n "$dlopen" && dlfiles="$dlfiles $dlopen" test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen" fi if test "$pass" = conv; then # Only check for convenience libraries deplibs="$lib $deplibs" if test -z "$libdir"; then if test -z "$old_library"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # It is a libtool convenience library, so add in its objects. convenience="$convenience $ladir/$objdir/$old_library" old_convenience="$old_convenience $ladir/$objdir/$old_library" tmp_libs= for deplib in $dependency_libs; do deplibs="$deplib $deplibs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done elif test "$linkmode" != prog && test "$linkmode" != lib; then func_fatal_error "\`$lib' is not a convenience library" fi continue fi # $pass = conv # Get the name of the library we link against. linklib= for l in $old_library $library_names; do linklib="$l" done if test -z "$linklib"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # This library was specified with -dlopen. if test "$pass" = dlopen; then if test -z "$libdir"; then func_fatal_error "cannot -dlopen a convenience library: \`$lib'" fi if test -z "$dlname" || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlname, no dlopen support or we're linking # statically, we need to preload. We also need to preload any # dependent libraries so libltdl's deplib preloader doesn't # bomb out in the load deplibs phase. dlprefiles="$dlprefiles $lib $dependency_libs" else newdlfiles="$newdlfiles $lib" fi continue fi # $pass = dlopen # We need an absolute path. case $ladir in [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;; *) abs_ladir=`cd "$ladir" && pwd` if test -z "$abs_ladir"; then func_warning "cannot determine absolute directory name of \`$ladir'" func_warning "passing it literally to the linker, although it might fail" abs_ladir="$ladir" fi ;; esac func_basename "$lib" laname="$func_basename_result" # Find the relevant object directory and library name. if test "X$installed" = Xyes; then if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then func_warning "library \`$lib' was moved." dir="$ladir" absdir="$abs_ladir" libdir="$abs_ladir" else dir="$libdir" absdir="$libdir" fi test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes else if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then dir="$ladir" absdir="$abs_ladir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" else dir="$ladir/$objdir" absdir="$abs_ladir/$objdir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" fi fi # $installed = yes func_stripname 'lib' '.la' "$laname" name=$func_stripname_result # This library was specified with -dlpreopen. if test "$pass" = dlpreopen; then if test -z "$libdir" && test "$linkmode" = prog; then func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" fi # Prefer using a static library (so that no silly _DYNAMIC symbols # are required to link). if test -n "$old_library"; then newdlprefiles="$newdlprefiles $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library" # Otherwise, use the dlname, so that lt_dlopen finds it. elif test -n "$dlname"; then newdlprefiles="$newdlprefiles $dir/$dlname" else newdlprefiles="$newdlprefiles $dir/$linklib" fi fi # $pass = dlpreopen if test -z "$libdir"; then # Link the convenience library if test "$linkmode" = lib; then deplibs="$dir/$old_library $deplibs" elif test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$dir/$old_library $compile_deplibs" finalize_deplibs="$dir/$old_library $finalize_deplibs" else deplibs="$lib $deplibs" # used for prog,scan pass fi continue fi if test "$linkmode" = prog && test "$pass" != link; then newlib_search_path="$newlib_search_path $ladir" deplibs="$lib $deplibs" linkalldeplibs=no if test "$link_all_deplibs" != no || test -z "$library_names" || test "$build_libtool_libs" = no; then linkalldeplibs=yes fi tmp_libs= for deplib in $dependency_libs; do case $deplib in -L*) func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; esac # Need to link against all dependency_libs? if test "$linkalldeplibs" = yes; then deplibs="$deplib $deplibs" else # Need to hardcode shared library paths # or/and link against static libraries newdependency_libs="$deplib $newdependency_libs" fi if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done # for deplib continue fi # $linkmode = prog... if test "$linkmode,$pass" = "prog,link"; then if test -n "$library_names" && { { test "$prefer_static_libs" = no || test "$prefer_static_libs,$installed" = "built,yes"; } || test -z "$old_library"; }; then # We need to hardcode the library path if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then # Make sure the rpath contains only unique directories. case "$temp_rpath:" in *"$absdir:"*) ;; *) temp_rpath="$temp_rpath$absdir:" ;; esac fi # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi # $linkmode,$pass = prog,link... if test "$alldeplibs" = yes && { test "$deplibs_check_method" = pass_all || { test "$build_libtool_libs" = yes && test -n "$library_names"; }; }; then # We only need to search for static libraries continue fi fi link_static=no # Whether the deplib will be linked statically use_static_libs=$prefer_static_libs if test "$use_static_libs" = built && test "$installed" = yes; then use_static_libs=no fi if test -n "$library_names" && { test "$use_static_libs" = no || test -z "$old_library"; }; then case $host in *cygwin* | *mingw* | *cegcc*) # No point in relinking DLLs because paths are not encoded notinst_deplibs="$notinst_deplibs $lib" need_relink=no ;; *) if test "$installed" = no; then notinst_deplibs="$notinst_deplibs $lib" need_relink=yes fi ;; esac # This is a shared library # Warn about portability, can't link against -module's on some # systems (darwin). Don't bleat about dlopened modules though! dlopenmodule="" for dlpremoduletest in $dlprefiles; do if test "X$dlpremoduletest" = "X$lib"; then dlopenmodule="$dlpremoduletest" break fi done if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then $ECHO if test "$linkmode" = prog; then $ECHO "*** Warning: Linking the executable $output against the loadable module" else $ECHO "*** Warning: Linking the shared library $output against the loadable module" fi $ECHO "*** $linklib is not portable!" fi if test "$linkmode" = lib && test "$hardcode_into_libs" = yes; then # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi if test -n "$old_archive_from_expsyms_cmds"; then # figure out the soname set dummy $library_names shift realname="$1" shift libname=`eval "\\$ECHO \"$libname_spec\""` # use dlname if we got it. it's perfectly good, no? if test -n "$dlname"; then soname="$dlname" elif test -n "$soname_spec"; then # bleh windows case $host in *cygwin* | mingw* | *cegcc*) func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; esac eval soname=\"$soname_spec\" else soname="$realname" fi # Make a new name for the extract_expsyms_cmds to use soroot="$soname" func_basename "$soroot" soname="$func_basename_result" func_stripname 'lib' '.dll' "$soname" newlib=libimp-$func_stripname_result.a # If the library has no export list, then create one now if test -f "$output_objdir/$soname-def"; then : else func_verbose "extracting exported symbol list from \`$soname'" func_execute_cmds "$extract_expsyms_cmds" 'exit $?' fi # Create $newlib if test -f "$output_objdir/$newlib"; then :; else func_verbose "generating import library for \`$soname'" func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?' fi # make sure the library variables are pointing to the new library dir=$output_objdir linklib=$newlib fi # test -n "$old_archive_from_expsyms_cmds" if test "$linkmode" = prog || test "$mode" != relink; then add_shlibpath= add_dir= add= lib_linked=yes case $hardcode_action in immediate | unsupported) if test "$hardcode_direct" = no; then add="$dir/$linklib" case $host in *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;; *-*-sysv4*uw2*) add_dir="-L$dir" ;; *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \ *-*-unixware7*) add_dir="-L$dir" ;; *-*-darwin* ) # if the lib is a (non-dlopened) module then we can not # link against it, someone is ignoring the earlier warnings if /usr/bin/file -L $add 2> /dev/null | $GREP ": [^:]* bundle" >/dev/null ; then if test "X$dlopenmodule" != "X$lib"; then $ECHO "*** Warning: lib $linklib is a module, not a shared library" if test -z "$old_library" ; then $ECHO $ECHO "*** And there doesn't seem to be a static archive available" $ECHO "*** The link will probably fail, sorry" else add="$dir/$old_library" fi elif test -n "$old_library"; then add="$dir/$old_library" fi fi esac elif test "$hardcode_minus_L" = no; then case $host in *-*-sunos*) add_shlibpath="$dir" ;; esac add_dir="-L$dir" add="-l$name" elif test "$hardcode_shlibpath_var" = no; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; relink) if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$dir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$dir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; *) lib_linked=no ;; esac if test "$lib_linked" != yes; then func_fatal_configuration "unsupported hardcode properties" fi if test -n "$add_shlibpath"; then case :$compile_shlibpath: in *":$add_shlibpath:"*) ;; *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;; esac fi if test "$linkmode" = prog; then test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs" test -n "$add" && compile_deplibs="$add $compile_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" if test "$hardcode_direct" != yes && test "$hardcode_minus_L" != yes && test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac fi fi fi if test "$linkmode" = prog || test "$mode" = relink; then add_shlibpath= add_dir= add= # Finalize command for both is simple: just hardcode it. if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$libdir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$libdir" add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac add="-l$name" elif test "$hardcode_automatic" = yes; then if test -n "$inst_prefix_dir" && test -f "$inst_prefix_dir$libdir/$linklib" ; then add="$inst_prefix_dir$libdir/$linklib" else add="$libdir/$linklib" fi else # We cannot seem to hardcode it, guess we'll fake it. add_dir="-L$libdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" fi if test "$linkmode" = prog; then test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs" test -n "$add" && finalize_deplibs="$add $finalize_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" fi fi elif test "$linkmode" = prog; then # Here we assume that one of hardcode_direct or hardcode_minus_L # is not unsupported. This is valid on all known static and # shared platforms. if test "$hardcode_direct" != unsupported; then test -n "$old_library" && linklib="$old_library" compile_deplibs="$dir/$linklib $compile_deplibs" finalize_deplibs="$dir/$linklib $finalize_deplibs" else compile_deplibs="-l$name -L$dir $compile_deplibs" finalize_deplibs="-l$name -L$dir $finalize_deplibs" fi elif test "$build_libtool_libs" = yes; then # Not a shared library if test "$deplibs_check_method" != pass_all; then # We're trying link a shared library against a static one # but the system doesn't support it. # Just print a warning and add the library to dependency_libs so # that the program can be linked against the static library. $ECHO $ECHO "*** Warning: This system can not link to static lib archive $lib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have." if test "$module" = yes; then $ECHO "*** But as you try to build a module library, libtool will still create " $ECHO "*** a static module, that should work as long as the dlopening application" $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi else deplibs="$dir/$old_library $deplibs" link_static=yes fi fi # link shared/static library? if test "$linkmode" = lib; then if test -n "$dependency_libs" && { test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes || test "$link_static" = yes; }; then # Extract -R from dependency_libs temp_deplibs= for libdir in $dependency_libs; do case $libdir in -R*) func_stripname '-R' '' "$libdir" temp_xrpath=$func_stripname_result case " $xrpath " in *" $temp_xrpath "*) ;; *) xrpath="$xrpath $temp_xrpath";; esac;; *) temp_deplibs="$temp_deplibs $libdir";; esac done dependency_libs="$temp_deplibs" fi newlib_search_path="$newlib_search_path $absdir" # Link against this library test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" # ... and its dependency_libs tmp_libs= for deplib in $dependency_libs; do newdependency_libs="$deplib $newdependency_libs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done if test "$link_all_deplibs" != no; then # Add the search paths of all dependency libraries for deplib in $dependency_libs; do path= case $deplib in -L*) path="$deplib" ;; *.la) func_dirname "$deplib" "" "." dir="$func_dirname_result" # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;; *) absdir=`cd "$dir" && pwd` if test -z "$absdir"; then func_warning "cannot determine absolute directory name of \`$dir'" absdir="$dir" fi ;; esac if $GREP "^installed=no" $deplib > /dev/null; then case $host in *-*-darwin*) depdepl= eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib` if test -n "$deplibrary_names" ; then for tmp in $deplibrary_names ; do depdepl=$tmp done if test -f "$absdir/$objdir/$depdepl" ; then depdepl="$absdir/$objdir/$depdepl" darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` if test -z "$darwin_install_name"; then darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` fi compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}" path= fi fi ;; *) path="-L$absdir/$objdir" ;; esac else eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" test "$absdir" != "$libdir" && \ func_warning "\`$deplib' seems to be moved" path="-L$absdir" fi ;; esac case " $deplibs " in *" $path "*) ;; *) deplibs="$path $deplibs" ;; esac done fi # link_all_deplibs != no fi # linkmode = lib done # for deplib in $libs if test "$pass" = link; then if test "$linkmode" = "prog"; then compile_deplibs="$new_inherited_linker_flags $compile_deplibs" finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" else compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` fi fi dependency_libs="$newdependency_libs" if test "$pass" = dlpreopen; then # Link the dlpreopened libraries before other libraries for deplib in $save_deplibs; do deplibs="$deplib $deplibs" done fi if test "$pass" != dlopen; then if test "$pass" != conv; then # Make sure lib_search_path contains only unique directories. lib_search_path= for dir in $newlib_search_path; do case "$lib_search_path " in *" $dir "*) ;; *) lib_search_path="$lib_search_path $dir" ;; esac done newlib_search_path= fi if test "$linkmode,$pass" != "prog,link"; then vars="deplibs" else vars="compile_deplibs finalize_deplibs" fi for var in $vars dependency_libs; do # Add libraries to $var in reverse order eval tmp_libs=\"\$$var\" new_libs= for deplib in $tmp_libs; do # FIXME: Pedantically, this is the right thing to do, so # that some nasty dependency loop isn't accidentally # broken: #new_libs="$deplib $new_libs" # Pragmatically, this seems to cause very few problems in # practice: case $deplib in -L*) new_libs="$deplib $new_libs" ;; -R*) ;; *) # And here is the reason: when a library appears more # than once as an explicit dependence of a library, or # is implicitly linked in more than once by the # compiler, it is considered special, and multiple # occurrences thereof are not removed. Compare this # with having the same library being listed as a # dependency of multiple other libraries: in this case, # we know (pedantically, we assume) the library does not # need to be listed more than once, so we keep only the # last copy. This is not always right, but it is rare # enough that we require users that really mean to play # such unportable linking tricks to link the library # using -Wl,-lname, so that libtool does not consider it # for duplicate removal. case " $specialdeplibs " in *" $deplib "*) new_libs="$deplib $new_libs" ;; *) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$deplib $new_libs" ;; esac ;; esac ;; esac done tmp_libs= for deplib in $new_libs; do case $deplib in -L*) case " $tmp_libs " in *" $deplib "*) ;; *) tmp_libs="$tmp_libs $deplib" ;; esac ;; *) tmp_libs="$tmp_libs $deplib" ;; esac done eval $var=\"$tmp_libs\" done # for var fi # Last step: remove runtime libs from dependency_libs # (they stay in deplibs) tmp_libs= for i in $dependency_libs ; do case " $predeps $postdeps $compiler_lib_search_path " in *" $i "*) i="" ;; esac if test -n "$i" ; then tmp_libs="$tmp_libs $i" fi done dependency_libs=$tmp_libs done # for pass if test "$linkmode" = prog; then dlfiles="$newdlfiles" fi if test "$linkmode" = prog || test "$linkmode" = lib; then dlprefiles="$newdlprefiles" fi case $linkmode in oldlib) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for archives" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for archives" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for archives" test -n "$xrpath" && \ func_warning "\`-R' is ignored for archives" test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for archives" test -n "$release" && \ func_warning "\`-release' is ignored for archives" test -n "$export_symbols$export_symbols_regex" && \ func_warning "\`-export-symbols' is ignored for archives" # Now set the variables for building old libraries. build_libtool_libs=no oldlibs="$output" objs="$objs$old_deplibs" ;; lib) # Make sure we only generate libraries of the form `libNAME.la'. case $outputname in lib*) func_stripname 'lib' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" ;; *) test "$module" = no && \ func_fatal_help "libtool library \`$output' must begin with \`lib'" if test "$need_lib_prefix" != no; then # Add the "lib" prefix for modules if required func_stripname '' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" else func_stripname '' '.la' "$outputname" libname=$func_stripname_result fi ;; esac if test -n "$objs"; then if test "$deplibs_check_method" != pass_all; then func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" else $ECHO $ECHO "*** Warning: Linking the shared library $output against the non-libtool" $ECHO "*** objects $objs is not portable!" libobjs="$libobjs $objs" fi fi test "$dlself" != no && \ func_warning "\`-dlopen self' is ignored for libtool libraries" set dummy $rpath shift test "$#" -gt 1 && \ func_warning "ignoring multiple \`-rpath's for a libtool library" install_libdir="$1" oldlibs= if test -z "$rpath"; then if test "$build_libtool_libs" = yes; then # Building a libtool convenience library. # Some compilers have problems with a `.al' extension so # convenience libraries should have the same extension an # archive normally would. oldlibs="$output_objdir/$libname.$libext $oldlibs" build_libtool_libs=convenience build_old_libs=yes fi test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for convenience libraries" test -n "$release" && \ func_warning "\`-release' is ignored for convenience libraries" else # Parse the version information argument. save_ifs="$IFS"; IFS=':' set dummy $vinfo 0 0 0 shift IFS="$save_ifs" test -n "$7" && \ func_fatal_help "too many parameters to \`-version-info'" # convert absolute version numbers to libtool ages # this retains compatibility with .la files and attempts # to make the code below a bit more comprehensible case $vinfo_number in yes) number_major="$1" number_minor="$2" number_revision="$3" # # There are really only two kinds -- those that # use the current revision as the major version # and those that subtract age and use age as # a minor version. But, then there is irix # which has an extra 1 added just for fun # case $version_type in darwin|linux|osf|windows|none) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_revision" ;; freebsd-aout|freebsd-elf|sunos) current="$number_major" revision="$number_minor" age="0" ;; irix|nonstopux) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_minor" lt_irix_increment=no ;; *) func_fatal_configuration "$modename: unknown library version type \`$version_type'" ;; esac ;; no) current="$1" revision="$2" age="$3" ;; esac # Check that each of the things are valid numbers. case $current in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "CURRENT \`$current' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $revision in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "REVISION \`$revision' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $age in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "AGE \`$age' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac if test "$age" -gt "$current"; then func_error "AGE \`$age' is greater than the current interface number \`$current'" func_fatal_error "\`$vinfo' is not valid version information" fi # Calculate the version variables. major= versuffix= verstring= case $version_type in none) ;; darwin) # Like Linux, but with the current version available in # verstring for coding it into the library header func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" # Darwin ld doesn't like 0 for these options... func_arith $current + 1 minor_current=$func_arith_result xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision" verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" ;; freebsd-aout) major=".$current" versuffix=".$current.$revision"; ;; freebsd-elf) major=".$current" versuffix=".$current" ;; irix | nonstopux) if test "X$lt_irix_increment" = "Xno"; then func_arith $current - $age else func_arith $current - $age + 1 fi major=$func_arith_result case $version_type in nonstopux) verstring_prefix=nonstopux ;; *) verstring_prefix=sgi ;; esac verstring="$verstring_prefix$major.$revision" # Add in all the interfaces that we are compatible with. loop=$revision while test "$loop" -ne 0; do func_arith $revision - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring_prefix$major.$iface:$verstring" done # Before this point, $major must not contain `.'. major=.$major versuffix="$major.$revision" ;; linux) func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" ;; osf) func_arith $current - $age major=.$func_arith_result versuffix=".$current.$age.$revision" verstring="$current.$age.$revision" # Add in all the interfaces that we are compatible with. loop=$age while test "$loop" -ne 0; do func_arith $current - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring:${iface}.0" done # Make executables depend on our current version. verstring="$verstring:${current}.0" ;; qnx) major=".$current" versuffix=".$current" ;; sunos) major=".$current" versuffix=".$current.$revision" ;; windows) # Use '-' rather than '.', since we only want one # extension on DOS 8.3 filesystems. func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; *) func_fatal_configuration "unknown library version type \`$version_type'" ;; esac # Clear the version info if we defaulted, and they specified a release. if test -z "$vinfo" && test -n "$release"; then major= case $version_type in darwin) # we can't check for "0.0" in archive_cmds due to quoting # problems, so we reset it completely verstring= ;; *) verstring="0.0" ;; esac if test "$need_version" = no; then versuffix= else versuffix=".0.0" fi fi # Remove version info from name if versioning should be avoided if test "$avoid_version" = yes && test "$need_version" = no; then major= versuffix= verstring="" fi # Check to see if the archive will have undefined symbols. if test "$allow_undefined" = yes; then if test "$allow_undefined_flag" = unsupported; then func_warning "undefined symbols not allowed in $host shared libraries" build_libtool_libs=no build_old_libs=yes fi else # Don't allow undefined symbols. allow_undefined_flag="$no_undefined_flag" fi fi func_generate_dlsyms "$libname" "$libname" "yes" libobjs="$libobjs $symfileobj" test "X$libobjs" = "X " && libobjs= if test "$mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. removelist= tempremovelist=`$ECHO "$output_objdir/*"` for p in $tempremovelist; do case $p in *.$objext | *.gcno) ;; $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) if test "X$precious_files_regex" != "X"; then if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 then continue fi fi removelist="$removelist $p" ;; *) ;; esac done test -n "$removelist" && \ func_show_eval "${RM}r \$removelist" fi # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then oldlibs="$oldlibs $output_objdir/$libname.$libext" # Transform .lo files to .o files. oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP` fi # Eliminate all temporary directories. #for path in $notinst_path; do # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"` # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"` # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"` #done if test -n "$xrpath"; then # If the user specified any rpath flags, then add them. temp_xrpath= for libdir in $xrpath; do temp_xrpath="$temp_xrpath -R$libdir" case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then dependency_libs="$temp_xrpath $dependency_libs" fi fi # Make sure dlfiles contains only unique files that won't be dlpreopened old_dlfiles="$dlfiles" dlfiles= for lib in $old_dlfiles; do case " $dlprefiles $dlfiles " in *" $lib "*) ;; *) dlfiles="$dlfiles $lib" ;; esac done # Make sure dlprefiles contains only unique files old_dlprefiles="$dlprefiles" dlprefiles= for lib in $old_dlprefiles; do case "$dlprefiles " in *" $lib "*) ;; *) dlprefiles="$dlprefiles $lib" ;; esac done if test "$build_libtool_libs" = yes; then if test -n "$rpath"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework deplibs="$deplibs System.ltframework" ;; *-*-netbsd*) # Don't link with libc until the a.out ld.so is fixed. ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work ;; *) # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then deplibs="$deplibs -lc" fi ;; esac fi # Transform deplibs into only deplibs that can be linked in shared. name_save=$name libname_save=$libname release_save=$release versuffix_save=$versuffix major_save=$major # I'm not sure if I'm treating the release correctly. I think # release should show up in the -l (ie -lgmp5) so we don't want to # add it in twice. Is that correct? release="" versuffix="" major="" newdeplibs= droppeddeps=no case $deplibs_check_method in pass_all) # Don't check for shared/static. Everything works. # This might be a little naive. We might want to check # whether the library exists or not. But this is on # osf3 & osf4 and I'm not really sure... Just # implementing what was already the behavior. newdeplibs=$deplibs ;; test_compile) # This code stresses the "libraries are programs" paradigm to its # limits. Maybe even breaks it. We compile a program, linking it # against the deplibs as a proxy for the library. Then we can check # whether they linked in statically or dynamically with ldd. $opt_dry_run || $RM conftest.c cat > conftest.c </dev/null` for potent_lib in $potential_libs; do # Follow soft links. if ls -lLd "$potent_lib" 2>/dev/null | $GREP " -> " >/dev/null; then continue fi # The statement above tries to avoid entering an # endless loop below, in case of cyclic links. # We might still enter an endless loop, since a link # loop can be closed while we follow links, # but so what? potlib="$potent_lib" while test -h "$potlib" 2>/dev/null; do potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'` case $potliblink in [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";; esac done if eval $file_magic_cmd \"\$potlib\" 2>/dev/null | $SED -e 10q | $EGREP "$file_magic_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for file magic test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a file magic. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` for a_deplib in $deplibs; do case $a_deplib in -l*) func_stripname -l '' "$a_deplib" name=$func_stripname_result if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $a_deplib "*) newdeplibs="$newdeplibs $a_deplib" a_deplib="" ;; esac fi if test -n "$a_deplib" ; then libname=`eval "\\$ECHO \"$libname_spec\""` for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do potential_libs=`ls $i/$libname[.-]* 2>/dev/null` for potent_lib in $potential_libs; do potlib="$potent_lib" # see symlink-check above in file_magic test if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \ $EGREP "$match_pattern_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a regex pattern. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; none | unknown | *) newdeplibs="" tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'` if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then for i in $predeps $postdeps ; do # can't use Xsed below, because $i might contain '/' tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"` done fi if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' | $GREP . >/dev/null; then $ECHO if test "X$deplibs_check_method" = "Xnone"; then $ECHO "*** Warning: inter-library dependencies are not supported in this platform." else $ECHO "*** Warning: inter-library dependencies are not known to be supported." fi $ECHO "*** All declared inter-library dependencies are being dropped." droppeddeps=yes fi ;; esac versuffix=$versuffix_save major=$major_save release=$release_save libname=$libname_save name=$name_save case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library with the System framework newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac if test "$droppeddeps" = yes; then if test "$module" = yes; then $ECHO $ECHO "*** Warning: libtool could not satisfy all declared inter-library" $ECHO "*** dependencies of module $libname. Therefore, libtool will create" $ECHO "*** a static module, that should work as long as the dlopening" $ECHO "*** application is linked with the -dlopen flag." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi else $ECHO "*** The inter-library dependencies that have been dropped here will be" $ECHO "*** automatically added whenever a program is linked with this library" $ECHO "*** or is declared to -dlopen it." if test "$allow_undefined" = no; then $ECHO $ECHO "*** Since this library must not contain undefined symbols," $ECHO "*** because either the platform does not support them or" $ECHO "*** it was explicitly requested with -no-undefined," $ECHO "*** libtool will only create a static version of it." if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi fi fi # Done checking deplibs! deplibs=$newdeplibs fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" case $host in *-*-darwin*) newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done deplibs="$new_libs" # All the library-specific variables (install_libdir is set above). library_names= old_library= dlname= # Test again, we may have decided not to build it any more if test "$build_libtool_libs" = yes; then if test "$hardcode_into_libs" = yes; then # Hardcode the library paths hardcode_libdirs= dep_rpath= rpath="$finalize_rpath" test "$mode" != relink && rpath="$compile_rpath$rpath" for libdir in $rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" dep_rpath="$dep_rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" if test -n "$hardcode_libdir_flag_spec_ld"; then eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\" else eval dep_rpath=\"$hardcode_libdir_flag_spec\" fi fi if test -n "$runpath_var" && test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" fi test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs" fi shlibpath="$finalize_shlibpath" test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath" if test -n "$shlibpath"; then eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" fi # Get the real and link names of the library. eval shared_ext=\"$shrext_cmds\" eval library_names=\"$library_names_spec\" set dummy $library_names shift realname="$1" shift if test -n "$soname_spec"; then eval soname=\"$soname_spec\" else soname="$realname" fi if test -z "$dlname"; then dlname=$soname fi lib="$output_objdir/$realname" linknames= for link do linknames="$linknames $link" done # Use standard objects if they are pic test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` test "X$libobjs" = "X " && libobjs= delfiles= if test -n "$export_symbols" && test -n "$include_expsyms"; then $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" export_symbols="$output_objdir/$libname.uexp" delfiles="$delfiles $export_symbols" fi orig_export_symbols= case $host_os in cygwin* | mingw* | cegcc*) if test -n "$export_symbols" && test -z "$export_symbols_regex"; then # exporting using user supplied symfile if test "x`$SED 1q $export_symbols`" != xEXPORTS; then # and it's NOT already a .def file. Must figure out # which of the given symbols are data symbols and tag # them as such. So, trigger use of export_symbols_cmds. # export_symbols gets reassigned inside the "prepare # the list of exported symbols" if statement, so the # include_expsyms logic still works. orig_export_symbols="$export_symbols" export_symbols= always_export_symbols=yes fi fi ;; esac # Prepare the list of exported symbols if test -z "$export_symbols"; then if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols cmds=$export_symbols_cmds save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" func_len " $cmd" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then func_show_eval "$cmd" 'exit $?' skipped_export=false else # The command line is too long to execute in one step. func_verbose "using reloadable object file for export list..." skipped_export=: # Break out early, otherwise skipped_export may be # set to false by a later but shorter cmd. break fi done IFS="$save_ifs" if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi fi if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi tmp_deplibs= for test_deplib in $deplibs; do case " $convenience " in *" $test_deplib "*) ;; *) tmp_deplibs="$tmp_deplibs $test_deplib" ;; esac done deplibs="$tmp_deplibs" if test -n "$convenience"; then if test -n "$whole_archive_flag_spec" && test "$compiler_needs_object" = yes && test -z "$libobjs"; then # extract the archives, so we have objects to list. # TODO: could optimize this to just extract one archive. whole_archive_flag_spec= fi if test -n "$whole_archive_flag_spec"; then save_libobjs=$libobjs eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= else gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $convenience libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi fi if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then eval flag=\"$thread_safe_flag_spec\" linker_flags="$linker_flags $flag" fi # Make a backup of the uninstalled library when relinking if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? fi # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then eval test_cmds=\"$module_expsym_cmds\" cmds=$module_expsym_cmds else eval test_cmds=\"$module_cmds\" cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then eval test_cmds=\"$archive_expsym_cmds\" cmds=$archive_expsym_cmds else eval test_cmds=\"$archive_cmds\" cmds=$archive_cmds fi fi if test "X$skipped_export" != "X:" && func_len " $test_cmds" && len=$func_len_result && test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then : else # The command line is too long to link in one step, link piecewise # or, if using GNU ld and skipped_export is not :, use a linker # script. # Save the value of $output and $libobjs because we want to # use them later. If we have whole_archive_flag_spec, we # want to use save_libobjs as it was before # whole_archive_flag_spec was expanded, because we can't # assume the linker understands whole_archive_flag_spec. # This may have to be revisited, in case too many # convenience libraries get linked in and end up exceeding # the spec. if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then save_libobjs=$libobjs fi save_output=$output output_la=`$ECHO "X$output" | $Xsed -e "$basename"` # Clear the reloadable object creation command queue and # initialize k to one. test_cmds= concat_cmds= objlist= last_robj= k=1 if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then output=${output_objdir}/${output_la}.lnkscript func_verbose "creating GNU ld script: $output" $ECHO 'INPUT (' > $output for obj in $save_libobjs do $ECHO "$obj" >> $output done $ECHO ')' >> $output delfiles="$delfiles $output" elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then output=${output_objdir}/${output_la}.lnk func_verbose "creating linker input file list: $output" : > $output set x $save_libobjs shift firstobj= if test "$compiler_needs_object" = yes; then firstobj="$1 " shift fi for obj do $ECHO "$obj" >> $output done delfiles="$delfiles $output" output=$firstobj\"$file_list_spec$output\" else if test -n "$save_libobjs"; then func_verbose "creating reloadable object files..." output=$output_objdir/$output_la-${k}.$objext eval test_cmds=\"$reload_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 # Loop over the list of objects to be linked. for obj in $save_libobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result if test "X$objlist" = X || test "$len" -lt "$max_cmd_len"; then func_append objlist " $obj" else # The command $test_cmds is almost too long, add a # command to the queue. if test "$k" -eq 1 ; then # The first file doesn't have a previous command to add. eval concat_cmds=\"$reload_cmds $objlist $last_robj\" else # All subsequent reloadable object files will link in # the last one created. eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\" fi last_robj=$output_objdir/$output_la-${k}.$objext func_arith $k + 1 k=$func_arith_result output=$output_objdir/$output_la-${k}.$objext objlist=$obj func_len " $last_robj" func_arith $len0 + $func_len_result len=$func_arith_result fi done # Handle the remaining objects by creating one last # reloadable object file. All subsequent reloadable object # files will link in the last one created. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\" if test -n "$last_robj"; then eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" fi delfiles="$delfiles $output" else output= fi if ${skipped_export-false}; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols libobjs=$output # Append the command to create the export file. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\" fi fi test -n "$save_libobjs" && func_verbose "creating a temporary reloadable object file: $output" # Loop through the commands generated above and execute them. save_ifs="$IFS"; IFS='~' for cmd in $concat_cmds; do IFS="$save_ifs" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" if test -n "$export_symbols_regex" && ${skipped_export-false}; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi if ${skipped_export-false}; then if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi fi libobjs=$output # Restore the value of output. output=$save_output if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= fi # Expand the library linking commands again to reset the # value of $libobjs for piecewise linking. # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then cmds=$module_expsym_cmds else cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then cmds=$archive_expsym_cmds else cmds=$archive_cmds fi fi fi if test -n "$delfiles"; then # Append the command to remove temporary files to $cmds. eval cmds=\"\$cmds~\$RM $delfiles\" fi # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $dlprefiles libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" # Restore the uninstalled library and exit if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? if test -n "$convenience"; then if test -z "$whole_archive_flag_spec"; then func_show_eval '${RM}r "$gentop"' fi fi exit $EXIT_SUCCESS fi # Create links to the real library. for linkname in $linknames; do if test "$realname" != "$linkname"; then func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?' fi done # If -module or -export-dynamic was specified, set the dlname. if test "$module" = yes || test "$export_dynamic" = yes; then # On all known operating systems, these are identical. dlname="$soname" fi fi ;; obj) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for objects" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for objects" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for objects" test -n "$xrpath" && \ func_warning "\`-R' is ignored for objects" test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for objects" test -n "$release" && \ func_warning "\`-release' is ignored for objects" case $output in *.lo) test -n "$objs$old_deplibs" && \ func_fatal_error "cannot build library object \`$output' from non-libtool objects" libobj=$output func_lo2o "$libobj" obj=$func_lo2o_result ;; *) libobj= obj="$output" ;; esac # Delete the old objects. $opt_dry_run || $RM $obj $libobj # Objects from convenience libraries. This assumes # single-version convenience libraries. Whenever we create # different ones for PIC/non-PIC, this we'll have to duplicate # the extraction. reload_conv_objs= gentop= # reload_cmds runs $LD directly, so let us get rid of # -Wl from whole_archive_flag_spec and hope we can get by with # turning comma into space.. wl= if test -n "$convenience"; then if test -n "$whole_archive_flag_spec"; then eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'` else gentop="$output_objdir/${obj}x" generated="$generated $gentop" func_extract_archives $gentop $convenience reload_conv_objs="$reload_objs $func_extract_archives_result" fi fi # Create the old-style object. reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test output="$obj" func_execute_cmds "$reload_cmds" 'exit $?' # Exit if we aren't doing a library object file. if test -z "$libobj"; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS fi if test "$build_libtool_libs" != yes; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi # Create an invalid libtool object if no PIC, so that we don't # accidentally link it into a program. # $show "echo timestamp > $libobj" # $opt_dry_run || eval "echo timestamp > $libobj" || exit $? exit $EXIT_SUCCESS fi if test -n "$pic_flag" || test "$pic_mode" != default; then # Only do commands if we really have different PIC objects. reload_objs="$libobjs $reload_conv_objs" output="$libobj" func_execute_cmds "$reload_cmds" 'exit $?' fi if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS ;; prog) case $host in *cygwin*) func_stripname '' '.exe' "$output" output=$func_stripname_result.exe;; esac test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for programs" test -n "$release" && \ func_warning "\`-release' is ignored for programs" test "$preload" = yes \ && test "$dlopen_support" = unknown \ && test "$dlopen_self" = unknown \ && test "$dlopen_self_static" = unknown && \ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support." case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac case $host in *-*-darwin*) # Don't allow lazy linking, it breaks C++ global constructors # But is supposedly fixed on 10.4 or later (yay!). if test "$tagname" = CXX ; then case ${MACOSX_DEPLOYMENT_TARGET-10.0} in 10.[0123]) compile_command="$compile_command ${wl}-bind_at_load" finalize_command="$finalize_command ${wl}-bind_at_load" ;; esac fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $compile_deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $compile_deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done compile_deplibs="$new_libs" compile_command="$compile_command $compile_deplibs" finalize_command="$finalize_command $finalize_deplibs" if test -n "$rpath$xrpath"; then # If the user specified any rpath flags, then add them. for libdir in $rpath $xrpath; do # This is the magic to use -rpath. case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done fi # Now hardcode the library paths rpath= hardcode_libdirs= for libdir in $compile_rpath $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$libdir:"*) ;; ::) dllsearchpath=$libdir;; *) dllsearchpath="$dllsearchpath:$libdir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) dllsearchpath="$dllsearchpath:$testbindir";; esac ;; esac done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi compile_rpath="$rpath" rpath= hardcode_libdirs= for libdir in $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$finalize_perm_rpath " in *" $libdir "*) ;; *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi finalize_rpath="$rpath" if test -n "$libobjs" && test "$build_old_libs" = yes; then # Transform all the library objects into standard objects. compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` fi func_generate_dlsyms "$outputname" "@PROGRAM@" "no" # template prelinking step if test -n "$prelink_cmds"; then func_execute_cmds "$prelink_cmds" 'exit $?' fi wrappers_required=yes case $host in *cygwin* | *mingw* ) if test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; *cegcc) # Disable wrappers for cegcc, we are cross compiling anyway. wrappers_required=no ;; *) if test "$need_relink" = no || test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; esac if test "$wrappers_required" = no; then # Replace the output file specification. compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` link_command="$compile_command$compile_rpath" # We have no uninstalled library dependencies, so finalize right now. exit_status=0 func_show_eval "$link_command" 'exit_status=$?' # Delete the generated files. if test -f "$output_objdir/${outputname}S.${objext}"; then func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"' fi exit $exit_status fi if test -n "$compile_shlibpath$finalize_shlibpath"; then compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command" fi if test -n "$finalize_shlibpath"; then finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command" fi compile_var= finalize_var= if test -n "$runpath_var"; then if test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done compile_var="$runpath_var=\"$rpath\$$runpath_var\" " fi if test -n "$finalize_perm_rpath"; then # We should set the runpath_var. rpath= for dir in $finalize_perm_rpath; do rpath="$rpath$dir:" done finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " fi fi if test "$no_install" = yes; then # We don't need to create a wrapper script. link_command="$compile_var$compile_command$compile_rpath" # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` # Delete the old output file. $opt_dry_run || $RM $output # Link the executable and exit func_show_eval "$link_command" 'exit $?' exit $EXIT_SUCCESS fi if test "$hardcode_action" = relink; then # Fast installation is not supported link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" func_warning "this platform does not like uninstalled shared libraries" func_warning "\`$output' will be relinked during installation" else if test "$fast_install" != no; then link_command="$finalize_var$compile_command$finalize_rpath" if test "$fast_install" = yes; then relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'` else # fast_install is set to needless relink_command= fi else link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" fi fi # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` # Delete the old output files. $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname func_show_eval "$link_command" 'exit $?' # Now create the wrapper script. func_verbose "creating $output" # Quote the relink command for shipping. if test -n "$relink_command"; then # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" fi done relink_command="(cd `pwd`; $relink_command)" relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` fi # Quote $ECHO for shipping. if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then case $progpath in [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";; *) qecho="$SHELL `pwd`/$progpath --fallback-echo";; esac qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"` else qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"` fi # Only actually do things if not in dry run mode. $opt_dry_run || { # win32 will think the script is a binary if it has # a .exe suffix, so we strip it off here. case $output in *.exe) func_stripname '' '.exe' "$output" output=$func_stripname_result ;; esac # test for cygwin because mv fails w/o .exe extensions case $host in *cygwin*) exeext=.exe func_stripname '' '.exe' "$outputname" outputname=$func_stripname_result ;; 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fi ;; esac done func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj" oldobjs="$oldobjs $gentop/$newobj" ;; *) oldobjs="$oldobjs $obj" ;; esac done fi eval cmds=\"$old_archive_cmds\" func_len " $cmds" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then cmds=$old_archive_cmds else # the command line is too long to link in one step, link in parts func_verbose "using piecewise archive linking..." save_RANLIB=$RANLIB RANLIB=: objlist= concat_cmds= save_oldobjs=$oldobjs oldobjs= # Is there a better way of finding the last object in the list? for obj in $save_oldobjs do last_oldobj=$obj done eval test_cmds=\"$old_archive_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 for obj in $save_oldobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result func_append objlist " $obj" if test "$len" -lt "$max_cmd_len"; then : else # the above command should be used before it gets too long oldobjs=$objlist if test "$obj" = "$last_oldobj" ; then RANLIB=$save_RANLIB fi test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\" objlist= len=$len0 fi done RANLIB=$save_RANLIB oldobjs=$objlist if test "X$oldobjs" = "X" ; then eval cmds=\"\$concat_cmds\" else eval cmds=\"\$concat_cmds~\$old_archive_cmds\" fi fi fi func_execute_cmds "$cmds" 'exit $?' done test -n "$generated" && \ func_show_eval "${RM}r$generated" # Now create the libtool archive. case $output in *.la) old_library= test "$build_old_libs" = yes && old_library="$libname.$libext" func_verbose "creating $output" # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; 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do case $lib in *.la) func_basename "$lib" name="$func_basename_result" eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" newdlfiles="$newdlfiles $libdir/$name" ;; *) newdlfiles="$newdlfiles $lib" ;; esac done dlfiles="$newdlfiles" newdlprefiles= for lib in $dlprefiles; do case $lib in *.la) # Only pass preopened files to the pseudo-archive (for # eventual linking with the app. that links it) if we # didn't already link the preopened objects directly into # the library: func_basename "$lib" name="$func_basename_result" eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib` test -z "$libdir" && \ func_fatal_error "\`$lib' is not a valid libtool archive" newdlprefiles="$newdlprefiles $libdir/$name" ;; esac done dlprefiles="$newdlprefiles" else newdlfiles= for lib in $dlfiles; do case $lib in [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; *) abs=`pwd`"/$lib" ;; esac newdlfiles="$newdlfiles $abs" done dlfiles="$newdlfiles" newdlprefiles= for lib in $dlprefiles; do case $lib in [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;; *) abs=`pwd`"/$lib" ;; esac newdlprefiles="$newdlprefiles $abs" done dlprefiles="$newdlprefiles" fi $RM $output # place dlname in correct position for cygwin tdlname=$dlname case $host,$output,$installed,$module,$dlname in *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;; esac $ECHO > $output "\ # $outputname - a libtool library file # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # Please DO NOT delete this file! # It is necessary for linking the library. # The name that we can dlopen(3). dlname='$tdlname' # Names of this library. library_names='$library_names' # The name of the static archive. old_library='$old_library' # Linker flags that can not go in dependency_libs. inherited_linker_flags='$new_inherited_linker_flags' # Libraries that this one depends upon. dependency_libs='$dependency_libs' # Names of additional weak libraries provided by this library weak_library_names='$weak_libs' # Version information for $libname. current=$current age=$age revision=$revision # Is this an already installed library? installed=$installed # Should we warn about portability when linking against -modules? shouldnotlink=$module # Files to dlopen/dlpreopen dlopen='$dlfiles' dlpreopen='$dlprefiles' # Directory that this library needs to be installed in: libdir='$install_libdir'" if test "$installed" = no && test "$need_relink" = yes; then $ECHO >> $output "\ relink_command=\"$relink_command\"" fi done } # Do a symbolic link so that the libtool archive can be found in # LD_LIBRARY_PATH before the program is installed. func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?' ;; esac exit $EXIT_SUCCESS } { test "$mode" = link || test "$mode" = relink; } && func_mode_link ${1+"$@"} # func_mode_uninstall arg... func_mode_uninstall () { $opt_debug RM="$nonopt" files= rmforce= exit_status=0 # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" for arg do case $arg in -f) RM="$RM $arg"; rmforce=yes ;; -*) RM="$RM $arg" ;; *) files="$files $arg" ;; esac done test -z "$RM" && \ func_fatal_help "you must specify an RM program" rmdirs= origobjdir="$objdir" for file in $files; do func_dirname "$file" "" "." dir="$func_dirname_result" if test "X$dir" = X.; then objdir="$origobjdir" else objdir="$dir/$origobjdir" fi func_basename "$file" name="$func_basename_result" test "$mode" = uninstall && objdir="$dir" # Remember objdir for removal later, being careful to avoid duplicates if test "$mode" = clean; then case " $rmdirs " in *" $objdir "*) ;; *) rmdirs="$rmdirs $objdir" ;; esac fi # Don't error if the file doesn't exist and rm -f was used. if { test -L "$file"; } >/dev/null 2>&1 || { test -h "$file"; } >/dev/null 2>&1 || test -f "$file"; then : elif test -d "$file"; then exit_status=1 continue elif test "$rmforce" = yes; then continue fi rmfiles="$file" case $name in *.la) # Possibly a libtool archive, so verify it. if func_lalib_p "$file"; then func_source $dir/$name # Delete the libtool libraries and symlinks. for n in $library_names; do rmfiles="$rmfiles $objdir/$n" done test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library" case "$mode" in clean) case " $library_names " in # " " in the beginning catches empty $dlname *" $dlname "*) ;; *) rmfiles="$rmfiles $objdir/$dlname" ;; esac test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i" ;; uninstall) if test -n "$library_names"; then # Do each command in the postuninstall commands. func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' fi if test -n "$old_library"; then # Do each command in the old_postuninstall commands. func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' fi # FIXME: should reinstall the best remaining shared library. ;; esac fi ;; *.lo) # Possibly a libtool object, so verify it. if func_lalib_p "$file"; then # Read the .lo file func_source $dir/$name # Add PIC object to the list of files to remove. if test -n "$pic_object" && test "$pic_object" != none; then rmfiles="$rmfiles $dir/$pic_object" fi # Add non-PIC object to the list of files to remove. if test -n "$non_pic_object" && test "$non_pic_object" != none; then rmfiles="$rmfiles $dir/$non_pic_object" fi fi ;; *) if test "$mode" = clean ; then noexename=$name case $file in *.exe) func_stripname '' '.exe' "$file" file=$func_stripname_result func_stripname '' '.exe' "$name" noexename=$func_stripname_result # $file with .exe has already been added to rmfiles, # add $file without .exe rmfiles="$rmfiles $file" ;; esac # Do a test to see if this is a libtool program. if func_ltwrapper_p "$file"; then if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" relink_command= func_source $func_ltwrapper_scriptname_result rmfiles="$rmfiles $func_ltwrapper_scriptname_result" else relink_command= func_source $dir/$noexename fi # note $name still contains .exe if it was in $file originally # as does the version of $file that was added into $rmfiles rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}" if test "$fast_install" = yes && test -n "$relink_command"; then rmfiles="$rmfiles $objdir/lt-$name" fi if test "X$noexename" != "X$name" ; then rmfiles="$rmfiles $objdir/lt-${noexename}.c" fi fi fi ;; esac func_show_eval "$RM $rmfiles" 'exit_status=1' done objdir="$origobjdir" # Try to remove the ${objdir}s in the directories where we deleted files for dir in $rmdirs; do if test -d "$dir"; then func_show_eval "rmdir $dir >/dev/null 2>&1" fi done exit $exit_status } { test "$mode" = uninstall || test "$mode" = clean; } && func_mode_uninstall ${1+"$@"} test -z "$mode" && { help="$generic_help" func_fatal_help "you must specify a MODE" } test -z "$exec_cmd" && \ func_fatal_help "invalid operation mode \`$mode'" if test -n "$exec_cmd"; then eval exec "$exec_cmd" exit $EXIT_FAILURE fi exit $exit_status # The TAGs below are defined such that we never get into a situation # in which we disable both kinds of libraries. Given conflicting # choices, we go for a static library, that is the most portable, # since we can't tell whether shared libraries were disabled because # the user asked for that or because the platform doesn't support # them. This is particularly important on AIX, because we don't # support having both static and shared libraries enabled at the same # time on that platform, so we default to a shared-only configuration. # If a disable-shared tag is given, we'll fallback to a static-only # configuration. But we'll never go from static-only to shared-only. # ### BEGIN LIBTOOL TAG CONFIG: disable-shared build_libtool_libs=no build_old_libs=yes # ### END LIBTOOL TAG CONFIG: disable-shared # ### BEGIN LIBTOOL TAG CONFIG: disable-static build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac` # ### END LIBTOOL TAG CONFIG: disable-static # Local Variables: # mode:shell-script # sh-indentation:2 # End: # vi:sw=2 odin-1.8.5/platforms/0000755000175000017500000000000011735135552011475 500000000000000odin-1.8.5/platforms/StandAlone/0000755000175000017500000000000011735135552013525 500000000000000odin-1.8.5/platforms/StandAlone/odinseq_standalone/0000755000175000017500000000000011735135552017377 500000000000000odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqstandalone.cpp0000644000175000017500000002354111735135552022671 00000000000000#include "seqstandalone.h" #include "seqacq_standalone.h" #include "seqacqepi_standalone.h" #include "seqdec_standalone.h" #include "seqdelay_standalone.h" #include "seqfreq_standalone.h" #include "seqgradchan_standalone.h" #include "seqgradtrapez_standalone.h" #include "seqlist_standalone.h" #include "seqcounter_standalone.h" #include "seqparallel_standalone.h" #include "seqphase_standalone.h" #include "seqpuls_standalone.h" #include "seqtrigg_standalone.h" #include #include const char* SeqStandAlone::get_compName() {return "StandAlone";} LOGGROUNDWORK(SeqStandAlone) int SeqStandAlone::process(int argc, char *argv[]) { #ifndef NO_CMDLINE Log odinlog("SeqStandAlone","process"); SeqMethodProxy method; SeqPlatformProxy pfinterface; char value[ODIN_MAXCHAR]; bool valid_command=false; STD_string action(argv[1]); if(action=="plot") { if(getCommandlineOption(argc,argv,"-p",value,ODIN_MAXCHAR)) method->load_protocol(value); pfinterface.set_current_platform(standalone); // overwrite result from load_protocol dump2console=true; if(method->prepare()) { eventContext context; context.action=seqRun; method->event(context); STD_cout << STD_endl; } else ODINLOG(odinlog,errorLog) << method->get_label() << +"->prepare() failed" << STD_endl; dump2console=false; valid_command=true; } if(action=="simulate") { STD_string samplefile; if(getCommandlineOption(argc,argv,"-s",value,ODIN_MAXCHAR)) samplefile=value; else { ODINLOG(odinlog,errorLog) << "(simulate): No virtual sample file specified" << STD_endl; return -1; } if(getCommandlineOption(argc,argv,"-p",value,ODIN_MAXCHAR)) method->load_protocol(value); pfinterface.set_current_platform(standalone); // overwrite result from load_protocol while(getCommandlineOption(argc,argv,"-m",value,ODIN_MAXCHAR)) { svector toks(tokens(value,'=')); if(toks.size()!=2) ODINLOG(odinlog,errorLog) << "syntax error in " << value << STD_endl; else method->set_sequenceParameter(toks[0],toks[1]); } if(!method->prepare()) { ODINLOG(odinlog,errorLog) << "(simulate): method->prepare() failed" << STD_endl; return -1; } if(!method->prep_acquisition()) { ODINLOG(odinlog,errorLog) << "(simulate): method->prep_acquisition() failed" << STD_endl; return -1; } plotData->get_opts(true,true).parse_cmdline_options(argc,argv); ProgressDisplayConsole pdc; ProgressMeter progmeter(pdc); create_plot_events(&progmeter); STD_string fidfile=systemInfo->get_scandir()+get_rawfile(); plotData->simulate(fidfile,samplefile,&progmeter,0); method->write_meas_contex(systemInfo->get_scandir()); plotData->get_opts(true,true).write(systemInfo->get_scandir()+"simopts"); valid_command=true; } // if(!valid_command) return -1; return int(valid_command); #endif return 0; } SeqCmdlineActionList SeqStandAlone::get_actions_usage() const { SeqCmdlineActionList result; #ifndef NO_CMDLINE SeqCmdlineAction plot("plot","Print plotting events to the console."); plot.add_opt_arg("p","The file with the measurement protocol"); result.push_back(plot); SeqCmdlineAction simulate("simulate","Creates a virtual MR signal by simulating the sequence."); simulate.opt_args=plotData->get_opts(true,true).get_cmdline_options(); simulate.add_req_arg("s","The virtual sample file"); simulate.add_opt_arg("p","The file with the measurement protocol"); simulate.add_opt_arg("m","protcol_parameter=value"); result.push_back(simulate); #endif return result; } void SeqStandAlone::pre_event(eventContext& context) const { Log odinlog(this,"pre_event"); ODINLOG(odinlog,normalDebug) << "resetting plotData" << STD_endl; plotData->reset(); new_plot_frame(context); } void SeqStandAlone::post_event(eventContext& context) const { flush_plot_frame(context); if(dump2console) { double totaldur=plotData->get_total_duration(); STD_cout << "---------- Curves: ---------------------" << STD_endl; STD_list::const_iterator begin,end; plotData->get_curves(begin, end, 0.0, totaldur, totaldur); for(STD_list::const_iterator it=begin; it!=end; ++it) { if(it->size) { STD_cout << it->x[0] << "\t" << it->label; if(it->has_freq_phase) STD_cout << "\tfreq/phase=" << it->freq << "/" << it->phase; if(it->gradmatrix) STD_cout << "\tgradmatrix=" << it->gradmatrix->print(); STD_cout << STD_endl; } } STD_cout << "---------- Markers: --------------------" << STD_endl; STD_list::const_iterator markbegin,markend; plotData->get_markers(markbegin, markend, 0.0, totaldur); for(STD_list::const_iterator markit=markbegin; markit!=markend; ++markit) { STD_cout << markit->x << "\t" << markit->label << STD_endl; } } } fvector SeqStandAlone::get_acq_channel_scale_factors() const { fvector result(numof_rec_channels()); result=1.0; return result; } void SeqStandAlone::new_plot_frame(eventContext& context) const { context.elapsed=0.0; } void SeqStandAlone::flush_plot_frame(eventContext& context) const { plotData->flush_frame(context.elapsed); context.elapsed=0.0; } SeqAcqDriver* SeqStandAlone::create_driver(SeqAcqDriver*) const {return new SeqAcqStandAlone;} SeqEpiDriver* SeqStandAlone::create_driver(SeqEpiDriver*) const {return new SeqEpiDriverDefault;} SeqDecouplingDriver* SeqStandAlone::create_driver(SeqDecouplingDriver*) const {return new SeqDecouplingStandalone;} SeqDelayDriver* SeqStandAlone::create_driver(SeqDelayDriver*) const {return new SeqDelayStandAlone;} SeqDelayVecDriver* SeqStandAlone::create_driver(SeqDelayVecDriver*) const {return new SeqDelayVecStandAlone;} SeqFreqChanDriver* SeqStandAlone::create_driver(SeqFreqChanDriver*) const {return new SeqFreqChanStandAlone;} SeqGradChanDriver* SeqStandAlone::create_driver(SeqGradChanDriver*) const {return new SeqGradChanStandAlone;} SeqGradChanParallelDriver* SeqStandAlone::create_driver(SeqGradChanParallelDriver*) const {return new SeqGradChanParallelStandAlone;} SeqGradTrapezDriver* SeqStandAlone::create_driver(SeqGradTrapezDriver*) const {return new SeqGradTrapezDefault;} SeqListDriver* SeqStandAlone::create_driver(SeqListDriver*) const {return new SeqListStandAlone;} SeqCounterDriver* SeqStandAlone::create_driver(SeqCounterDriver*) const {return new SeqCounterStandAlone;} SeqParallelDriver* SeqStandAlone::create_driver(SeqParallelDriver*) const {return new SeqParallelStandAlone;} SeqPhaseDriver* SeqStandAlone::create_driver(SeqPhaseDriver*) const {return new SeqPhaseStandAlone;} SeqPulsDriver* SeqStandAlone::create_driver(SeqPulsDriver*) const {return new SeqPulsStandAlone;} SeqTriggerDriver* SeqStandAlone::create_driver(SeqTriggerDriver*) const {return new SeqTriggerStandAlone;} unsigned int SeqStandAlone::numof_rec_channels() const { return plotData->numof_rec_channels(); } void SeqStandAlone::append_curve2plot(double starttime, const SeqPlotCurve* curve_ptr) const { plotData->append_curve(starttime,curve_ptr); } void SeqStandAlone::append_curve2plot(double starttime, const SeqPlotCurve* curve_ptr, double freq, double phase) const { plotData->append_curve(starttime,curve_ptr,freq,phase); } void SeqStandAlone::append_curve2plot(double starttime, const SeqPlotCurve* curve_ptr, const RotMatrix* gradrotmatrix) const { plotData->append_curve(starttime,curve_ptr,gradrotmatrix); } void SeqStandAlone::set_systemInfo_defaults() { Log odinlog(this,"set_systemInfo_defaults"); SystemInterface::systemInfo_platform[standalone]->platformstr=get_label(); // hide unused settings SystemInterface::systemInfo_platform[standalone]->reference_gain.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->transmit_coil_name.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->delay_rastertime.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->rf_rastertime.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->acq_rastertime.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->grad_rastertime.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->min_grad_rastertime.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->inter_grad_delay.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->max_rf_samples.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->max_grad_samples.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->datatype.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->grad_reson_center.set_parmode(hidden); SystemInterface::systemInfo_platform[standalone]->grad_reson_width.set_parmode(hidden); } SeqPlotDataAbstract* SeqStandAlone::get_plot_data() {return plotData.unlocked_ptr();} bool SeqStandAlone::create_plot_events(ProgressMeter* progmeter) { SeqMethodProxy method; eventContext context; // count events first if(progmeter) { context.action=countEvents; unsigned int eventscount=method->SeqMethod::event(context); context.event_progmeter=progmeter; context.event_progmeter->new_task(eventscount,"Creating sequence plot"); } context.action=seqRun; method->SeqMethod::event(context); return true; } void SeqStandAlone::init_static() { plotData.init("plotData"); } void SeqStandAlone::destroy_static() { plotData.destroy(); } template class SingletonHandler; SingletonHandler SeqStandAlone::plotData; double SeqStandAlone::current_rf_rec_freq=0.0; double SeqStandAlone::current_rf_rec_phase=0.0; const RotMatrix* SeqStandAlone::current_rotmatrix=0; bool SeqStandAlone::dump2console=false; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqacq_standalone.cpp0000644000175000017500000000352011735135552023510 00000000000000#include "seqacq_standalone.h" SeqAcqStandAlone::SeqAcqStandAlone(const SeqAcqStandAlone& sas) { set_label(sas.get_label()); } bool SeqAcqStandAlone::prep_driver(kSpaceCoord& recoindex, double sweepwidth,unsigned int nAcqPoints, double acqcenter, int freqchannel) { Log odinlog(this,"prep_driver"); adc_curve.label=get_label().c_str(); adc_curve.channel=rec_plotchan; adc_curve.spikes=true; double acqdur=secureDivision(double(nAcqPoints),sweepwidth); double dt=secureInv(sweepwidth); ODINLOG(odinlog,normalDebug) << "acqdur/dt/nAcqPoints=" << acqdur << "/" << dt << "/" << nAcqPoints << STD_endl; adc_curve.resize(nAcqPoints); for(unsigned int i=0; i=0.0 && acqcenter<=acqdur) { adc_curve.marker=acquisition_marker; adc_curve.marklabel=markLabel[acquisition_marker]; adc_curve.marker_x=acqcenter; } if(dump2console) { STD_cout << adc_curve << STD_endl; STD_cout << adc_curve_nomark << STD_endl; STD_cout << endacq_mark << STD_endl; } return true; } void SeqAcqStandAlone::event(eventContext& context, double start) const { Log odinlog(this,"event"); // plot center and end marker append_curve2plot(start,&adc_curve,current_rf_rec_freq,current_rf_rec_phase); append_curve2plot(start,&endacq_mark); } odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqgradchan_standalone.cpp0000644000175000017500000001313711735135552024520 00000000000000#include "seqgradchan_standalone.h" void SeqGradChanStandAlone::common_int() { veccurve_cache=0; current_vec=-1; } void SeqGradChanStandAlone::common_prep(SeqGradPlotCurve& gradcurve) { for(int i=0; iget_max_slew_rate(); if(gradduration<0.0) gradduration=0.0; float maxstrength_dur=slewrate*gradduration; if(fabs(strength)>maxstrength_dur) { float sign=secureDivision(strength,fabs(strength)); strength=sign*maxstrength_dur; } double rampdur=secureDivision(fabs(strength),slewrate); if(rampdur>0.0 && strength!=0.0) { for(int i=0; i odinlog(this,"prep_vector"); unsigned int n=gradvec.size(); ODINLOG(odinlog,normalDebug) << "gradvec(" << n << ")=" << gradvec.printbody() << STD_endl; veccurve_cache=new SeqGradPlotCurve[n]; for(unsigned int j=0; j odinlog(this,"prep_vector_iteration"); ODINLOG(odinlog,normalDebug) << "count=" << count << STD_endl; current_vec=count; return true; } bool SeqGradChanStandAlone::prep_trapez(float strength, const fvector& strengthfactor, double ruptime, const fvector& rupshape, double consttime, double rdowntime, const fvector& rdownshape) { common_prep(curve); unsigned int n_up =rupshape.size(); unsigned int n_down=rdownshape.size(); unsigned int n_total=n_up+2+n_down; unsigned int j; for(int i=0; i odinlog(this,"event"); ODINLOG(odinlog,normalDebug) << "start=" << start << STD_endl; for(int i=0; i=0) { ODINLOG(odinlog,normalDebug) << "current_vec=" << current_vec << STD_endl; if(veccurve_cache[current_vec].grad[i].x.size()) { append_curve2plot(start,&(veccurve_cache[current_vec].grad[i]),current_rotmatrix); } } } else { if(curve.grad[i].x.size()) { append_curve2plot(start,&(curve.grad[i]),current_rotmatrix); } } } } odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqacqepi_standalone.cpp0000644000175000017500000000012111735135552024200 00000000000000#include "seqacqepi_standalone.h" // empty, because SeqEpiDriverDefault is used odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqparallel_standalone.cpp0000644000175000017500000000004511735135552024537 00000000000000#include "seqparallel_standalone.h" odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqcounter_standalone.cpp0000644000175000017500000000004311735135552024420 00000000000000#include "seqcounter_standalone.h" odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqdec_standalone.h0000644000175000017500000000430211735135552023143 00000000000000/*************************************************************************** seqdec_standalone.h - description ------------------- begin : Fri Jul 23 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDEC_STANDALONE_H #define SEQDEC_STANDALONE_H #include #include "seqstandalone.h" #define ON_OFF_DELAY 1.0e-6 /** * @ingroup odinseq_internals * The Standalone driver for decoupling periods */ class SeqDecouplingStandalone : public SeqDecouplingDriver, public SeqStandAlone { public: SeqDecouplingStandalone() {} SeqDecouplingStandalone(const SeqDecouplingStandalone& sds); ~SeqDecouplingStandalone() {} // overloading virtual functions from SeqDecouplingDriver bool prep_driver(double decdur, int channel, float decpower, const STD_string& program, double pulsedur); void event(eventContext& context, double start) const; double get_preduration() const {return 0.0;} double get_postduration() const {return 0.0;} STD_string get_preprogram(programContext& context, const STD_string& iteratorcommand) const {return "";} STD_string get_postprogram(programContext& context) const {return "";} SeqDecouplingDriver* clone_driver() const {return new SeqDecouplingStandalone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} private: SeqPlotCurve curve; }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqstandalone.h0000644000175000017500000001126011735135552022331 00000000000000/*************************************************************************** seqstandalone.h - description ------------------- begin : Fri Jul 23 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQSTANDALONE_H #define SEQSTANDALONE_H #include #include #include class SeqPlotCurve; // forward declaration class SeqPlotData; // forward declaration //////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Base class for all sequence objects that deal with functionality specific to the ODIN stand-alone platform */ class SeqStandAlone : public SeqPlatform, public StaticHandler { public: SeqStandAlone() {} SeqStandAlone(const PlatformRegistration&) {set_label("StandAlone");set_systemInfo_defaults();} // name of debugging component static const char* get_compName(); // overloadded functions from SeqPlatform void init() {} void reset_before_prep() {} void prepare_measurement(unsigned int) {} SeqAcqDriver* create_driver(SeqAcqDriver*) const; SeqEpiDriver* create_driver(SeqEpiDriver*) const; SeqDecouplingDriver* create_driver(SeqDecouplingDriver*) const; SeqDelayDriver* create_driver(SeqDelayDriver*) const; SeqDelayVecDriver* create_driver(SeqDelayVecDriver*) const; SeqFreqChanDriver* create_driver(SeqFreqChanDriver*) const; SeqGradChanDriver* create_driver(SeqGradChanDriver*) const; SeqGradChanParallelDriver* create_driver(SeqGradChanParallelDriver*) const; SeqGradTrapezDriver* create_driver(SeqGradTrapezDriver*) const; SeqListDriver* create_driver(SeqListDriver*) const; SeqCounterDriver* create_driver(SeqCounterDriver*) const; SeqParallelDriver* create_driver(SeqParallelDriver*) const; SeqPhaseDriver* create_driver(SeqPhaseDriver*) const; SeqPulsDriver* create_driver(SeqPulsDriver*) const; SeqTriggerDriver* create_driver(SeqTriggerDriver*) const; int process(int argc, char *argv[]); SeqCmdlineActionList get_actions_usage() const; void pre_event (eventContext& context) const; void post_event(eventContext& context) const; fvector get_acq_channel_scale_factors() const; STD_string get_program(programContext& context) const {return "";} STD_string get_rawdatatype() const {return TypeTraits::type2label(float(0));} STD_string get_rawfile() const {return "signal.float";} unsigned int get_rawheader_size() const {return 0;} STD_string get_image_proc() const {return "";} bool create_recoInfo() const {return true;} int write_rf_waveform (const STD_string& filename, const cvector& waveform) const {return -1;} int load_rf_waveform (const STD_string& filename, cvector& result) const {return -1;} int get_max_methodname_length() const {return -1;} void set_eventlogging(eventLogging loggflag) {} void set_idea_pars(void* pmp,void* psl,void* pse, bool onlineReco) {} SeqPlotDataAbstract* get_plot_data(); bool create_plot_events(ProgressMeter* progmeter); // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); unsigned int numof_rec_channels() const; protected: void append_curve2plot(double starttime, const SeqPlotCurve* curve_ptr) const; void append_curve2plot(double starttime, const SeqPlotCurve* curve_ptr, double freq, double phase) const; void append_curve2plot(double starttime, const SeqPlotCurve* curve_ptr, const RotMatrix* gradrotmatrix) const; void new_plot_frame(eventContext& context) const; void flush_plot_frame(eventContext& context) const; static double current_rf_rec_freq; static double current_rf_rec_phase; static const RotMatrix* current_rotmatrix; static bool dump2console; private: void set_systemInfo_defaults(); static SingletonHandler plotData; }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqcounter_standalone.h0000644000175000017500000000575011735135552024077 00000000000000/*************************************************************************** seqcounter_standalone.h - description ------------------- begin : Sat Apr 17 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQCOUNTER_STANDALONE_H #define SEQCOUNTER_STANDALONE_H #include ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for counter objects */ class SeqCounterStandAlone : public SeqCounterDriver { public: SeqCounterStandAlone() {} SeqCounterStandAlone(const SeqCounterStandAlone& sls) {set_label(sls.get_label());} ~SeqCounterStandAlone() {} // overloading virtual functions from SeqCounterDriver bool prep_driver() {return true;} void update_driver(const SeqCounter* counter, const SeqObjList* seqlist, const List* vectors) const {}; double get_preduration () const {return 0.0;} double get_postduration() const {return 0.0;} double get_preduration_inloop() const {return 0.0;} double get_postduration_inloop() const {return 0.0;} bool create_program(programContext& context, const STD_string& loopkernel) const {return true;} STD_string get_program_head(programContext& context, const STD_string& loopkernel, unsigned int times) const {return "";} STD_string get_program_tail(programContext& context, const STD_string& loopkernel, unsigned int times) const {return "";} STD_string get_program_head_unrolled(programContext& context, unsigned int index) const {return "";} STD_string get_program_iterator(programContext& context) const {return "";} void pre_vecprepevent (eventContext& context) const {} void post_vecprepevent(eventContext& context, int repcounter) const {} void outdate_cache() const {} bool unroll_program(const SeqCounter* counter, const SeqObjList* seqlist, const List* vectors, programContext& context) const {return false;} SeqCounterDriver* clone_driver() const {return new SeqCounterStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqgradchan_standalone.h0000644000175000017500000001111311735135552024155 00000000000000/*************************************************************************** seqgradchan_standalone.h - description ------------------- begin : Fri Jul 23 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADCHAN_STANDALONE_H #define SEQGRADCHAN_STANDALONE_H #include #include #include "seqstandalone.h" ////////////////////////////////////////////////////////////////// struct SeqGradPlotCurve { SeqGradPlotCurve() { for(int i=0; i #include #include SeqTimecourseOpts::SeqTimecourseOpts() : JcampDxBlock("Timecourse Options") { JcampDxBlock::set_embedded(true); EddyCurrentAmpl=0.0; EddyCurrentAmpl.set_minmaxval(0.0,10.0); EddyCurrentAmpl.set_unit("%"); EddyCurrentAmpl.set_description("Amplitude of eddy currents relative to the inducing gradient."); EddyCurrentAmpl.set_cmdline_option("ecamp"); EddyCurrentTimeConst=2.0; EddyCurrentTimeConst.set_minmaxval(0.0,10.0); EddyCurrentTimeConst.set_unit(ODIN_TIME_UNIT); EddyCurrentTimeConst.set_description("Time constant of the exponentially decaying eddy currents."); EddyCurrentTimeConst.set_cmdline_option("ectime"); append_member(EddyCurrentAmpl,"EddyCurrentAmpl"); append_member(EddyCurrentTimeConst,"EddyCurrentTimeConst"); } SeqSimulationOpts::SeqSimulationOpts() : JcampDxBlock("Simulation Options"), transm_coil(0), receiv_coil(0), coil_cache_up2date(false) { JcampDxBlock::set_embedded(true); SimThreads=numof_cores(); SimThreads.set_minmaxval(1,16); SimThreads.set_description("Number of concurrent threads (parallel processing) during simulation"); SimThreads.set_cmdline_option("j"); IntraVoxelMagnGrads=true; IntraVoxelMagnGrads.set_description("Consider intra-voxel magnetization gradients during simulation"); IntraVoxelMagnGrads.set_cmdline_option("magsi"); MagnMonitor=false; MagnMonitor.set_description("Monitor magnetization vector using vtk"); MagnMonitor.set_cmdline_option("mon"); ReceiverNoise=0.0; ReceiverNoise.set_minmaxval(0.0,10.0); ReceiverNoise.set_unit("%"); ReceiverNoise.set_description("Noise generated by the receiver in percentage of the maximum available, in-phase signal of the sample."); ReceiverNoise.set_cmdline_option("noise"); TransmitterCoil.set_suffix("coi"); TransmitterCoil.set_description("RF coil used for transmission. Leave blank for homogeneous coil."); TransmitterCoil.set_cmdline_option("tcoil"); ReceiverCoil.set_suffix("coi"); ReceiverCoil.set_description("RF coil used for acquisition. Leave blank for homogeneous coil."); ReceiverCoil.set_cmdline_option("rcoil"); InitialMagnVector[0]=0.0; InitialMagnVector[1]=0.0; InitialMagnVector[2]=1.0; InitialMagnVector.set_description("Initial magnetization vector."); #ifndef NO_THREADS append_member(SimThreads,"SimThreads"); #endif append_member(IntraVoxelMagnGrads,"IntraVoxelMagnGrads"); append_member(MagnMonitor,"MagnMonitor"); append_member(ReceiverNoise,"ReceiverNoise"); append_member(TransmitterCoil,"TransmitterCoil"); append_member(ReceiverCoil,"ReceiverCoil"); append_member(InitialMagnVector,"InitialMagnVector"); } void SeqSimulationOpts::update_coil_cache() const { if(coil_cache_up2date) return; outdate_coil_cache(); if(filesize(TransmitterCoil.c_str())>0) { transm_coil=new CoilSensitivity("Transmitter Coil"); if(transm_coil->load(TransmitterCoil)<=0) { delete transm_coil; transm_coil=0; } else SeqMethodProxy()->get_systemInfo().set_transmit_coil_name(TransmitterCoil.get_basename()); // update protocol } if(filesize(ReceiverCoil.c_str())>0) { receiv_coil=new CoilSensitivity("Receiver Coil"); if(receiv_coil->load(ReceiverCoil)<=0) { delete receiv_coil; receiv_coil=0; } } coil_cache_up2date=true; } void SeqSimulationOpts::outdate_coil_cache() const { if(transm_coil) delete transm_coil; transm_coil=0; if(receiv_coil) delete receiv_coil; receiv_coil=0; coil_cache_up2date=false; } /////////////////////////////////////////////////////////////// STD_ostream& operator << (STD_ostream& os, const SeqPlotCurve& spc) { os << "---------------------------------------------" << STD_endl; os << "label=" << spc.label << " "; os << "channel=" << spc.channel << " "; os << "spikes=" << spc.spikes << " "; os << STD_endl; for(unsigned int i=0; ix.size(); if(!curvesize) return false; double curvestart=start+ptr->x[0]; double curveend =start+ptr->x[curvesize-1]; return( (curvestart<=timep) && (timep<=curveend) ); } double SeqPlotCurveRef::interpolate_timepoint(double timep) const { double result=0.0; unsigned int curvesize=ptr->x.size(); for(unsigned int i=0; i<(curvesize-1); i++) { double curr_x=start+ptr->x[i]; double next_x=start+ptr->x[i+1]; double curr_y=ptr->y[i]; double next_y=ptr->y[i+1]; if(timep==curr_x) { if(curr_x==next_x) result=STD_max(curr_y,next_y); else result=curr_y; break; } if(timep==next_x) { result=next_y; break; } if(!ptr->spikes && curr_xchannel; bool src_is_gradchan= ( (src_channel>=Gread_plotchan) && (src_channel<=Gslice_plotchan) ); if(src_is_gradchan && gradmatrix) { for(int target_channel=Gread_plotchan; target_channel<=Gslice_plotchan; target_channel++) { double rotfactor=(*gradmatrix)[target_channel-Gread_plotchan][src_channel-Gread_plotchan]; sp.val[target_channel]+=rotfactor*value; } } else { sp.val[src_channel]+=value; } if(has_freq_phase) { sp.val[freq_plotchan]=freq; sp.val[phase_plotchan]=phase; } } ///////////////////////////////////////////////////////////////////////////////////////////// struct CurvePointRef { CurvePointRef() : curveref(0), index(0) {} const SeqPlotCurveRef* curveref; int index; }; ///////////////////////////////////////////////////////////////////////////////////////////// struct FrameTimepoint { FrameTimepoint(double timep, plotChannel curvechannel, const SeqPlotCurveRef* curve, int curveindex) : t(timep), markerref(0) { curve_point[curvechannel].curveref=curve; curve_point[curvechannel].index=curveindex; } FrameTimepoint(double timep, const SeqPlotCurveRef* marker) : t(timep), markerref(marker) {} double t; CurvePointRef curve_point[numof_plotchan]; const SeqPlotCurveRef* markerref; bool contains_curve(const SeqPlotCurveRef* curve) const { for(int ichan=0; ichan& synclist, double framestart) const { STD_list::const_iterator refit; STD_list::const_iterator tpit; int ichan; STD_list timepoints_in_frame; // create a list of all timepoints and the corresponding curves for(refit=begin(); refit!=end(); ++refit) { const SeqPlotCurve& plotcurve=*(refit->ptr); unsigned int curvesize=plotcurve.x.size(); for(unsigned int i=0; istart+plotcurve.x[i]; timepoints_in_frame.push_back(FrameTimepoint(curve_timepoint_in_frame, plotcurve.channel, &(*refit),i)); } if(plotcurve.marker!=no_marker) { double marker_timepoint_in_frame=refit->start+plotcurve.marker_x; timepoints_in_frame.push_back(FrameTimepoint(marker_timepoint_in_frame, &(*refit))); } } timepoints_in_frame.sort(); STD_list merged_timepoints_in_frame; // merge timepoints with the same time tpit=timepoints_in_frame.begin(); while(tpit!=timepoints_in_frame.end()) { FrameTimepoint ft=(*tpit); ++tpit; while(tpit!=timepoints_in_frame.end() && ft.merge(*tpit)) ++tpit; merged_timepoints_in_frame.push_back(ft); } // create syncpoints from the list of timepoints for(tpit=merged_timepoints_in_frame.begin(); tpit!=merged_timepoints_in_frame.end(); ++tpit) { double syncpoint_timepoint_in_frame=tpit->t; SeqPlotSyncPoint sp(framestart+syncpoint_timepoint_in_frame); // deal with curves that are explicitely part of the TimePoint for(ichan=0; ichancurve_point[ichan].curveref; if(curveref) { int curveindex=tpit->curve_point[ichan].index; double value=curveref->ptr->y[curveindex]; curveref->copy_to_syncpoint(sp,value); } } // interpolate remaining curves for(refit=begin(); refit!=end(); ++refit) { if(!tpit->contains_curve(&(*refit))) { if(refit->contains_timepoint(syncpoint_timepoint_in_frame)) { double value=refit->interpolate_timepoint(syncpoint_timepoint_in_frame); refit->copy_to_syncpoint(sp,value); } } } // deal with marker if(tpit->markerref) { sp.marker=tpit->markerref->ptr->marker; sp.marklabel=tpit->markerref->ptr->label; } synclist.push_back(sp); } } double SeqPlotFrame::get_latest_point() const { double result=0.0; for(STD_list::const_iterator refit=begin(); refit!=end(); ++refit) { const SeqPlotCurve& plotcurve=*(refit->ptr); unsigned int curvesize=plotcurve.x.size(); if(curvesize) { double latest=refit->start+plotcurve.x[curvesize-1]; if(latest>result) result=latest; } } return result; } ///////////////////////////////////////////////////////////////// void SeqTimecourse::allocate(unsigned int allocsize) { size=allocsize; x=new double[allocsize]; for(int ichan=0; ichan& synclist, const SeqTimecourse* eddy_tcourse, ProgressMeter* progmeter) : signal_x(0), signal_y(0) { Log odinlog("SeqTimecourse",""); allocate(synclist.size()); if(eddy_tcourse) ODINLOG(odinlog,normalDebug) << "eddy_tcourse->size=" << eddy_tcourse->size << STD_endl; else ODINLOG(odinlog,normalDebug) << "no eddy_tcourse" << STD_endl; unsigned int index=0; int ichan; for(STD_list::const_iterator syncit=synclist.begin(); syncit!=synclist.end(); ++syncit) { x[index]=syncit->timep; for(ichan=0; ichanval[ichan]; if(eddy_tcourse && ichan>=Gread_plotchan && ichan<=Gslice_plotchan) { y[ichan][index]+=eddy_tcourse->y[ichan][index]; } } if(syncit->val[rec_plotchan]>0.0) n_rec_points++; if(progmeter) progmeter->increase_counter(); index++; } create_marker_values(synclist,progmeter); } void SeqTimecourse::create_marker_values(const STD_list& synclist, ProgressMeter* progmeter) { markers.clear(); unsigned int index=0; for(STD_list::const_iterator syncit=synclist.begin(); syncit!=synclist.end(); ++syncit) { if(syncit->marker!=no_marker) { TimecourseMarker4Qwt tm4q; tm4q.x=x[index]; for(int ichan=0; ichanmarker; markers.push_back(tm4q); } index++; if(progmeter) progmeter->refresh_display(); } markers.reset_subcache(); } SeqTimecourse::~SeqTimecourse() { if(x) delete x; for(int i=0; itimepoint) break; } if(x[result]>timepoint) { while(result!=0 && x[result]>timepoint) result--; } else { while(result odinlog("SeqTimecourse","get_subtimecourse"); static SeqTimecourseData result; if(!size) return &result; unsigned int beginindex=get_index(starttime); unsigned int endindex=get_index(endtime); if(beginindex>EXTRA_TIMECOURSE_POINTS) beginindex-=EXTRA_TIMECOURSE_POINTS; else beginindex=0; if(endindex<(size-EXTRA_TIMECOURSE_POINTS)) endindex +=EXTRA_TIMECOURSE_POINTS; else endindex=size-1; result.size=endindex-beginindex; result.x=&(x[beginindex]); for(int i=0; iget_geometry().get_gradrotmatrix(true)); Nuclei nuc; float gamma=nuc.get_gamma(method->get_main_nucleus()); unsigned int ichan,nchan=1; CoilSensitivity* rec_coil=opts.get_receiv_coil(); if(rec_coil) nchan=rec_coil->get_numof_channels(); signal_label.resize(nchan); for(ichan=0; ichan endacqindices; // create cache for simulation mag.prepare_simulation(sample,opts.get_transm_coil(),opts.get_receiv_coil(),progmeter); magplot.prepare_simulation(sampleplot); // prepare noise generator, do this after 'prepare_simulation()' RandomDist noisegen; double noisefactor=0.01*opts.ReceiverNoise; float noisedev=0.0; if(noisefactor>0.0) { float sdsum=sample.get_spinDensity().sum(); noisedev=noisefactor*sdsum; ODINLOG(odinlog,normalDebug) << "noisefactor/sdsum/noisedev=" << noisefactor << "/" << sdsum << "/" << noisedev << STD_endl; } progmeter->new_task(size,"Simulating NMR Signal"); cvector signal; Profiler* prof=new Profiler("simulate"); // iterate through list of syncpoints i=0; for(STD_list::const_iterator syncit=synclist.begin(); syncit!=synclist.end(); ++syncit) { y[signal_plotchan][i]=0.0; if(i) { SeqSimInterval simvals; simvals.dt=x[i]-x[i-1]; // simvals.t=0.5*(x[i]+x[i-1]); double B1re= 0.5*(y[B1re_plotchan][i] +y[B1re_plotchan][i-1]); double B1im= 0.5*(y[B1im_plotchan][i] +y[B1im_plotchan][i-1]); simvals.B1=STD_complex(B1re,B1im); simvals.freq= 0.5*(y[freq_plotchan][i] +y[freq_plotchan][i-1]); simvals.phase=0.5*(y[phase_plotchan][i] +y[phase_plotchan][i-1]); simvals.Gx= 0.5*(y[Gread_plotchan][i] +y[Gread_plotchan][i-1]); simvals.Gy= 0.5*(y[Gphase_plotchan][i]+y[Gphase_plotchan][i-1]); simvals.Gz= 0.5*(y[Gslice_plotchan][i]+y[Gslice_plotchan][i-1]); simvals.rec=y[rec_plotchan][i]; // acquire at end of simulation interval signal=mag.simulate(simvals,gamma); if(feedback) { float Mvec[3]; float dM[3]; double max_dt_fields=0.050; if( (cabs(simvals.B1) || simvals.Gx || simvals.Gy || simvals.Gz) && (simvals.dt>max_dt_fields) ) { unsigned int n_sub_dt=(unsigned int)(simvals.dt/max_dt_fields+0.5); simvals.dt=secureDivision(simvals.dt,n_sub_dt); ODINLOG(odinlog,normalDebug) << "splitting simulation into " << n_sub_dt << " sub intervals at t=" << x[i] << STD_endl; for(unsigned int isub=0; isubplot_vector(x[i-1]+isub*simvals.dt,Mvec,dM); } else feedback->plot_vector(x[i-1]+isub*simvals.dt,Mvec,0); progmeter->refresh_display(); } } else { magplot.simulate(simvals,gamma); Mvec[0]=magplot.get_Mx()[0]; Mvec[1]=magplot.get_My()[0]; Mvec[2]=magplot.get_Mz()[0]; float timestamp=0.5*(x[i]+x[i-1]); if(opts.IntraVoxelMagnGrads) { dM[0]=magplot.dMx[0][0]; dM[1]=magplot.dMy[0][0]; dM[2]=magplot.dMz[0][0]; feedback->plot_vector(timestamp,Mvec,dM); } feedback->plot_vector(timestamp,Mvec,0); } } if(simvals.rec>0.0) { // add noise to the signal if(noisedev>0.0) { for(ichan=0; ichanmarker==endacq_marker) { endacqindices.push_back(recindex); for(ichan=0; ichanmarker==snapshot_marker) { STD_string snap_fname(syncit->marklabel); if(snap_fname!="") { unsigned int totalsize=mag.get_total_size(); ODINLOG(odinlog,normalDebug) << "dumping snapshot at " << x[i] << ODIN_TIME_UNIT << " of size " << totalsize << " to file " << syncit->marklabel << STD_endl; fvector dumpmagn(3*totalsize); fvector data; unsigned int offset=0; unsigned int i; data=mag.get_Mx(); for(i=0; imarker==reset_marker) mag.reset_magnetization(); } progmeter->increase_counter(); i++; } mag.finalize_simulation(); // transfer signal curves to plotting window unsigned int last_endof_acq=0; for(STD_list::const_iterator it=endacqindices.begin(); it!=endacqindices.end(); ++it) { unsigned int acqwindow_size=(*it)-last_endof_acq; unsigned int acqwindow_start=last_endof_acq; ODINLOG(odinlog,normalDebug) << "endof_acq n_rec_points/start/size=" << n_rec_points << "/" << acqwindow_start << "/" << acqwindow_size << STD_endl; for(ichan=0; ichanadd_signal_curve(signal_curve); } last_endof_acq=(*it); } delete prof; delete[] acqresult; return true; } ///////////////////////////////////////////////////////////////// template SeqGradMomentTimecourse::SeqGradMomentTimecourse(const STD_list& synclist, const SeqTimecourse& plain_tcourse, const STD_string& nucleus, ProgressMeter* progmeter) : SeqTimecourse(plain_tcourse) { allocate(size); // allocate new arrays int igrad,ichan; Nuclei n; double gamma=n.get_gamma(nucleus); double tau[3]; for(igrad=0; igrad<3; igrad++) tau[igrad]=0.0; double moment_integral[3]; for(igrad=0; igrad<3; igrad++) moment_integral[igrad]=0.0; unsigned int index=0; for(STD_list::const_iterator syncit=synclist.begin(); syncit!=synclist.end(); ++syncit) { x[index]=plain_tcourse.x[index]; double x1=x[index]; double x0=0.0; if(index) x0=x[index-1]; double dx=x1-x0; bool active_transverse=true; for(ichan=0; ichan=Gread_plotchan && ichan<=Gslice_plotchan) { int gradchan=ichan-Gread_plotchan; if(active_transverse) { double y0=0.0; double y1=0.0; if(ConstGrad) { y0=1.0; y1=1.0; } else { y1=plain_tcourse.y[ichan][index]; if(index) y0=plain_tcourse.y[ichan][index-1]; } double dy=y1-y0; double m=secureDivision(dy,dx); double x0_tau=tau[gradchan]; double x1_tau=tau[gradchan]+dx; double moment_increment= m/double(Nth_moment+2)*(pow(x1_tau,Nth_moment+2)-pow(x0_tau,Nth_moment+2)); moment_increment+=(y0-m*x0_tau)/double(Nth_moment+1)*(pow(x1_tau,Nth_moment+1)-pow(x0_tau,Nth_moment+1)); moment_integral[gradchan]+=gamma*moment_increment; } if(syncit->marker==excitation_marker) { // reset moment_integral[gradchan]=0.0; tau[gradchan]=0.0; active_transverse=true; } if(syncit->marker==refocusing_marker || syncit->marker==recallMagn_marker) { // invert phase moment_integral[gradchan]=-moment_integral[gradchan]; active_transverse=true; } if(syncit->marker==storeMagn_marker) { // disable accumulation of integral active_transverse=false; } y[ichan][index]=moment_integral[gradchan]; tau[gradchan]+=dx; } } if(progmeter) progmeter->increase_counter(); index++; } create_marker_values(synclist,progmeter); } //////////////////////////////////////////////////////////// SeqTwoFuncIntegralTimecourse::SeqTwoFuncIntegralTimecourse(const STD_list& synclist, const SeqTimecourse& ka_tcourse, const SeqTimecourse& kb_tcourse, ProgressMeter* progmeter) : SeqTimecourse(ka_tcourse) { allocate(size); // allocate new arrays int igrad,ichan; double integral[3]; for(igrad=0; igrad<3; igrad++) integral[igrad]=0.0; unsigned int index=0; for(STD_list::const_iterator syncit=synclist.begin(); syncit!=synclist.end(); ++syncit) { x[index]=ka_tcourse.x[index]; double x1=x[index]; double x0=0.0; if(index) x0=x[index-1]; double dx=x1-x0; for(ichan=0; ichan=Gread_plotchan && ichan<=Gslice_plotchan) { int gradchan=ichan-Gread_plotchan; double ka1=ka_tcourse.y[ichan][index]; double kb1=kb_tcourse.y[ichan][index]; double ka0=0.0; double kb0=0.0; if(index) { ka0=ka_tcourse.y[ichan][index-1]; kb0=kb_tcourse.y[ichan][index-1]; } double dka=ka1-ka0; double dkb=kb1-kb0; double incr = ( (6.0*dx*ka0 + 3.0*dka*dx)*kb0 + 3.0*dkb*dx*ka0 + 2.0*dka*dkb*dx) / 6.0; // integrate((ka0+x/dx*dka)*(kb0+x/dx*dkb),x,0,dx); // double incr = dx * ( k0*k0 + k0*dk + dk*dk/3.0 ); // integrate((kval_last+t/dx*dk)^2,t,0,dx); integral[gradchan]+= incr; y[ichan][index]=integral[gradchan]; if(syncit->marker==excitation_marker) { integral[gradchan]=0.0; } } } if(progmeter) progmeter->increase_counter(); index++; } create_marker_values(synclist,progmeter); } //////////////////////////////////////////////////////////// SeqSlewRateTimecourse::SeqSlewRateTimecourse(const STD_list& synclist, const SeqTimecourse& plain_tcourse, ProgressMeter* progmeter) : SeqTimecourse(plain_tcourse) { allocate(size); // allocate new arrays int ichan; double maxslewrate=SeqMethodProxy()->get_systemInfo().get_max_slew_rate(); unsigned int index=0; for(STD_list::const_iterator syncit=synclist.begin(); syncit!=synclist.end(); ++syncit) { x[index]=plain_tcourse.x[index]; double x1=x[index]; double x0=0.0; if(index) x0=x[index-1]; double dx=x1-x0; for(ichan=0; ichan=Gread_plotchan && ichan<=Gslice_plotchan) { double y1=plain_tcourse.y[ichan][index]; double y0=0.0; if(index) y0=plain_tcourse.y[ichan][index-1]; double dy=y1-y0; double sr=secureDivision(dy,dx); if(fabs(sr)>maxslewrate) { double sign=secureDivision(sr,fabs(sr)); sr=sign*maxslewrate; } y[ichan][index]=sr; } } if(progmeter) progmeter->increase_counter(); index++; } create_marker_values(synclist,progmeter); } //////////////////////////////////////////////////////////// SeqEddyCurrentTimecourse::SeqEddyCurrentTimecourse(const STD_list& synclist, const SeqTimecourse& slew_rate_tcourse, const SeqTimecourseOpts& opts, ProgressMeter* progmeter) : SeqTimecourse(slew_rate_tcourse) { Log odinlog("SeqEddyCurrentTimecourse",""); allocate(size); // allocate new arrays double ec_ampl=opts.EddyCurrentAmpl/100.0; double ec_time=opts.EddyCurrentTimeConst; ODINLOG(odinlog,normalDebug) << "ec_time/ec_ampl=" << ec_time << "/" << ec_ampl << STD_endl; int ichan; for(unsigned int index=0; index=Gread_plotchan && ichan<=Gslice_plotchan) { double x1=x[index]; double x0=0.0; if(index) x0=x[index-1]; double dx=x1-x0; // eddy currents induced by the previous interval double additional_eddy_currents = - ec_ampl * slew_rate_tcourse.y[ichan][index] * dx; double decay_factor = exp(-dx/ec_time); y[ichan][index]=0.0; if(index) y[ichan][index]=decay_factor * y[ichan][index-1] + additional_eddy_currents; } } if(progmeter) progmeter->increase_counter(); } create_marker_values(synclist,progmeter); } //////////////////////////////////////////////////////////// SeqPlotData::SeqPlotData(const STD_string& objlabel) : Labeled(objlabel.c_str()), curves4qwt_cache_done(false), markers4qwt_cache_done(false), synclist_cache_done(false) { for(int itc=0; itc odinlog("SeqPlotData","flush_frame"); double latest=current_frame.get_latest_point(); double framedur_total=framestart_offset+framedur; double diff=latest-framedur_total; ODINLOG(odinlog,normalDebug) << "latest/framedur_total/diff=" << latest << "/" << framedur_total << "/" << diff << STD_endl; if(diff>1e-6) { // check whether there are remaining points leaping into next frame framestart_offset+=framedur; } else { unsigned int framesize=current_frame.size(); ODINLOG(odinlog,normalDebug) << "appending frame with size=" << framesize << STD_endl; if(framesize || framedur_total>0.0) { current_frame.frameduration=framedur_total; push_back(current_frame); } current_frame.clear(); framestart_offset=0.0; } } void SeqPlotData::reset() { Log odinlog("SeqPlotData","reset"); ODINLOG(odinlog,normalDebug) << "mem(pre )=" << Profiler::get_memory_usage() << STD_endl; STD_list::clear(); ODINLOG(odinlog,normalDebug) << "size()=" << size() << STD_endl; current_frame.clear(); signal_curves.reset(); framestart_offset=0.0; clear_curves4qwt_cache(); curves4qwt_cache_done=false; clear_markers4qwt_cache(); markers4qwt_cache_done=false; clear_synclist_cache(); for(int itc=0; itc::iterator qwtit; for(qwtit=curves4qwt_cache.begin(); qwtit!=curves4qwt_cache.end(); ++qwtit) { if(qwtit->x) delete[] qwtit->x; if(qwtit->y) delete[] qwtit->y; } curves4qwt_cache.clear(); for(qwtit=curves4qwt_cache_lowres.begin(); qwtit!=curves4qwt_cache_lowres.end(); ++qwtit) { if(qwtit->x) delete[] qwtit->x; if(qwtit->y) delete[] qwtit->y; } curves4qwt_cache_lowres.clear(); } void SeqPlotData::clear_markers4qwt_cache() const { markers4qwt_cache.clear(); } void SeqPlotData::clear_synclist_cache() const { synclist_cache.clear(); synclist_cache_done=false; } void SeqPlotData::clear_timecourse_cache(timecourseMode type) const { Log odinlog("SeqPlotData","clear_timecourse_cache"); ODINLOG(odinlog,normalDebug) << "timecourse_cache[" << type << "]=" << timecourse_cache[type] << STD_endl; if(timecourse_cache[type]) delete timecourse_cache[type]; timecourse_cache[type]=0; } void SeqPlotData::create_curves4qwt_cache() const { if(curves4qwt_cache_done) return; clear_curves4qwt_cache(); double framestart=0.0; int i; for(int ichan=0; ichan::const_iterator frameit=begin(); frameit!=end(); ++frameit) { for(STD_list::const_iterator refit=frameit->begin(); refit!=frameit->end(); ++refit) { int curvesize=refit->ptr->x.size(); if(curvesize) { Curve4Qwt c4q; c4q.label=refit->ptr->label; c4q.channel=refit->ptr->channel; c4q.size=curvesize+2; // create points with y=0 at beginning/end of curve c4q.spikes=refit->ptr->spikes; c4q.x=new double[c4q.size]; c4q.y=new double[c4q.size]; double min_y=0.0; double max_y=0.0; for(i=0; istart+refit->ptr->x[i]; double yval=refit->ptr->y[i]; c4q.y[i+1]=yval; if(yvalmax_y) max_y=yval; } // points at beginning/end of curve c4q.x[0]=c4q.x[1]; c4q.y[0]=0.0; c4q.x[c4q.size-1]=c4q.x[c4q.size-2]; c4q.y[c4q.size-1]=0.0; c4q.has_freq_phase=refit->has_freq_phase; c4q.freq=refit->freq; c4q.phase=refit->phase; c4q.gradmatrix=refit->gradmatrix; curves4qwt_cache.push_back(c4q); STD_list lowres_x; STD_list lowres_y; lowres_x.push_back(c4q.x[0]); lowres_y.push_back(c4q.y[0]); for(i=1; i<(c4q.size-1); i++) { double last_y=c4q.y[i-1]; double curr_y=c4q.y[i]; double next_y=c4q.y[i+1]; bool significant_point=false; if(last_y<=curr_y && next_y=curr_y && next_y>curr_y) significant_point=true; if(last_ycurr_y && next_y>=curr_y) significant_point=true; if(significant_point) { lowres_x.push_back(c4q.x[i]); lowres_y.push_back(c4q.y[i]); } } lowres_x.push_back(c4q.x[c4q.size-1]); lowres_y.push_back(c4q.y[c4q.size-1]); Curve4Qwt c4q_lowres; c4q_lowres=c4q; c4q_lowres.size=lowres_x.size(); c4q_lowres.x=new double[c4q_lowres.size]; c4q_lowres.y=new double[c4q_lowres.size]; i=0; STD_list::const_iterator yit=lowres_y.begin(); for(STD_list::const_iterator xit=lowres_x.begin(); xit!=lowres_x.end(); ++xit) { c4q_lowres.x[i]=(*xit); c4q_lowres.y[i]=(*yit); i++; ++yit; } curves4qwt_cache_lowres.push_back(c4q_lowres); has_curves_on_channel_cache[c4q.channel]=true; } } framestart+=frameit->frameduration; } curves4qwt_cache.reset_subcache(); curves4qwt_cache_lowres.reset_subcache(); curves4qwt_cache_done=true; } void SeqPlotData::get_curves(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime, double max_highres_interval ) const { Log odinlog("SeqPlotData","get_curves"); create_curves4qwt_cache(); double interval=endtime-starttime; if(interval>max_highres_interval) { curves4qwt_cache_lowres.get_sublist(result_begin, result_end, starttime, endtime); } else { curves4qwt_cache.get_sublist(result_begin, result_end, starttime, endtime); } } void SeqPlotData::get_signal_curves(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const { Log odinlog("SeqPlotData","get_signal_curves"); ODINLOG(odinlog,normalDebug) << "size()=" << signal_curves.size() << STD_endl; signal_curves.get_sublist(result_begin, result_end, starttime, endtime); } void SeqPlotData::create_markers4qwt_cache() const { clear_markers4qwt_cache(); double framestart=0.0; for(STD_list::const_iterator frameit=begin(); frameit!=end(); ++frameit) { for(STD_list::const_iterator refit=frameit->begin(); refit!=frameit->end(); ++refit) { if((refit->ptr->marker)!=no_marker) { Marker4Qwt m4q; m4q.label=refit->ptr->marklabel; m4q.x=framestart+refit->start+refit->ptr->marker_x; m4q.type=refit->ptr->marker; markers4qwt_cache.push_back(m4q); } } framestart+=frameit->frameduration; } markers4qwt_cache.reset_subcache(); markers4qwt_cache_done=true; } void SeqPlotData::get_markers(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const { Log odinlog("SeqPlotData","get_markers"); if(!markers4qwt_cache_done) create_markers4qwt_cache(); markers4qwt_cache.get_sublist(result_begin, result_end, starttime, endtime); } void SeqPlotData::create_synclist_cache(ProgressMeter* progmeter) const { Log odinlog("SeqPlotData","create_synclist_cache"); clear_synclist_cache(); SeqPlotSyncPoint sp_start(0.0); synclist_cache.push_back(sp_start); SeqPlotSyncPoint sp_frameend(0.0); double framestart=0.0; for(STD_list::const_iterator frameit=begin(); frameit!=end(); ++frameit) { frameit->append_syncpoints(synclist_cache,framestart); framestart+=frameit->frameduration; sp_frameend.timep=framestart; synclist_cache.push_back(sp_frameend); if(progmeter) progmeter->increase_counter(); } SeqPlotSyncPoint sp_end(framestart); synclist_cache.push_back(sp_end); synclist_cache_done=true; } void SeqPlotData::create_timecourse_cache(timecourseMode type, const STD_string& nucleus, ProgressMeter* progmeter) const { Log odinlog("SeqPlotData","create_timecourse_cache"); clear_timecourse_cache(type); SeqTimecourse* result=0; // exception safe unsigned int tcourse_size=synclist_cache.size(); STD_string progtxt=STD_string("Creating ")+timecourseLabel[type]+" Timecourse"; if(type==tcmode_plain) { create_timecourses(tcmode_eddy_currents,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqTimecourse(synclist_cache,timecourse_cache[tcmode_eddy_currents],progmeter); } if(type==tcmode_kspace) { create_timecourses(tcmode_plain,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqGradMomentTimecourse<0>(synclist_cache,*(timecourse_cache[tcmode_plain]),nucleus,progmeter); } if(type==tcmode_M1) { create_timecourses(tcmode_plain,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqGradMomentTimecourse<1>(synclist_cache,*(timecourse_cache[tcmode_plain]),nucleus,progmeter); } if(type==tcmode_M2) { create_timecourses(tcmode_plain,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqGradMomentTimecourse<2>(synclist_cache,*(timecourse_cache[tcmode_plain]),nucleus,progmeter); } if(type==tcmode_b_trace) { create_timecourses(tcmode_kspace,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqTwoFuncIntegralTimecourse(synclist_cache,*(timecourse_cache[tcmode_kspace]),*(timecourse_cache[tcmode_kspace]),progmeter); } if(type==tcmode_backgr_kspace) { create_timecourses(tcmode_plain,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqGradMomentTimecourse<0,true>(synclist_cache,*(timecourse_cache[tcmode_plain]),nucleus,progmeter); } if(type==tcmode_backgr_crossterm) { create_timecourses(tcmode_kspace,nucleus,progmeter); create_timecourses(tcmode_backgr_kspace,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqTwoFuncIntegralTimecourse(synclist_cache,*(timecourse_cache[tcmode_kspace]),*(timecourse_cache[tcmode_backgr_kspace]),progmeter); } if(type==tcmode_slew_rate) { SeqTimecourse* plain_tc_without_eddy_currents=new SeqTimecourse(synclist_cache,0,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqSlewRateTimecourse(synclist_cache,*plain_tc_without_eddy_currents,progmeter); delete plain_tc_without_eddy_currents; } if(type==tcmode_eddy_currents) { if(timecourse_opts.EddyCurrentAmpl>0.0 && timecourse_opts.EddyCurrentTimeConst>0.0) { create_timecourses(tcmode_slew_rate,nucleus,progmeter); if(progmeter) progmeter->new_task(tcourse_size,progtxt.c_str()); result=new SeqEddyCurrentTimecourse(synclist_cache,*(timecourse_cache[tcmode_slew_rate]),timecourse_opts,progmeter); } } ODINLOG(odinlog,normalDebug) << "result[" << type << "]=" << result << STD_endl; timecourse_cache[type]=result; } bool SeqPlotData::create_timecourses(timecourseMode type, const STD_string& nucleus, ProgressMeter* progmeter) const { Log odinlog("SeqPlotData","create_timecourses"); if(!synclist_cache_done) create_synclist_cache(progmeter); if(!timecourse_cache[type]) create_timecourse_cache(type, nucleus, progmeter); return bool(timecourse_cache[type]); } const SeqTimecourseData* SeqPlotData::get_timecourse(timecourseMode type) const { return timecourse_cache[type]; } const SeqTimecourseData* SeqPlotData::get_subtimecourse(timecourseMode type, double starttime, double endtime) const { if(timecourse_cache[type]) return timecourse_cache[type]->get_subtimecourse(starttime, endtime); return 0; } void SeqPlotData::get_timecourse_markers(timecourseMode type, STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const { if(timecourse_cache[type]) timecourse_cache[type]->get_markers(result_begin,result_end,starttime,endtime); } double SeqPlotData::get_total_duration() const { double result=0.0; for(STD_list::const_iterator frameit=begin(); frameit!=end(); ++frameit) { result+=frameit->frameduration; } return result; } unsigned int SeqPlotData::numof_rec_channels() const { unsigned int result=1; CoilSensitivity* rec_coil=sim_opts.get_receiv_coil(); if(rec_coil) result=rec_coil->get_numof_channels(); return result; } JcampDxBlock& SeqPlotData::get_opts(bool include_timecourse_opts, bool include_simulation_opts) const { all_opts.clear(); all_opts.set_label("Options"); if(include_timecourse_opts) all_opts.merge(timecourse_opts); if(include_simulation_opts) { all_opts.merge(sim_opts); sim_opts.outdate_coil_cache(); // might be changed } return all_opts; } void SeqPlotData::set_coilsdir(const STD_string& coilsdir) const { sim_opts.TransmitterCoil.set_defaultdir(coilsdir); sim_opts.ReceiverCoil.set_defaultdir(coilsdir); } bool SeqPlotData::simulate(const STD_string& fidfile, const STD_string& samplefile, ProgressMeter* progmeter, SeqSimFeedbackAbstract* feedback) const { if(!create_timecourses(tcmode_plain,"",progmeter)) return false; return timecourse_cache[tcmode_plain]->simulate(synclist_cache,fidfile,samplefile,sim_opts,progmeter,feedback,this); } bool SeqPlotData::has_curves_on_channel(plotChannel chan) const { create_curves4qwt_cache(); return has_curves_on_channel_cache[chan]; } odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqtrigg_standalone.h0000644000175000017500000000422711735135552023532 00000000000000/*************************************************************************** seqtrigg_standalone.h - description ------------------- begin : Mon Apr 12 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQTRIGG_STANDALONE_H #define SEQTRIGG_STANDALONE_H #include #include "seqstandalone.h" ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for external trigger events */ class SeqTriggerStandAlone : public SeqTriggerDriver, public SeqStandAlone { public: SeqTriggerStandAlone() {} SeqTriggerStandAlone(const SeqTriggerStandAlone& sts) {set_label(sts.get_label());} ~SeqTriggerStandAlone() {} // overloading virtual functions from SeqTriggerDriver double get_postduration() const {return 0.0;} bool prep_exttrigger(double duration); bool prep_halttrigger(); bool prep_snaptrigger(const STD_string& snapshot_fname); bool prep_resettrigger(); void event(eventContext& context, double startelapsed) const; STD_string get_program(programContext& context) const {return "";} SeqTriggerDriver* clone_driver() const {return new SeqTriggerStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} private: SeqPlotCurve trigg_marker; }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqacqepi_standalone.h0000644000175000017500000000224111735135552023652 00000000000000/*************************************************************************** seqacqepi_standalone.h - description ------------------- begin : Fri Jul 23 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQACQEPI_STANDALONE_H #define SEQACQEPI_STANDALONE_H #include // empty, because SeqEpiDriverDefault is used #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqlist_standalone.h0000644000175000017500000000461111735135552023366 00000000000000/*************************************************************************** seqlist_standalone.h - description ------------------- begin : Sat Apr 17 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQLIST_STANDALONE_H #define SEQLIST_STANDALONE_H #include #include "seqstandalone.h" ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for lists of sequence objects */ class SeqListStandAlone : public SeqListDriver, public SeqStandAlone { public: SeqListStandAlone() {} SeqListStandAlone(const SeqListStandAlone& sls) {set_label(sls.get_label());} ~SeqListStandAlone() {} // overloading virtual functions from SeqListDriver STD_string pre_program (programContext& context, const SeqRotMatrixVector* rotmats) const {return "";} STD_string post_program(programContext& context, const SeqRotMatrixVector* rotmats) const {return "";} STD_string get_itemprogram(const SeqTreeObj* item, programContext& context) const {return "";} void pre_event (eventContext& context, const RotMatrix* rotmatrix) const; void post_event(eventContext& context, const RotMatrix* rotmatrix) const; void pre_itemevent (const SeqTreeObj* item, eventContext& context) const; void post_itemevent(const SeqTreeObj* item, eventContext& context) const; bool prep_driver() {return true;} SeqListDriver* clone_driver() const {return new SeqListStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqpuls_standalone.h0000644000175000017500000000531411735135552023377 00000000000000/*************************************************************************** seqpuls_standalone.h - description ------------------- begin : Sat Apr 3 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPULS_STANDALONE_H #define SEQPULS_STANDALONE_H #include #include "seqstandalone.h" ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for RF pulses */ class SeqPulsStandAlone : public SeqPulsDriver, public SeqStandAlone { public: SeqPulsStandAlone() {current_pls=0;} ~SeqPulsStandAlone() {} SeqPulsStandAlone(const SeqPulsStandAlone& sps); // overloading virtual functions from SeqPulsDriver bool prep_driver(const cvector& wave, double pulsduration, double pulscenter, float b1max, float power, float flipangle, const fvector& flipscales, pulseType plstype); void event(eventContext& context, double start) const; double get_rf_energy() const {return rf_energy[current_pls];} bool prep_flipangle_iteration(unsigned int count); double get_predelay() const {return 0.0;} double get_postdelay() const {return 0.0;} STD_string get_program(programContext& context, unsigned int phaselistindex,int channel, const STD_string& iteratorcommand) const {return "";} STD_string get_instr_label() const {return "";} svector get_flipvector_commands(const STD_string& iterator) const {return svector();} void new_freq(double newfreq) const {} bool has_new_freq() const {return true;} SeqPulsDriver* clone_driver() const {return new SeqPulsStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} private: STD_vector B1re_curve; STD_vector B1im_curve; dvector rf_energy; unsigned int current_pls; bool has_real; bool has_imag; STD_string relabel,imlabel; }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqplot_standalone.h0000644000175000017500000003613711735135552023401 00000000000000/*************************************************************************** seqplot_standalone.h - description ------------------- begin : Fri Jul 23 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPLOT_STANDALONE_H #define SEQPLOT_STANDALONE_H #include #include #include #define TIMECOURSE_HASH_INTERVAL 100 #define EXTRA_UPDOWN_ITERATIONS 5 #define EXTRA_TIMECOURSE_POINTS 2 ///////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Data structure to hold parameters for timecourse generation */ struct SeqTimecourseOpts : public JcampDxBlock { SeqTimecourseOpts(); JDXdouble EddyCurrentAmpl; JDXdouble EddyCurrentTimeConst; }; ///////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Data structure to hold parameters for simulation */ struct SeqSimulationOpts : public JcampDxBlock { SeqSimulationOpts(); ~SeqSimulationOpts() {outdate_coil_cache();} JDXint SimThreads; JDXbool IntraVoxelMagnGrads; JDXbool MagnMonitor; JDXdouble ReceiverNoise; JDXfileName TransmitterCoil; JDXfileName ReceiverCoil; JDXtriple InitialMagnVector; CoilSensitivity* get_transm_coil() const {update_coil_cache(); return transm_coil;} CoilSensitivity* get_receiv_coil() const {update_coil_cache(); return receiv_coil;} private: friend class SeqPlotData; void update_coil_cache() const; void outdate_coil_cache() const; mutable CoilSensitivity* transm_coil; mutable CoilSensitivity* receiv_coil; mutable bool coil_cache_up2date; }; ///////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Data structure to hold data for sequence plotting of a single 'sequence atom', e.g. an RF pulse */ struct SeqPlotCurve { SeqPlotCurve() : label(0), channel(plotChannel(0)), spikes(false), marklabel(0), marker(no_marker), marker_x(0.0) {} void resize(unsigned int newsize) {x.resize(newsize); y.resize(newsize);} bool operator == (const SeqPlotCurve& spc) const {return (channel==spc.channel) && (x==spc.x) && (y==spc.y);} friend STD_ostream& operator << (STD_ostream& os, const SeqPlotCurve& spc); const char* label; plotChannel channel; STD_vector x; STD_vector y; bool spikes; // values will not be interpolated between points const char* marklabel; markType marker; double marker_x; }; ///////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Data structure to hold a discrete value synchronously on all channels */ struct SeqPlotSyncPoint { SeqPlotSyncPoint(double timepoint) : timep(timepoint), marker(no_marker), marklabel(0) {for(int i=0; i { double frameduration; void append_syncpoints(STD_list& synclist, double framestart) const; double get_latest_point() const; }; ///////////////////////////////////////////////////// template class PlotList : public STD_list { public: PlotList() {reset_subcache();} void reset_subcache() { subbegin_cache=STD_list::begin(); subend_cache =STD_list::end(); } void reset() { STD_list::clear(); reset_subcache(); } typename STD_list::const_iterator& get_iterator(double timepoint, bool below ) const { Log odinlog("PlotList","get_iterator"); typename STD_list::const_iterator current_iterator; // take iterator from last call for fast scrolling through the the curves if(below) current_iterator=subbegin_cache; else current_iterator=subend_cache; // go one item back if we are already at the end if(current_iterator==STD_list::end()) --current_iterator; // maximum boundaries for the search typename STD_list::const_iterator lower_bound=STD_list::begin(); typename STD_list::const_iterator upper_bound=STD_list::end(); unsigned int niter=0; double current_timepoint=current_iterator->get_bounds(below); // iterate current_iterator while we are below the first boundary if(current_timepoint>timepoint) { while(current_iterator!=lower_bound && current_iterator->get_bounds(below)>timepoint) { --current_iterator; niter++; } } // iterate current_iterator while we are above the last boundary if(current_timepointget_bounds(below)::end(); result_end= STD_list::end(); if(starttime>=endtime) return; if(STD_list::begin() == STD_list::end()) return; result_begin=get_iterator(starttime,true); result_end =get_iterator(endtime,false); } private: mutable typename STD_list::const_iterator subbegin_cache; mutable typename STD_list::const_iterator subend_cache; }; ///////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Class to calculate plain timecourses */ class SeqTimecourse : public SeqTimecourseData { public: SeqTimecourse(const STD_list& synclist, const SeqTimecourse* eddy_tcourse, ProgressMeter* progmeter); ~SeqTimecourse(); const SeqTimecourseData* get_subtimecourse(double starttime, double endtime) const; void get_markers(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const; bool simulate(const STD_list& synclist, const STD_string& fidfile, const STD_string& samplefile, const SeqSimulationOpts& opts, ProgressMeter* progmeter, SeqSimFeedbackAbstract* feedback, const SeqPlotDataAbstract* plotdata) const; protected: void allocate(unsigned int allocsize); void create_marker_values(const STD_list& synclist, ProgressMeter* progmeter); private: unsigned int get_index(double timepoint) const; PlotList markers; // signal data used for for curves in Qwt mutable double* signal_x; mutable double** signal_y; // ptr2ptr for multi-channel coils mutable unsigned int signal_nchan; // cache for numof channels mutable svector signal_label; }; ////////////////////////////// /** * @ingroup odinseq_internals * Class to calculate gradient moments */ template class SeqGradMomentTimecourse : public SeqTimecourse { public: SeqGradMomentTimecourse(const STD_list& synclist, const SeqTimecourse& plain_tcourse, const STD_string& nucleus, ProgressMeter* progmeter); }; ////////////////////////////// /** * @ingroup odinseq_internals * Class to integrate the product of two functions, e.g. to calculate b-Values */ class SeqTwoFuncIntegralTimecourse : public SeqTimecourse { public: SeqTwoFuncIntegralTimecourse(const STD_list& synclist, const SeqTimecourse& ka_tcourse, const SeqTimecourse& kb_tcourse, ProgressMeter* progmeter); }; ////////////////////////////// /** * @ingroup odinseq_internals * Class to calculate gradient slew rates */ class SeqSlewRateTimecourse : public SeqTimecourse { public: SeqSlewRateTimecourse(const STD_list& synclist, const SeqTimecourse& plain_tcourse, ProgressMeter* progmeter); }; ////////////////////////////// /** * @ingroup odinseq_internals * Class to calculate gradients caused by eddy currents */ class SeqEddyCurrentTimecourse : public SeqTimecourse { public: SeqEddyCurrentTimecourse(const STD_list& synclist, const SeqTimecourse& slew_rate_tcourse, const SeqTimecourseOpts& opts, ProgressMeter* progmeter); }; ///////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Class which holds all frames of a sequence plot and which serves * as an interface to access the plotting data in various ways */ class SeqPlotData : public STD_list, public virtual SeqPlotDataAbstract, public Labeled { public: SeqPlotData(const STD_string& objlabel="unnamedSeqPlotData"); ~SeqPlotData() {reset();} void append_curve(double starttime, const SeqPlotCurve* curve_ptr) { current_frame.push_back(SeqPlotCurveRef(framestart_offset+starttime,curve_ptr)); } void append_curve(double starttime, const SeqPlotCurve* curve_ptr, double freq, double phase) { current_frame.push_back(SeqPlotCurveRef(framestart_offset+starttime,curve_ptr,freq,phase)); } void append_curve(double starttime, const SeqPlotCurve* curve_ptr, const RotMatrix* gradrotmatrix) { current_frame.push_back(SeqPlotCurveRef(framestart_offset+starttime,curve_ptr,gradrotmatrix)); } void flush_frame(double framedur); void reset(); void add_signal_curve(const Curve4Qwt& signal_curve) const; void get_curves(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime, double max_highres_interval ) const; void get_signal_curves(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const; void get_markers(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const; bool timecourse_created(timecourseMode type) const {return bool(timecourse_cache[type]);} bool create_timecourses(timecourseMode type, const STD_string& nucleus, ProgressMeter* progmeter) const; const SeqTimecourseData* get_timecourse(timecourseMode type) const; const SeqTimecourseData* get_subtimecourse(timecourseMode type, double starttime, double endtime) const; void get_timecourse_markers(timecourseMode type, STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const; double get_total_duration() const; unsigned int numof_rec_channels() const; unsigned int n_frames() const {return size();} JcampDxBlock& get_opts(bool include_timecourse_opts, bool include_simulation_opts) const; void set_coilsdir(const STD_string& coilsdir) const; bool monitor_simulation() const {return sim_opts.MagnMonitor;} bool simulate(const STD_string& fidfile, const STD_string& samplefile, ProgressMeter* progmeter, SeqSimFeedbackAbstract* feedback) const; bool has_curves_on_channel(plotChannel chan) const; private: void clear_curves4qwt_cache() const; void clear_markers4qwt_cache() const; void clear_synclist_cache() const; void clear_timecourse_cache(timecourseMode type) const; void create_curves4qwt_cache() const; void create_markers4qwt_cache() const; void create_synclist_cache(ProgressMeter* progmeter) const; void create_timecourse_cache(timecourseMode type, const STD_string& nucleus, ProgressMeter* progmeter) const; mutable SeqTimecourseOpts timecourse_opts; mutable SeqSimulationOpts sim_opts; mutable JcampDxBlock all_opts; SeqPlotFrame current_frame; double framestart_offset; mutable PlotList curves4qwt_cache; mutable PlotList curves4qwt_cache_lowres; mutable bool curves4qwt_cache_done; mutable PlotList markers4qwt_cache; mutable bool markers4qwt_cache_done; mutable STD_list synclist_cache; mutable bool synclist_cache_done; mutable SeqTimecourse* timecourse_cache[numof_tcmodes]; mutable PlotList signal_curves; mutable bool has_curves_on_channel_cache[numof_plotchan]; }; ///////////////////////////////////////////////////////////////// #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqfreq_standalone.h0000644000175000017500000000510311735135552023345 00000000000000/*************************************************************************** seqfreq_standalone.h - description ------------------- begin : Sat Apr 3 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQFREQ_STANDALONE_H #define SEQFREQ_STANDALONE_H #include #include "seqstandalone.h" ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for transmit/receive channels */ class SeqFreqChanStandAlone : public SeqFreqChanDriver, public SeqStandAlone { public: SeqFreqChanStandAlone() {} ~SeqFreqChanStandAlone() {} SeqFreqChanStandAlone(const SeqFreqChanStandAlone& sfcs) {set_label(sfcs.get_label());} // overloading virtual functions from SeqFreqChanDriver bool prep_driver(const STD_string& nucleus, const dvector& freqlist) {return true;} void prep_iteration(double current_frequency, double current_phase, double freqchan_duration) const; int get_channel() const {return 0;} STD_string get_iteratorcommand(objCategory cat,int freqlistindex) const {return "";} svector get_freqvec_commands(const STD_string& iterator, const STD_string& instr) const {return svector();} STD_string get_pre_program(programContext& context, objCategory cat, const STD_string& instr_label, double default_frequency, double default_phase) const {return "";} void pre_event (eventContext& context,double starttime) const; void post_event(eventContext& context,double starttime) const {} SeqFreqChanDriver* clone_driver() const {return new SeqFreqChanStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} private: mutable double freq_cache; mutable double phase_cache; }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqfreq_standalone.cpp0000644000175000017500000000106511735135552023703 00000000000000#include "seqfreq_standalone.h" void SeqFreqChanStandAlone::prep_iteration(double current_frequency, double current_phase, double freqchan_duration) const { Log odinlog(this,"prep_iteration"); ODINLOG(odinlog,normalDebug) << "current_frequency/current_phase=" << current_frequency << "/" << current_phase << STD_endl; freq_cache =current_frequency; phase_cache=current_phase; } void SeqFreqChanStandAlone::pre_event(eventContext& context,double starttime) const { current_rf_rec_freq =freq_cache; current_rf_rec_phase=phase_cache; } odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqparallel_standalone.h0000644000175000017500000000414211735135552024206 00000000000000/*************************************************************************** seqparallel_standalone.h - description ------------------- begin : Fri Apr 16 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPARALLEL_STANDALONE_H #define SEQPARALLEL_STANDALONE_H #include ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for parallel RF/gradient handling */ class SeqParallelStandAlone : public SeqParallelDriver, public SeqStandAlone { public: SeqParallelStandAlone() {} SeqParallelStandAlone(const SeqParallelStandAlone& sps) {set_label(sps.get_label());} ~SeqParallelStandAlone() {} // overloading virtual functions from SeqParallelDriver STD_string get_program(programContext& context, const SeqObjBase* soa, const SeqGradObjInterface* sgoa) const {return "";} double get_duration (const SeqObjBase* soa, const SeqGradObjInterface* sgoa) const {return 0.0;} double get_predelay (const SeqObjBase* soa, const SeqGradObjInterface* sgoa) const {return 0.0;} SeqParallelDriver* clone_driver() const {return new SeqParallelStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqdelay_standalone.cpp0000644000175000017500000000004111735135552024035 00000000000000#include "seqdelay_standalone.h" odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqgradtrapez_standalone.h0000644000175000017500000000223511735135552024556 00000000000000/*************************************************************************** seqgradtrapez_standalone.h - description ------------------- begin : Tue Apr 27 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADTRAPEZ_STANDALONE_H #define SEQGRADTRAPEZ_STANDALONE_H #include // using default driver #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqlist_standalone.cpp0000644000175000017500000000125211735135552023717 00000000000000#include "seqlist_standalone.h" void SeqListStandAlone::pre_event (eventContext& context, const RotMatrix* rotmatrix) const { if(rotmatrix) SeqStandAlone::current_rotmatrix=rotmatrix; } void SeqListStandAlone::post_event(eventContext& context, const RotMatrix* rotmatrix) const { if(rotmatrix) SeqStandAlone::current_rotmatrix=0; } void SeqListStandAlone::pre_itemevent (const SeqTreeObj* item, eventContext& context) const { if(context.action==seqRun && !context.noflush) new_plot_frame(context); } void SeqListStandAlone::post_itemevent(const SeqTreeObj* item, eventContext& context) const { if(context.action==seqRun && !context.noflush) flush_plot_frame(context); } odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqacq_standalone.h0000644000175000017500000000451011735135552023155 00000000000000/*************************************************************************** seqacq_standalone.h - description ------------------- begin : Fri Jul 23 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQACQ_STANDALONE_H #define SEQACQ_STANDALONE_H #include #include "seqstandalone.h" /** * @ingroup odinseq_internals * The Standalone driver for acquisition windows */ class SeqAcqStandAlone : public SeqAcqDriver, public SeqStandAlone { public: SeqAcqStandAlone() {} ~SeqAcqStandAlone() {} SeqAcqStandAlone(const SeqAcqStandAlone& sas); // overloading virtual functions from SeqAcqDriver double adjust_sweepwidth(double desired_sweep_widht) const {return desired_sweep_widht;} bool prep_driver(kSpaceCoord& recoindex, double sweepwidth,unsigned int nAcqPoints, double acqcenter, int freqchannel); double get_predelay() const {return 0.0;} double get_postdelay(double) const {return 0.0;} void event(eventContext& context, double start) const; STD_string get_program(programContext& context, unsigned int phaselistindex) const {return "";} STD_string get_instr_label() const {return "";} unsigned int get_numof_channels() const {return SeqStandAlone::numof_rec_channels();} SeqAcqDriver* clone_driver() const {return new SeqAcqStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} private: SeqPlotCurve adc_curve; SeqPlotCurve adc_curve_nomark; SeqPlotCurve endacq_mark; }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqdelay_standalone.h0000644000175000017500000000523211735135552023511 00000000000000/*************************************************************************** seqdelay_standalone.h - description ------------------- begin : Fri Jul 23 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDELAY_STANDALONE_H #define SEQDELAY_STANDALONE_H #include #include ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for delays */ class SeqDelayStandAlone : public SeqDelayDriver { public: SeqDelayStandAlone() {} SeqDelayStandAlone(const SeqDelayStandAlone& sds) {set_label(sds.get_label());} ~SeqDelayStandAlone() {} // overloading virtual functions from SeqDelayDriver SeqDelayDriver* clone_driver() const {return new SeqDelayStandAlone(*this);} STD_string get_program(programContext& context, double duration, const STD_string& cmd, const STD_string& durcmd) const {return "";} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} }; ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for delay vectors */ class SeqDelayVecStandAlone : public SeqDelayVecDriver { public: SeqDelayVecStandAlone() {} SeqDelayVecStandAlone(const SeqDelayVecStandAlone& sdvs) {set_label(sdvs.get_label());} ~SeqDelayVecStandAlone() {} // overloading virtual functions from SeqDelayVecDriver SeqDelayVecDriver* clone_driver() const {return new SeqDelayVecStandAlone(*this);} bool prep_driver() {return true;} STD_string get_program(programContext& context, double duration) const {return "";} bool unroll_program() const {return false;} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqphase_standalone.cpp0000644000175000017500000000004111735135552024037 00000000000000#include "seqphase_standalone.h" odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqphase_standalone.h0000644000175000017500000000400411735135552023507 00000000000000/*************************************************************************** seqphase_standalone.h - description ------------------- begin : Tue Apr 6 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPHASE_STANDALONE_H #define SEQPHASE_STANDALONE_H #include ////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Standalone driver for phase lists */ class SeqPhaseStandAlone : public SeqPhaseDriver { public: SeqPhaseStandAlone() {} ~SeqPhaseStandAlone() {} SeqPhaseStandAlone(const SeqPhaseStandAlone& sps) {set_label(sps.get_label());} // overloading virtual functions from SeqPhaseDriver void prep_driver(const dvector& phaselist) {} unsigned int get_phaselistindex(const dvector& phaselist) const {return 0;} STD_string get_loopcommand(const dvector& phaselist) const {return "";} svector get_phasevec_commands(const STD_string& iterator, const STD_string& instr) const {return svector();} SeqPhaseDriver* clone_driver() const {return new SeqPhaseStandAlone(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} }; #endif odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqpuls_standalone.cpp0000644000175000017500000000517511735135552023737 00000000000000#include "seqpuls_standalone.h" SeqPulsStandAlone::SeqPulsStandAlone(const SeqPulsStandAlone& sps) { set_label(sps.get_label()); rf_energy=sps.rf_energy; current_pls=0; } bool SeqPulsStandAlone::prep_driver(const cvector& wave, double pulsduration, double pulscenter, float b1max, float power, float flipangle, const fvector& flipscales, pulseType plstype) { Log odinlog(this,"prep_driver"); fvector b1maxvals; if(flipscales.size()) { b1maxvals=b1max*flipscales; } else { b1maxvals.resize(1); b1maxvals[0]=b1max; } unsigned int n_flips=b1maxvals.size(); ODINLOG(odinlog,normalDebug) << "n_flips=" << n_flips << STD_endl; unsigned int n=wave.size(); double dt=secureDivision(pulsduration,n); B1re_curve.resize(n_flips); B1im_curve.resize(n_flips); rf_energy.resize(n_flips); fvector amp=amplitude(wave); amp=amp*amp; float ampsum=amp.sum(); has_real=false; has_imag=false; relabel=STD_string(get_label())+"_re"; imlabel=STD_string(get_label())+"_im"; for(unsigned int iflp=0; iflp odinlog(this,"prep_driver"); curve.resize(4); curve.channel=B1re_plotchan; curve.label=get_label().c_str(); curve.x[0]=0.0; curve.y[0]=0.0; curve.x[1]=ON_OFF_DELAY; curve.y[1]=decpower; curve.x[2]=decdur-ON_OFF_DELAY; curve.y[2]=decpower; curve.x[3]=decdur; curve.y[3]=0.0; if(dump2console) STD_cout << curve << STD_endl; return true; } void SeqDecouplingStandalone::event(eventContext& context, double start) const { Log odinlog(this,"event"); ODINLOG(odinlog,normalDebug) << "start=" << start << STD_endl; append_curve2plot(start,&curve,current_rf_rec_freq,current_rf_rec_phase); } odin-1.8.5/platforms/StandAlone/odinseq_standalone/seqtrigg_standalone.cpp0000644000175000017500000000260211735135552024060 00000000000000#include "seqtrigg_standalone.h" bool SeqTriggerStandAlone::prep_exttrigger(double duration) { trigg_marker.label=get_label().c_str(); trigg_marker.marklabel=markLabel[exttrigger_marker]; trigg_marker.marker=exttrigger_marker; trigg_marker.marker_x=0.0; if(dump2console) STD_cout << trigg_marker << STD_endl; return true; } bool SeqTriggerStandAlone::prep_halttrigger() { trigg_marker.label=get_label().c_str(); trigg_marker.marklabel=markLabel[halttrigger_marker]; trigg_marker.marker=halttrigger_marker; trigg_marker.marker_x=0.0; if(dump2console) STD_cout << trigg_marker << STD_endl; return true; } bool SeqTriggerStandAlone::prep_snaptrigger(const STD_string& snapshot_fname) { trigg_marker.label=snapshot_fname.c_str(); trigg_marker.marklabel=markLabel[snapshot_marker]; trigg_marker.marker=snapshot_marker; trigg_marker.marker_x=0.0; rmfile(snapshot_fname.c_str()); if(dump2console) STD_cout << trigg_marker << STD_endl; return true; } bool SeqTriggerStandAlone::prep_resettrigger() { trigg_marker.label="Magnetization Reset"; trigg_marker.marklabel=markLabel[reset_marker]; trigg_marker.marker=reset_marker; trigg_marker.marker_x=0.0; if(dump2console) STD_cout << trigg_marker << STD_endl; return true; } void SeqTriggerStandAlone::event(eventContext& context, double startelapsed) const { append_curve2plot(startelapsed,&trigg_marker); } odin-1.8.5/configure0000755000175000017500000223472011734622600011321 00000000000000#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.67. # # # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, # 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software # Foundation, Inc. # # # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. ## -------------------- ## ## M4sh Initialization. ## ## -------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which # is contrary to our usage. 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Even if it were fixed, the result of this # check would be larger than it should be. lt_cv_sys_max_cmd_len=12288; # 12K is about right ;; gnu*) # Under GNU Hurd, this test is not required because there is # no limit to the length of command line arguments. # Libtool will interpret -1 as no limit whatsoever lt_cv_sys_max_cmd_len=-1; ;; cygwin* | mingw* | cegcc*) # On Win9x/ME, this test blows up -- it succeeds, but takes # about 5 minutes as the teststring grows exponentially. # Worse, since 9x/ME are not pre-emptively multitasking, # you end up with a "frozen" computer, even though with patience # the test eventually succeeds (with a max line length of 256k). # Instead, let's just punt: use the minimum linelength reported by # all of the supported platforms: 8192 (on NT/2K/XP). lt_cv_sys_max_cmd_len=8192; ;; amigaos*) # On AmigaOS with pdksh, this test takes hours, literally. # So we just punt and use a minimum line length of 8192. lt_cv_sys_max_cmd_len=8192; ;; netbsd* | freebsd* | openbsd* | darwin* | dragonfly*) # This has been around since 386BSD, at least. Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else # Make teststring a little bigger before we do anything with it. # a 1K string should be a reasonable start. for i in 1 2 3 4 5 6 7 8 ; do teststring=$teststring$teststring done SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \ = "XX$teststring$teststring"; } >/dev/null 2>&1 && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done # Only check the string length outside the loop. lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` teststring= # Add a significant safety factor because C++ compilers can tack on # massive amounts of additional arguments before passing them to the # linker. It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5 $as_echo "$lt_cv_sys_max_cmd_len" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5 $as_echo "none" >&6; } fi max_cmd_len=$lt_cv_sys_max_cmd_len : ${CP="cp -f"} : ${MV="mv -f"} : ${RM="rm -f"} { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5 $as_echo_n "checking whether the shell understands some XSI constructs... " >&6; } # Try some XSI features xsi_shell=no ( _lt_dummy="a/b/c" test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \ = c,a/b,, \ && eval 'test $(( 1 + 1 )) -eq 2 \ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \ && xsi_shell=yes { $as_echo "$as_me:${as_lineno-$LINENO}: result: $xsi_shell" >&5 $as_echo "$xsi_shell" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands \"+=\"" >&5 $as_echo_n "checking whether the shell understands \"+=\"... " >&6; } lt_shell_append=no ( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \ >/dev/null 2>&1 \ && lt_shell_append=yes { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_shell_append" >&5 $as_echo "$lt_shell_append" >&6; } if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then lt_unset=unset else lt_unset=false fi # test EBCDIC or ASCII case `echo X|tr X '\101'` in A) # ASCII based system # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr lt_SP2NL='tr \040 \012' lt_NL2SP='tr \015\012 \040\040' ;; *) # EBCDIC based system lt_SP2NL='tr \100 \n' lt_NL2SP='tr \r\n \100\100' ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $LD option to reload object files" >&5 $as_echo_n "checking for $LD option to reload object files... " >&6; } if test "${lt_cv_ld_reload_flag+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_reload_flag='-r' fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5 $as_echo "$lt_cv_ld_reload_flag" >&6; } reload_flag=$lt_cv_ld_reload_flag case $reload_flag in "" | " "*) ;; *) reload_flag=" $reload_flag" ;; esac reload_cmds='$LD$reload_flag -o $output$reload_objs' case $host_os in darwin*) if test "$GCC" = yes; then reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs' else reload_cmds='$LD$reload_flag -o $output$reload_objs' fi ;; esac if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args. set dummy ${ac_tool_prefix}objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OBJDUMP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$OBJDUMP"; then ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OBJDUMP=$ac_cv_prog_OBJDUMP if test -n "$OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5 $as_echo "$OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OBJDUMP"; then ac_ct_OBJDUMP=$OBJDUMP # Extract the first word of "objdump", so it can be a program name with args. set dummy objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OBJDUMP"; then ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OBJDUMP="objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP if test -n "$ac_ct_OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5 $as_echo "$ac_ct_OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OBJDUMP" = x; then OBJDUMP="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OBJDUMP=$ac_ct_OBJDUMP fi else OBJDUMP="$ac_cv_prog_OBJDUMP" fi test -z "$OBJDUMP" && OBJDUMP=objdump { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5 $as_echo_n "checking how to recognize dependent libraries... " >&6; } if test "${lt_cv_deplibs_check_method+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_deplibs_check_method='unknown' # Need to set the preceding variable on all platforms that support # interlibrary dependencies. # 'none' -- dependencies not supported. # `unknown' -- same as none, but documents that we really don't know. # 'pass_all' -- all dependencies passed with no checks. # 'test_compile' -- check by making test program. # 'file_magic [[regex]]' -- check by looking for files in library path # which responds to the $file_magic_cmd with a given extended regex. # If you have `file' or equivalent on your system and you're not sure # whether `pass_all' will *always* work, you probably want this one. case $host_os in aix[4-9]*) lt_cv_deplibs_check_method=pass_all ;; beos*) lt_cv_deplibs_check_method=pass_all ;; bsdi[45]*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/shlib/libc.so ;; cygwin*) # func_win32_libid is a shell function defined in ltmain.sh lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' ;; mingw* | pw32*) # Base MSYS/MinGW do not provide the 'file' command needed by # func_win32_libid shell function, so use a weaker test based on 'objdump', # unless we find 'file', for example because we are cross-compiling. if ( file / ) >/dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]' lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[3-9]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5 $as_echo "$lt_cv_deplibs_check_method" >&6; } file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args. set dummy ${ac_tool_prefix}ar; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_AR+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AR="${ac_tool_prefix}ar" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_AR"; then ac_ct_AR=$AR # Extract the first word of "ar", so it can be a program name with args. set dummy ar; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_AR+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_AR="ar" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi else AR="$ac_cv_prog_AR" fi test -z "$AR" && AR=ar test -z "$AR_FLAGS" && AR_FLAGS=cru if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi test -z "$STRIP" && STRIP=: if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_RANLIB+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi test -z "$RANLIB" && RANLIB=: # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" fi # If no C compiler was specified, use CC. LTCC=${LTCC-"$CC"} # If no C compiler flags were specified, use CFLAGS. LTCFLAGS=${LTCFLAGS-"$CFLAGS"} # Allow CC to be a program name with arguments. compiler=$CC # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then : $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[ABCDGISTW]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK '"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then # Now try to grab the symbols. nlist=conftest.nm if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\""; } >&5 (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 $as_echo "ok" >&6; } fi # Check whether --enable-libtool-lock was given. if test "${enable_libtool_lock+set}" = set; then : enableval=$enable_libtool_lock; fi test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes # Some flags need to be propagated to the compiler or linker for good # libtool support. case $host in ia64-*-hpux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '#line 6834 "configure"' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then if test "$lt_cv_prog_gnu_ld" = yes; then case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -melf32bsmip" ;; *N32*) LD="${LD-ld} -melf32bmipn32" ;; *64-bit*) LD="${LD-ld} -melf64bmip" ;; esac else case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -32" ;; *N32*) LD="${LD-ld} -n32" ;; *64-bit*) LD="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ s390*-*linux*|s390*-*tpf*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *32-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_i386_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_i386" ;; ppc64-*linux*|powerpc64-*linux*) LD="${LD-ld} -m elf32ppclinux" ;; s390x-*linux*) LD="${LD-ld} -m elf_s390" ;; sparc64-*linux*) LD="${LD-ld} -m elf32_sparc" ;; esac ;; *64-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_x86_64_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*|s390*-*tpf*) LD="${LD-ld} -m elf64_s390" ;; sparc*-*linux*) LD="${LD-ld} -m elf64_sparc" ;; esac ;; esac fi rm -rf conftest* ;; *-*-sco3.2v5*) # On SCO OpenServer 5, we need -belf to get full-featured binaries. SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5 $as_echo_n "checking whether the C compiler needs -belf... " >&6; } if test "${lt_cv_cc_needs_belf+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_cc_needs_belf=yes else lt_cv_cc_needs_belf=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5 $as_echo "$lt_cv_cc_needs_belf" >&6; } if test x"$lt_cv_cc_needs_belf" != x"yes"; then # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf CFLAGS="$SAVE_CFLAGS" fi ;; sparc*-*solaris*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *64-bit*) case $lt_cv_prog_gnu_ld in yes*) LD="${LD-ld} -m elf64_sparc" ;; *) if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then LD="${LD-ld} -64" fi ;; esac ;; esac fi rm -rf conftest* ;; esac need_locks="$enable_libtool_lock" case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_DSYMUTIL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_NMEDIT+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_NMEDIT"; then ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_NMEDIT="nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT if test -n "$ac_ct_NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5 $as_echo "$ac_ct_NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_NMEDIT" = x; then NMEDIT=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac NMEDIT=$ac_ct_NMEDIT fi else NMEDIT="$ac_cv_prog_NMEDIT" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. set dummy ${ac_tool_prefix}lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_LIPO+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$LIPO"; then ac_cv_prog_LIPO="$LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_LIPO="${ac_tool_prefix}lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi LIPO=$ac_cv_prog_LIPO if test -n "$LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5 $as_echo "$LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_LIPO"; then ac_ct_LIPO=$LIPO # Extract the first word of "lipo", so it can be a program name with args. set dummy lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_LIPO"; then ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_LIPO="lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO if test -n "$ac_ct_LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5 $as_echo "$ac_ct_LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_LIPO" = x; then LIPO=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac LIPO=$ac_ct_LIPO fi else LIPO="$ac_cv_prog_LIPO" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. set dummy ${ac_tool_prefix}otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OTOOL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL"; then ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OTOOL="${ac_tool_prefix}otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL=$ac_cv_prog_OTOOL if test -n "$OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5 $as_echo "$OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL"; then ac_ct_OTOOL=$OTOOL # Extract the first word of "otool", so it can be a program name with args. set dummy otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL"; then ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OTOOL="otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL if test -n "$ac_ct_OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5 $as_echo "$ac_ct_OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL" = x; then OTOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL=$ac_ct_OTOOL fi else OTOOL="$ac_cv_prog_OTOOL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. set dummy ${ac_tool_prefix}otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OTOOL64+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL64"; then ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL64=$ac_cv_prog_OTOOL64 if test -n "$OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5 $as_echo "$OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL64"; then ac_ct_OTOOL64=$OTOOL64 # Extract the first word of "otool64", so it can be a program name with args. set dummy otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL64"; then ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OTOOL64="otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 if test -n "$ac_ct_OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5 $as_echo "$ac_ct_OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL64" = x; then OTOOL64=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL64=$ac_ct_OTOOL64 fi else OTOOL64="$ac_cv_prog_OTOOL64" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5 $as_echo_n "checking for -single_module linker flag... " >&6; } if test "${lt_cv_apple_cc_single_mod+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_apple_cc_single_mod=no if test -z "${LT_MULTI_MODULE}"; then # By default we will add the -single_module flag. You can override # by either setting the environment variable LT_MULTI_MODULE # non-empty at configure time, or by adding -multi_module to the # link flags. rm -rf libconftest.dylib* echo "int foo(void){return 1;}" > conftest.c echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c" >&5 $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err _lt_result=$? if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then lt_cv_apple_cc_single_mod=yes else cat conftest.err >&5 fi rm -rf libconftest.dylib* rm -f conftest.* fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5 $as_echo "$lt_cv_apple_cc_single_mod" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5 $as_echo_n "checking for -exported_symbols_list linker flag... " >&6; } if test "${lt_cv_ld_exported_symbols_list+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_exported_symbols_list=no save_LDFLAGS=$LDFLAGS echo "_main" > conftest.sym LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_ld_exported_symbols_list=yes else lt_cv_ld_exported_symbols_list=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_exported_symbols_list" >&5 $as_echo "$lt_cv_ld_exported_symbols_list" >&6; } case $host_os in rhapsody* | darwin1.[012]) _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;; darwin1.*) _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; darwin*) # darwin 5.x on # if running on 10.5 or later, the deployment target defaults # to the OS version, if on x86, and 10.4, the deployment # target defaults to 10.4. Don't you love it? case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in 10.0,*86*-darwin8*|10.0,*-darwin[91]*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; 10.[012]*) _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; 10.*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; esac ;; esac if test "$lt_cv_apple_cc_single_mod" = "yes"; then _lt_dar_single_mod='$single_module' fi if test "$lt_cv_ld_exported_symbols_list" = "yes"; then _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym' else _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}' fi if test "$DSYMUTIL" != ":"; then _lt_dsymutil='~$DSYMUTIL $lib || :' else _lt_dsymutil= fi ;; esac ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 $as_echo_n "checking how to run the C preprocessor... " >&6; } # On Suns, sometimes $CPP names a directory. if test -n "$CPP" && test -d "$CPP"; then CPP= fi if test -z "$CPP"; then if test "${ac_cv_prog_CPP+set}" = set; then : $as_echo_n "(cached) " >&6 else # Double quotes because CPP needs to be expanded for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" do ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # Prefer to if __STDC__ is defined, since # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include #else # include #endif Syntax error _ACEOF if ac_fn_c_try_cpp "$LINENO"; then : else # Broken: fails on valid input. continue fi rm -f conftest.err conftest.i conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if ac_fn_c_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else # Passes both tests. ac_preproc_ok=: break fi rm -f conftest.err conftest.i conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.i conftest.err conftest.$ac_ext if $ac_preproc_ok; then : break fi done ac_cv_prog_CPP=$CPP fi CPP=$ac_cv_prog_CPP else ac_cv_prog_CPP=$CPP fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 $as_echo "$CPP" >&6; } ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # Prefer to if __STDC__ is defined, since # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include #else # include #endif Syntax error _ACEOF if ac_fn_c_try_cpp "$LINENO"; then : else # Broken: fails on valid input. continue fi rm -f conftest.err conftest.i conftest.$ac_ext # OK, works on sane cases. 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The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi export_dynamic_flag_spec='${wl}-bexpall' # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols=yes if test "$aix_use_runtimelinking" = yes; then # Warning - without using the other runtime loading flags (-brtl), # -berok will link without error, but may produce a broken library. allow_undefined_flag='-berok' # Determine the default libpath from the value encoded in an # empty executable. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag="-z nodefs" archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an # empty executable. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. no_undefined_flag=' ${wl}-bernotok' allow_undefined_flag=' ${wl}-berok' # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec='$convenience' archive_cmds_need_lc=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; bsdi[45]*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_from_new_cmds='true' # FIXME: Should let the user specify the lib program. old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes=yes ;; darwin* | rhapsody*) archive_cmds_need_lc=no hardcode_direct=no hardcode_automatic=yes hardcode_shlibpath_var=unsupported whole_archive_flag_spec='' link_all_deplibs=yes allow_undefined_flag="$_lt_dar_allow_undefined" case $cc_basename in ifort*) _lt_dar_can_shared=yes ;; *) _lt_dar_can_shared=$GCC ;; esac if test "$_lt_dar_can_shared" = "yes"; then output_verbose_link_cmd=echo archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else ld_shlibs=no fi ;; dgux*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-L$libdir' hardcode_shlibpath_var=no ;; freebsd1*) ld_shlibs=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes export_dynamic_flag_spec='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_flag_spec_ld='+b $libdir' hardcode_libdir_separator=: hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: case $host_cpu in hppa*64*|ia64*) hardcode_direct=no hardcode_shlibpath_var=no ;; *) hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int foo(void) {} _ACEOF if ac_fn_c_try_link "$LINENO"; then : archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: inherit_rpath=yes link_all_deplibs=yes ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; newsos6) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: hardcode_shlibpath_var=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct=yes hardcode_shlibpath_var=no hardcode_direct_absolute=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-R$libdir' ;; *) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec='-rpath $libdir' fi archive_cmds_need_lc='no' hardcode_libdir_separator=: ;; solaris*) no_undefined_flag=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' ;; esac fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. 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# No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\"" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then : shlibpath_overrides_runpath=yes fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS=$save_LDFLAGS libdir=$save_libdir # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. Since this was broken with cross compilers, # most powerpc-linux boxes support dynamic linking these days and # people can always --disable-shared, the test was removed, and we # assume the GNU/Linux dynamic linker is in use. dynamic_linker='GNU/Linux ld.so' ;; netbsdelf*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='NetBSD ld.elf_so' ;; netbsd*) version_type=sunos need_lib_prefix=no need_version=no if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' dynamic_linker='NetBSD (a.out) ld.so' else library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='NetBSD ld.elf_so' fi shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes ;; newsos6) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[89] | openbsd2.[89].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. Preferred cross-host = GNU/Linux. version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; uts4*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH ;; *) dynamic_linker=no ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5 $as_echo "$dynamic_linker" >&6; } test "$dynamic_linker" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" fi if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5 $as_echo_n "checking how to hardcode library paths into programs... " >&6; } hardcode_action= if test -n "$hardcode_libdir_flag_spec" || test -n "$runpath_var" || test "X$hardcode_automatic" = "Xyes" ; then # We can hardcode non-existent directories. if test "$hardcode_direct" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no && test "$hardcode_minus_L" != no; then # Linking always hardcodes the temporary library directory. hardcode_action=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. hardcode_action=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. hardcode_action=unsupported fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action" >&5 $as_echo "$hardcode_action" >&6; } if test "$hardcode_action" = relink || test "$inherit_rpath" = yes; then # Fast installation is not supported enable_fast_install=no elif test "$shlibpath_overrides_runpath" = yes || test "$enable_shared" = no; then # Fast installation is not necessary enable_fast_install=needless fi if test "x$enable_dlopen" != xyes; then enable_dlopen=unknown enable_dlopen_self=unknown enable_dlopen_self_static=unknown else lt_cv_dlopen=no lt_cv_dlopen_libs= case $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32* | cegcc*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if test "${ac_cv_lib_dl_dlopen+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes fi ;; *) ac_fn_c_check_func "$LINENO" "shl_load" "ac_cv_func_shl_load" if test "x$ac_cv_func_shl_load" = x""yes; then : lt_cv_dlopen="shl_load" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shl_load in -ldld" >&5 $as_echo_n "checking for shl_load in -ldld... " >&6; } if test "${ac_cv_lib_dld_shl_load+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char shl_load (); int main () { return shl_load (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dld_shl_load=yes else ac_cv_lib_dld_shl_load=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_shl_load" >&5 $as_echo "$ac_cv_lib_dld_shl_load" >&6; } if test "x$ac_cv_lib_dld_shl_load" = x""yes; then : lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld" else ac_fn_c_check_func "$LINENO" "dlopen" "ac_cv_func_dlopen" if test "x$ac_cv_func_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if test "${ac_cv_lib_dl_dlopen+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -lsvld" >&5 $as_echo_n "checking for dlopen in -lsvld... " >&6; } if test "${ac_cv_lib_svld_dlopen+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsvld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_svld_dlopen=yes else ac_cv_lib_svld_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5 $as_echo "$ac_cv_lib_svld_dlopen" >&6; } if test "x$ac_cv_lib_svld_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5 $as_echo_n "checking for dld_link in -ldld... " >&6; } if test "${ac_cv_lib_dld_dld_link+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dld_link (); int main () { return dld_link (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dld_dld_link=yes else ac_cv_lib_dld_dld_link=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_dld_link" >&5 $as_echo "$ac_cv_lib_dld_dld_link" >&6; } if test "x$ac_cv_lib_dld_dld_link" = x""yes; then : lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld" fi fi fi fi fi fi ;; esac if test "x$lt_cv_dlopen" != xno; then enable_dlopen=yes else enable_dlopen=no fi case $lt_cv_dlopen in dlopen) save_CPPFLAGS="$CPPFLAGS" test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H" save_LDFLAGS="$LDFLAGS" wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\" save_LIBS="$LIBS" LIBS="$lt_cv_dlopen_libs $LIBS" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program can dlopen itself" >&5 $as_echo_n "checking whether a program can dlopen itself... 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esac ;; gnu*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH hardcode_into_libs=yes ;; hpux9* | hpux10* | hpux11*) # Give a soname corresponding to the major version so that dld.sl refuses to # link against other versions. version_type=sunos need_lib_prefix=no need_version=no case $host_cpu in ia64*) shrext_cmds='.so' hardcode_into_libs=yes dynamic_linker="$host_os dld.so" shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' if test "X$HPUX_IA64_MODE" = X32; then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; 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irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux else version_type=irix fi ;; esac need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; # No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; wl=\"$lt_prog_compiler_wl_CXX\"; \ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec_CXX\"" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_cxx_try_link "$LINENO"; then : if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then : shlibpath_overrides_runpath=yes fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS=$save_LDFLAGS libdir=$save_libdir # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. 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"Please install the GNU Scientific Library (There is probably a precompiled package for your UNIX/Linux distribution, otherwise see http://www.gnu.org/software/gsl)" "$LINENO" 5 fi if test "x$macos" = "xyes" ; then { $as_echo "$as_me:${as_lineno-$LINENO}: Using vecLib for lapack support" >&5 $as_echo "$as_me: Using vecLib for lapack support" >&6;} valid_lapack=yes lapack_libname="vecLib" else if test "$lapack_libname" = "lapack" ; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for i_indx in -lg2c" >&5 $as_echo_n "checking for i_indx in -lg2c... " >&6; } if test "${ac_cv_lib_g2c_i_indx+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lg2c $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. 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"Please install Blitz++ (Version 0.8 or higher) in order to use the reconstruction library (There is probably a precompiled package for your UNIX/Linux distribution, otherwise see http://www.oonumerics.org/blitz)" "$LINENO" 5 fi if test ! "x$enable_niftisupport" = "xno" ; then lib_nifti=yes if test -d ${extra_include_base}/nifti ; then all_includes="-I${extra_include_base}/nifti $all_includes" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lznz" >&5 $as_echo_n "checking for main in -lznz... " >&6; } if test "${ac_cv_lib_znz_main+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lznz $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_cxx_try_link "$LINENO"; then : ac_cv_lib_znz_main=yes else ac_cv_lib_znz_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_znz_main" >&5 $as_echo "$ac_cv_lib_znz_main" >&6; } if test "x$ac_cv_lib_znz_main" = x""yes; then : LIBS="-lznz $LIBS"; DATALIBS="-lznz $DATALIBS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for nifti_image_read in -lniftiio" >&5 $as_echo_n "checking for nifti_image_read in -lniftiio... " >&6; } if test "${ac_cv_lib_niftiio_nifti_image_read+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lniftiio $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. 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"libniftiio missing" "$LINENO" 5 else { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: NIFTI I/O library not found, NIFTI support will be disabled" >&5 $as_echo "$as_me: WARNING: NIFTI I/O library not found, NIFTI support will be disabled" >&2;} fi fi fi if test ! "x$enable_vtksupport" = "xno" ; then lib_vtk=yes { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lvtkIO" >&5 $as_echo_n "checking for main in -lvtkIO... 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"VTK library missing" "$LINENO" 5 else { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: VTK library (Version 4.4 or higher) not found, VTK support will be disabled" >&5 $as_echo "$as_me: WARNING: VTK library (Version 4.4 or higher) not found, VTK support will be disabled" >&2;} fi fi fi if test ! "x$enable_dcmtksupport" = "xno" ; then lib_dcmtk=yes if test -d ${extra_include_base}/dcmtk ; then all_includes="-I${extra_include_base}/dcmtk -I${extra_include_base}/dcmtk/dcmdata -I${extra_include_base}/dcmtk/ofstd $all_includes" fi CPPFLAGS_CACHE="$CPPFLAGS" CPPFLAGS="-DHAVE_CONFIG_H $all_includes $CPPFLAGS" ac_fn_cxx_check_header_mongrel "$LINENO" "dcmtk/dcmdata/dcdatset.h" "ac_cv_header_dcmtk_dcmdata_dcdatset_h" "$ac_includes_default" if test "x$ac_cv_header_dcmtk_dcmdata_dcdatset_h" = x""yes; then : else lib_dcmtk=no fi ac_fn_cxx_check_header_mongrel "$LINENO" "dcmtk/dcmimgle/dcmimage.h" "ac_cv_header_dcmtk_dcmimgle_dcmimage_h" "$ac_includes_default" if test "x$ac_cv_header_dcmtk_dcmimgle_dcmimage_h" = x""yes; then : else lib_dcmtk=no fi CPPFLAGS="$CPPFLAGS_CACHE" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lwsock32" >&5 $as_echo_n "checking for main in -lwsock32... " >&6; } if test "${ac_cv_lib_wsock32_main+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lwsock32 $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_cxx_try_link "$LINENO"; then : ac_cv_lib_wsock32_main=yes else ac_cv_lib_wsock32_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_wsock32_main" >&5 $as_echo "$ac_cv_lib_wsock32_main" >&6; } if test "x$ac_cv_lib_wsock32_main" = x""yes; then : LIBS="-lwsock32 $LIBS"; DATALIBS="-lwsock32 $DATALIBS" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lofstd" >&5 $as_echo_n "checking for main in -lofstd... 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"write failure creating $CONFIG_STATUS" "$LINENO" 5 # configure is writing to config.log, and then calls config.status. # config.status does its own redirection, appending to config.log. # Unfortunately, on DOS this fails, as config.log is still kept open # by configure, so config.status won't be able to write to it; its # output is simply discarded. So we exec the FD to /dev/null, # effectively closing config.log, so it can be properly (re)opened and # appended to by config.status. When coming back to configure, we # need to make the FD available again. if test "$no_create" != yes; then ac_cs_success=: ac_config_status_args= test "$silent" = yes && ac_config_status_args="$ac_config_status_args --quiet" exec 5>/dev/null $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. $ac_cs_success || as_fn_exit 1 fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi odin-1.8.5/cmdline-utils/0000755000175000017500000000000011735135552012237 500000000000000odin-1.8.5/cmdline-utils/swab.cpp0000644000175000017500000000562011322062353013610 00000000000000#include #include #include /** * \page swab Swap adjacent bytes * \verbinclude cmdline-utils/swab.usage */ int main(int argc, char* argv[]) { if(argc < 4 || argc > 5){ std::cout << "swab: Mirrors bytes, in the case of 2, it swaps adjacent bytes" << std::endl; std::cout << "Usage: swab " << std::endl; exit(0); } char *temp1,*temp2; unsigned long n_bytes; unsigned long block_size,i,k,n_data,j; std::ofstream out_data; n_bytes = atoi(argv[1]); std::ifstream in_data(argv[2],std::ios::in|std::ios::binary); if(in_data == NULL){ std::cerr << "swab: ERROR: can't open file " << argv[2] << std::endl; exit(1); } in_data.seekg(0,std::ios::end); if(argc == 5) block_size = (unsigned)atol(argv[4])*1000000; else block_size = in_data.tellg(); block_size-= block_size%n_bytes; n_data=in_data.tellg(); if(block_size > n_data){ // std::cerr << "swab: block size exceeding file size !" << std::endl // << "setting block size to file size (=" << n_data/1000000. << "MB)" << std::endl; block_size = n_data; } in_data.seekg(0,std::ios::beg); if((float)n_data/(float)n_bytes-n_data/n_bytes){ std::cerr << "swab: ERROR: swab: size of \n" << argv[2] << "not a multiple of no. of swap bytes (" << n_bytes << ")" << std::endl; exit(1); } temp1=new char[block_size]; temp2=new char[block_size]; for(k=0;k #include #include #include #include /** * \page gencoil Generate a coil file * \verbinclude cmdline-utils/gencoil.usage */ void usage() { STD_cout << STD_endl; STD_cout << "gencoil: Generates a virtual coil suitable for sequence simulation in ODIN" << STD_endl; STD_cout << STD_endl; STD_cout << "Usage and options:" << STD_endl; STD_cout << " Generate a radially inhomogenous coil:" << STD_endl; STD_cout << " gencoil -rad -n -fov -R -o " << STD_endl; STD_cout << " Generate an array coil by rotating pre-existing image file:" << STD_endl; STD_cout << " gencoil -rot -n -fov -nc -i -sl -o " << STD_endl; STD_cout << " Generate an array coil consisting of simple loops:" << STD_endl; STD_cout << " gencoil -arr -n -nc -fov -R -o " << STD_endl; STD_cout << " Generate coil with a B1 gradient:" << STD_endl; STD_cout << " gencoil -grad -n -fov -g -o " << STD_endl; STD_cout << "Other options:" << STD_endl; STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; } int main(int argc, char* argv[]) { LogBase::set_log_levels(argc,argv); Log odinlog("gencoil","main"); if(hasHelpOption(argc,argv)) {usage(); return 0;} Range all=Range::all(); char optval[ODIN_MAXCHAR]; STD_string coil_fname; if(getCommandlineOption(argc,argv,"-o",optval,ODIN_MAXCHAR)) coil_fname=optval; else {usage();exit(0);} CoilSensitivity sens("Coil Sensitivity"); bool valid_mode=false; ///////////////////////////////////////////////////////////////////////////// if(isCommandlineOption(argc,argv,"-rad")) { int n; float R,fov; if(getCommandlineOption(argc,argv,"-n",optval,ODIN_MAXCHAR)) n=atoi(optval); else {usage();exit(0);} if(getCommandlineOption(argc,argv,"-R",optval,ODIN_MAXCHAR)) R=0.01*atof(optval); else {usage();exit(0);} if(getCommandlineOption(argc,argv,"-fov",optval,ODIN_MAXCHAR)) fov=atof(optval); else {usage();exit(0);} carray sens_map(1,1,n,n); int nx_center=n/2; int ny_center=n/2; double a=-4.0*R; double c=1.0+R; STD_complex b1factor; ndim nn=sens_map.get_extent(); ndim indexvec; for(int i=0; i rotation; TinyVector offset; offset=0.0; carray sens_map(nc,1,n,n); Data imgdata(img.get_magnitude()); TinyVector newshape(n,n); ODINLOG(odinlog,infoLog) << "Congridding map ... " << STD_endl; Data onecoil=imgdata(0,sl,all,all); onecoil.congrid(newshape); float maxmap=max(onecoil); float sum=0.0; float nvals=0.0; for(int i=0; i0.1*maxmap) { sum+=val; nvals+=1.0; } } float mean=sum/nvals; onecoil/=(2.0*mean); // factor to account for overlapping adjacent coils ODINLOG(odinlog,infoLog) << "Polynomial fit ... " << STD_endl; onecoil=polyniomial_fit(onecoil,onecoil,2,6.0); Data onecoil_transform(newshape); for(int ic=0; ic rotate(onecoil_transform.shape(), rotation, offset, 2.0); onecoil_transform=rotate(onecoil); for(int iy=0; iy rotmat[nc]; Array offset[nc]; ODINLOG(odinlog,infoLog) << "Preparing rotmat/offset ... " << STD_endl; for(int icoil=0; icoil x(3); x(0)=fov*secureDivision(double(ix-nx_center),nx_center); x(1)=fov*secureDivision(double(iy-ny_center),ny_center); x(2)=0.0; int nloopsegments=100; float dphi=2.0*PII/nloopsegments; Array dl(3); Array r(3); Array r0(3); Array dB(3); STD_complex B1(0.0); for(int iseg=0; iseg0.0) { B1+=STD_complex(dB(0),dB(1))/r2; } } sens_map(indexvec)=B1/float(2.0*PII); // will be normalized to ~ 1 at center of loop } sens.set_sensitivity_map(sens_map,fov,fov,fov); valid_mode=true; } ///////////////////////////////////////////////////////////////////////////// if(isCommandlineOption(argc,argv,"-grad")) { int n; float fov,grad; if(getCommandlineOption(argc,argv,"-n",optval,ODIN_MAXCHAR)) n=atoi(optval); else {usage();exit(0);} if(getCommandlineOption(argc,argv,"-g",optval,ODIN_MAXCHAR)) grad=atof(optval); else {usage();exit(0);} if(getCommandlineOption(argc,argv,"-fov",optval,ODIN_MAXCHAR)) fov=atof(optval); else {usage();exit(0);} carray sens_map(1,1,n,n); int nx_center=n/2; ndim nn=sens_map.get_extent(); ndim indexvec; for(int i=0; i #include #include #include #include #include /** * \page micalc Basic calculations with medical image data * \verbinclude cmdline-utils/micalc.usage * * \section micalc_examples Some examples how to use micalc: * * Calculate the difference between two DICOM files 'image1.dcm' 'and image2.dcm' and store it in * float-type raw data file 'diff.float': * \verbatim micalc -if1 image1.dcm -op '-' -if2 image2.dcm -of diff.float \endverbatim * * * Multiply image magnitude of Nifti file 'image.nii' by a factor 10: * \verbatim micalc -if1 image.nii -op '*' -in2 10 -of image.nii \endverbatim * * * Accumulate all values in file 'image.float' and write result to console: * \verbatim micalc -if image.float -op '+' \endverbatim * * * Negate values (invert sign) of file image.hdr and write result to neg.hdr * \verbatim micalc -if image.hdr -op '-' neg.hdr \endverbatim * * * Print statistics about file 'data.asc' to console: * \verbatim micalc -if data.asc \endverbatim * * * Write time-course mean and fluctuation (relative standard deviation over time) of * file 'tcourse.v' to file 'mean.v' and 'stdev.v', respectively: * \verbatim micalc -if tcourse.v -mean mean.v -fluct stdev.v \endverbatim * * * Calculate histogram in interval (0.0,100.0) with 64 steps of DICOMs in directory cbv: * \verbatim micalc -if cbv -hist histogram.asc -histmin 0.0 -histmax 100.0 -histslots 64 \endverbatim * * * Please note that it might be necessary to quote the operation argument (as shown above) * in order to prevent the shell from expanding it. */ void usage(const Protocol& prot) { FileReadOpts ropts; FileWriteOpts wopts; FilterFactory filter; STD_cout << "micalc: Performs basic mathematics with data sets" << STD_endl; STD_cout << " File formats are automatically identified by their file extension." << STD_endl; STD_cout << "micalc can be used in one of the following modes:" << STD_endl; STD_cout << " Binary operation with data sets and/or scalar numbers:" << STD_endl; STD_cout << " micalc [-if1 | -in1 ] -op [-if2 | -in2 ] -of " << STD_endl; STD_cout << " Accumulation of one data set:" << STD_endl; STD_cout << " micalc -if -op " << STD_endl; STD_cout << " Transformation (magnitude, logarithm, negation, inversion, or acos) of one data set:" << STD_endl; STD_cout << " micalc -if -op -of " << STD_endl; STD_cout << " Statistics of one data set:" << STD_endl; STD_cout << " micalc -if [-mean ] [-stdev ] [-fluct ] [-tcourse ] [-hist -histmin -histmax -histslots -rightstairs -histfract]" << STD_endl; STD_cout << "Extra options:" << STD_endl; STD_cout << "\t-mask " << STD_endl; STD_cout << "\t-weightmask " << STD_endl; STD_cout << "File read options:" << STD_endl; STD_cout << prot.get_cmdline_usage("\t"); STD_cout << ropts.get_cmdline_usage("\t"); STD_cout << "File write options:" << STD_endl; STD_cout << wopts.get_cmdline_usage("\t"); STD_cout << "Filters applied to input file(s):" << STD_endl; STD_cout << filter.get_cmdline_usage("\t"); STD_cout << "Other options:" << STD_endl; STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; STD_cout << "Supported file extensions(formats):" << STD_endl; STD_cout << FileIO::autoformats_str("\t") << STD_endl; } bool read_infile(const STD_string& filename, Data& data, const FileReadOpts& ropts, Protocol& prot, const FilterChain& filterchain, const Data& weightmaskdata) { Log odinlog("micalc","read_infile"); Range all=Range::all(); Data datain; if(datain.autoread(filename,ropts,&prot)<0) return false; if(!filterchain.apply(prot,datain)) return false; data.resize(datain.shape()); if(weightmaskdata.size()) { if( weightmaskdata.extent(0) && same_shape(data, weightmaskdata, TinyVector(0,1,1,1) ) ) { for(int irep=0; irep odinlog("micalc","main"); Range all=Range::all(); FileReadOpts ropts; FileWriteOpts wopts; Protocol prot; if(hasHelpOption(argc,argv)) {usage(prot); return 0;} // set defaults prot.seqpars.set_MatrixSize(readDirection,1); prot.seqpars.set_MatrixSize(phaseDirection,1); prot.seqpars.set_MatrixSize(sliceDirection,1); char optval[ODIN_MAXCHAR]; STD_string operation; STD_string infile1; STD_string infile2; STD_string outfile; STD_string maskfile; STD_string weightmaskfile; float innumber1=0.0; float innumber2=0.0; bool i1flag=false; bool i2flag=false; bool offlag=false; bool ifflag=false; bool opflag=false; bool binaryop=false; bool accumulate=false; bool transform=false; bool stateval=false; // command line parsing, parse before filters to remove options if(getCommandlineOption(argc,argv,"-op",optval,ODIN_MAXCHAR)) {operation=optval; opflag=true;} if(getCommandlineOption(argc,argv,"-if1",optval,ODIN_MAXCHAR)) {infile1=optval; i1flag=true;} if(getCommandlineOption(argc,argv,"-if2",optval,ODIN_MAXCHAR)) {infile2=optval; i2flag=true;} if(getCommandlineOption(argc,argv,"-if",optval,ODIN_MAXCHAR)) {infile1=optval; ifflag=true;} if(getCommandlineOption(argc,argv,"-in1",optval,ODIN_MAXCHAR)) {innumber1=atof(optval); i1flag=true;} if(getCommandlineOption(argc,argv,"-in2",optval,ODIN_MAXCHAR)) {innumber2=atof(optval); i2flag=true;} if(getCommandlineOption(argc,argv,"-of",optval,ODIN_MAXCHAR)) {outfile=optval; offlag=true;} if(getCommandlineOption(argc,argv,"-mask",optval,ODIN_MAXCHAR)) {maskfile=optval;} if(getCommandlineOption(argc,argv,"-weightmask",optval,ODIN_MAXCHAR)) {weightmaskfile=optval;} STD_string histfile; if(getCommandlineOption(argc,argv,"-hist",optval,ODIN_MAXCHAR)) histfile=optval; STD_string meanfile; STD_string fluctfile; STD_string stdevfile; STD_string tcoursefile; STD_string histslots; STD_string histmin; STD_string histmax; if(getCommandlineOption(argc,argv,"-mean",optval,ODIN_MAXCHAR)) meanfile=optval; if(getCommandlineOption(argc,argv,"-fluct",optval,ODIN_MAXCHAR)) fluctfile=optval; if(getCommandlineOption(argc,argv,"-stdev",optval,ODIN_MAXCHAR)) stdevfile=optval; if(getCommandlineOption(argc,argv,"-tcourse",optval,ODIN_MAXCHAR)) tcoursefile=optval; if(getCommandlineOption(argc,argv,"-histslots",optval,ODIN_MAXCHAR)) histslots=optval; if(getCommandlineOption(argc,argv,"-histmin",optval,ODIN_MAXCHAR)) histmin=optval; if(getCommandlineOption(argc,argv,"-histmax",optval,ODIN_MAXCHAR)) histmax=optval; bool rightstairs=isCommandlineOption(argc,argv,"-rightstairs"); bool histfract=isCommandlineOption(argc,argv,"-histfract"); // Parse before filters to remove options ropts.parse_cmdline_options(argc,argv); wopts.parse_cmdline_options(argc,argv); prot.parse_cmdline_options(argc,argv); FilterChain filterchain(argc,argv); if(i1flag && i2flag && opflag) binaryop=true; if(ifflag && opflag) { if(offlag) transform=true; else accumulate=true; } if(ifflag && (!opflag)) stateval=true; if( !( binaryop || accumulate || transform || stateval ) ) {usage(prot); return 0;} if(accumulate || stateval) FileIO::set_trace_status(false); if(binaryop && infile1=="" && infile2=="") { ODINLOG(odinlog,errorLog) << "Specifiy at least one file" << STD_endl; return -1; } Data data1; Data data2; Data weightmaskdata; if(weightmaskfile!="") { if(weightmaskdata.autoread(weightmaskfile,ropts)<0) return -1; } if(infile1!="") { if(!read_infile(infile1, data1, ropts, prot, filterchain, weightmaskdata)) return -1; } if(binaryop && infile2!="") { if(!read_infile(infile2, data2, ropts, prot, filterchain, weightmaskdata)) return -1; } TinyVector outshape; if(binaryop || transform) { bool has_shape1=sum(data1.shape()); bool has_shape2=sum(data2.shape()); if( has_shape1 && has_shape2 && !same_shape(data1,data2) ) { ODINLOG(odinlog,errorLog) << "Shape mismatch: data1shape/data2shape=" << data1.shape() << "/" << data2.shape() << STD_endl; return -1; } else outshape=data1.shape(); if(has_shape1 && !has_shape2) { outshape=data1.shape(); data2.resize(outshape); data2=innumber2; } if(!has_shape1 && has_shape2) { outshape=data2.shape(); data1.resize(outshape); data1=innumber1; } if(!has_shape1 && !has_shape2) { ODINLOG(odinlog,errorLog) << "Specifiy at least one valid file" << STD_endl; return -1; } } Data* maskptr=0; Data maskdata; Data inmaskdata; if(maskfile!="") { if(inmaskdata.autoread(maskfile,ropts)<0) return -1; if( inmaskdata.extent(0) && same_shape(data1, inmaskdata, TinyVector(0,1,1,1) ) ) { maskdata.resize(data1.shape()); maskdata=0.0; for(int i=0; i index=data1.create_index(i); TinyVector maskindex=index; maskindex(0)=0; if(inmaskdata(maskindex)>0.0) maskdata(index)=1.0; } maskptr=&maskdata; } else { ODINLOG(odinlog,errorLog) << "Shape mismatch: datashape/maskshape=" << data1.shape() << "/" << inmaskdata.shape() << STD_endl; return -1; } } prot.system.set_data_type(TypeTraits::type2label(float(0))); // Store results in float if(binaryop) { if(maskptr) { ODINLOG(odinlog,normalDebug) << "data1/data2/maskdata" << data1.shape() << "/" << data2.shape() << "/" << maskdata.shape() << STD_endl; data1=data1*maskdata; data2=data2*maskdata; } if(operation=="lcorr" || operation=="kcorr") { int npts=data1.size(); if(maskptr) npts=int(sum(*maskptr)+0.5); Array vec1(npts); Array vec2(npts); int vecindex=0; for(int i=0; i index=data1.create_index(i); bool include=true; if( maskptr && (*maskptr)(index)<=0.0 ) include=false; if(include) { vec1(vecindex)=data1(index); vec2(vecindex)=data2(index); vecindex++; } } correlationResult coresult; if(operation=="lcorr") coresult=correlation(vec1, vec2); if(operation=="kcorr") coresult=kendall(vec1, vec2); STD_cout << "r/p/z(" << npts << ")=" << coresult.r << "/" << coresult.p << "/" << coresult.z << STD_endl; } else { Data result(outshape); ODINLOG(odinlog,infoLog) << "calculating " << data1.shape() << " " << operation << " " << data2.shape() << " ..." << STD_endl; bool validop=false; if(operation=="+") {validop=true; result=data1+data2;} if(operation=="-") {validop=true; result=data1-data2;} if(operation=="*") {validop=true; result=data1*data2;} if(operation=="/") {validop=true; result=secureDivision(data1,data2);} if(!validop) { ODINLOG(odinlog,errorLog) << "invalid binary operation: " << operation << STD_endl; return -1; } if(result.autowrite(outfile,wopts,&prot)<0) return -1; } return 0; } if(accumulate) { if(maskptr) { data1=data1*maskdata; } double accuresult=0.0; bool validop=false; if(operation=="+") {validop=true; accuresult=sum(data1);} if(operation=="*") {validop=true; accuresult=product(data1);} if(!validop) { ODINLOG(odinlog,errorLog) << "invalid accumulation operator: " << operation << STD_endl; return -1; } STD_cout << accuresult << STD_endl; } if(transform) { if(maskptr) { data1=data1*maskdata; } Data result(outshape); ODINLOG(odinlog,infoLog) << "Calculating " << operation << " " << data1.shape() << " ..." << STD_endl; bool validop=false; if(operation=="abs") {validop=true; result=fabs(data1);} if(operation=="log") {validop=true; result=where(Array(data1)>0.0, Array(log(data1)), float(0.0));} if(operation=="-") {validop=true; result=-data1;} if(operation=="/") {validop=true; result=where(Array(data1)!=0.0, Array(1.0/data1), float(0.0));} if(operation=="acos") {validop=true; result=where(Array(data1)>=-1.0 && Array(data1)<=1.0, Array(acos(data1)), float(0.0));} if(!validop) { ODINLOG(odinlog,errorLog) << "invalid unary operation: " << operation << STD_endl; return -1; } if(result.autowrite(outfile,wopts,&prot)<0) return -1; return 0; } if(stateval) { if(histfile!="") { int nvals=data1.numElements(); if(maskptr) { nvals=0; for(int i=0; inumElements(); i++) { TinyVector index=maskptr->create_index(i); if( (*maskptr)(index)>0.0 ) { nvals++; } } } if(histslots=="") {usage(prot); return -1;} int nslots=atoi(histslots.c_str()); if(histmin=="") {usage(prot); return -1;} float minval=atof(histmin.c_str()); if(histmax=="") {usage(prot); return -1;} float maxval=atof(histmax.c_str()); ODINLOG(odinlog,infoLog) << "calculating histogram with nslots/minval/maxval=" << nslots << "/" << minval << "/" << maxval << STD_endl; if(minval>=maxval) { ODINLOG(odinlog,errorLog) << "histmax must be larger than histmin" << STD_endl; return -1; } float stairoffset=0.5; // centered stairs if(rightstairs) stairoffset=0.0; // assume rightstairs when plotting (xmgrace) Data xvals(nslots); Data yvals(nslots); yvals=0.0; if(minval>0.0 && maxval>0.0) { // Use log histogram float minpow=log10(minval); float maxpow=log10(maxval); float powrange=maxpow-minpow; float step=secureDivision(powrange,nslots); ODINLOG(odinlog,normalDebug) << "minpow/maxpow/powrange/step=" << minpow << "/" << maxpow << "/" << powrange << "/" << step << STD_endl; for(int i=0; i index=data1.create_index(i); if( !(maskptr && (*maskptr)(index)==0.0) ) { float pow=log10(data1(index)); int slot=int(secureDivision(pow-minpow,powrange)*nslots); ODINLOG(odinlog,normalDebug) << "pow/slot=" << pow << "/" << slot << STD_endl; if(slot>=0 && slot index=data1.create_index(i); if( !(maskptr && (*maskptr)(index)==0.0) ) { float val=data1(index); int slot=int(secureDivision(val-minval,range)*nslots); ODINLOG(odinlog,normalDebug) << "val/slot=" << val << "/" << slot << STD_endl; if(slot>=0 && slot meanresult(outshape); meanresult=0.0; Data fluctresult(outshape); fluctresult=0.0; Data stdevresult(outshape); stdevresult=0.0; Data tcourseresult(data1.extent(0)); tcourseresult=0.0; int tcoursepts=0; for(int i=0; i index=meanresult.create_index(i); if(!index(0)) { // only once for all repetitions if( !(maskptr && (*maskptr)(index)==0.0) ) { statisticResult stats=statistics(data1(all,index(1),index(2),index(3))); meanresult(index)= stats.mean; fluctresult(index)=secureDivision(stats.stdev,stats.mean); stdevresult(index)=stats.stdev; tcourseresult(all)+=data1(all,index(1),index(2),index(3)); tcoursepts++; ODINLOG(odinlog,normalDebug) << "mean/stdev(" << index << ")=" << stats.mean << "/" << stats.stdev << STD_endl; } } } if(weightmaskdata.size()) { tcourseresult/=sum(weightmaskdata(0,all,all,all)); } else { tcourseresult/=float(tcoursepts); } if(meanfile!="") if(meanresult.autowrite(meanfile,wopts,&prot)<0) return -1; if(fluctfile!="") if(fluctresult.autowrite(fluctfile,wopts,&prot)<0) return -1; if(stdevfile!="") if(stdevresult.autowrite(stdevfile,wopts,&prot)<0) return -1; if(tcoursefile!="") if(tcourseresult.autowrite(tcoursefile,wopts,&prot)<0) return -1; } else { STD_cout << statistics(data1,maskptr) << STD_endl; } // STD_cout << "median = " << median(data1) << STD_endl; } return 0; } odin-1.8.5/cmdline-utils/miconv.cpp0000644000175000017500000001441411725203123014147 00000000000000#include #include #include /** * \page miconv Conversion utility for medical images * \verbinclude cmdline-utils/miconv.usage * * \section miconv_examples Some examples how to use miconv: * * Read a bunch of DICOM files (format 'dcm'), produced by Siemens, from directory 'mosaic' and convert it to NIFTI file 'mosaic.nii' * with a dialect suitable for FSL: * \verbatim miconv -rf dcm -rdialect siemens -wdialect fsl mosaic mosaic.nii \endverbatim * * Converting a short (16 bit) raw data file '2dseq' of size 256x256 to a DICOM file 'image.dcm': * \verbatim miconv -nx 256 -ny 256 -rf short 2dseq image.dcm \endverbatim */ struct MiConvOpts : JcampDxBlock { JDXstring protfile; JDXstring parlist; MiConvOpts() { protfile.set_cmdline_option("p").set_description("Load this protcol for defaults"); append_member(protfile,"protfile"); parlist.set_cmdline_option("l").set_description("Lists space-separated set of protocol parameters and exits. Use '-l help' to get a list of possible parameters and '-l all' to list all parameters. The parameter 'output-file' must be omitted when using this option."); append_member(parlist,"parlist"); } }; //////////////////////////////////////// void usage(const Protocol& prot) { FileReadOpts ropts; FileWriteOpts wopts; MiConvOpts mopts; FilterFactory filter; STD_cout << "miconv: Converts medical image data between formats." << STD_endl; STD_cout << " File formats are automatically identified by their file extension." << STD_endl; STD_cout << " It expects at least two filenames/directories (for the input and output file) at the end of the command line." << STD_endl; STD_cout << " An exception is the option '-l' which requires only one filename/directory to list its content." << STD_endl; STD_cout << "Usage: miconv [options] []" << STD_endl; STD_cout << "General options:" << STD_endl; STD_cout << mopts.get_cmdline_usage("\t"); STD_cout << "Protocol options:" << STD_endl; STD_cout << prot.get_cmdline_usage("\t"); STD_cout << "File read options:" << STD_endl; STD_cout << ropts.get_cmdline_usage("\t"); STD_cout << "File write options:" << STD_endl; STD_cout << wopts.get_cmdline_usage("\t"); STD_cout << "Filters:" << STD_endl; STD_cout << filter.get_cmdline_usage("\t"); STD_cout << "Other options:" << STD_endl; STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; STD_cout << "Supported file extensions(formats):" << STD_endl; STD_cout << FileIO::autoformats_str("\t") << STD_endl; } //////////////////////////////////////// int main(int argc, char* argv[]) { if(LogBase::set_log_levels(argc,argv)) return 0; Log odinlog("miconv","main"); char optval[ODIN_MAXCHAR]; Protocol prot_template; FileReadOpts ropts; FileWriteOpts wopts; MiConvOpts mopts; if(hasHelpOption(argc,argv)) {usage(prot_template); return 0;} if(argc<3) {usage(prot_template); return 0;} // set defaults prot_template.seqpars.set_MatrixSize(readDirection,1); prot_template.seqpars.set_MatrixSize(phaseDirection,1); prot_template.seqpars.set_MatrixSize(sliceDirection,1); mopts.parse_cmdline_options(argc,argv); STD_string infile; STD_string outfile; if(mopts.parlist!="") { infile=argv[argc-1]; } else { infile=argv[argc-2]; outfile=argv[argc-1]; } if(mopts.parlist=="help") { STD_cout << "Possible protocol parameters:" << STD_endl; for(unsigned int i=0; ifirst.printval(pars[ipar]), "\n", ""); // truncate after first newline } STD_ostringstream oss; oss << pdit->second.shape(); table(npars,imap)=oss.str(); imap++; } STD_cout << print_table(table); return 0; } ODINLOG(odinlog,normalDebug) << "mem(in ): " << Profiler::get_memory_usage() << STD_endl; // Create copy of protocol-data map, thereby modify protocol FileIO::ProtocolDataMap pdmap_out; for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap_in.begin(); pdit!=pdmap_in.end(); ++pdit) { Protocol prot(pdit->first); prot.parse_cmdline_options(argc,argv); // override parameters of infile pdmap_out[prot].reference(pdit->second); } ODINLOG(odinlog,normalDebug) << "mem(out): " << Profiler::get_memory_usage() << STD_endl; // Parse before filters to remove options wopts.parse_cmdline_options(argc,argv); FilterChain filterchain(argc,argv); //apply filters on pdmap_out if(!filterchain.apply(pdmap_out)) return -1; // Write data int result=FileIO::autowrite(pdmap_out, outfile, wopts); if(result>0) result=0; return result; } odin-1.8.5/cmdline-utils/micalc.10000644000175000017500000002173211734623251013473 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH MICALC "1" "March 2012" "micalc 1.8.5" "User Commands" .SH NAME micalc \- Performs basic mathematics with data sets .SH DESCRIPTION micalc: Performs basic mathematics with data sets .IP File formats are automatically identified by their file extension. .SS "micalc can be used in one of the following modes:" .IP Binary operation with data sets and/or scalar numbers: .IP micalc [\-if1 | \fB\-in1\fR ] \fB\-op\fR [\-if2 | \fB\-in2\fR ] \fB\-of\fR .IP Accumulation of one data set: .IP micalc \fB\-if\fR \fB\-op\fR .IP Transformation (magnitude, logarithm, negation, inversion, or acos) of one data set: .IP micalc \fB\-if\fR \fB\-op\fR \fB\-of\fR .IP Statistics of one data set: .IP micalc \fB\-if\fR [\-mean ] [\-stdev ] [\-fluct ] [\-tcourse ] [\-hist \fB\-histmin\fR \fB\-histmax\fR \fB\-histslots\fR \fB\-rightstairs\fR \fB\-histfract]\fR .SS "Extra options:" .HP \fB\-mask\fR .HP \fB\-weightmask\fR .SS "File read options:" .HP \fB\-date\fR: Date of scan [yyyymmdd] (default=20120328yyyymmdd) .HP \fB\-fp\fR: FOV in phase direction [mm] (default=220.0mm) .HP \fB\-fr\fR: FOV in read direction [mm] (default=220.0mm) .HP \fB\-fs\fR: FOV in slice direction [mm] (default=5.0mm) .HP \fB\-nr\fR: Number of consecutive measurements (default=1) .HP \fB\-nx\fR: Number of points in read direction (default=128) .HP \fB\-ny\fR: Number of points in phase direction (default=128) .HP \fB\-nz\fR: Number of points in slice direction (default=1) .HP \fB\-pbirth\fR: Patients date of birth [yyyymmdd] (default=00000000yyyymmdd) .HP \fB\-pid\fR: Unique patient identifier (default=Unknown) .HP \fB\-pname\fR: Full patient name (default=Unknown) .HP \fB\-psex\fR: Patients sex (options=M F O , default=O) .HP \fB\-pweight\fR: Patients weight [kg] (default=50.0kg) .HP \fB\-scient\fR: Scientist Name (default=Unknown) .HP \fB\-sd\fR: Inter\-slice distance (from center to center) [mm] (default=10.0mm) .HP \fB\-serd\fR: Series Description (default=Unknown) .HP \fB\-serno\fR: Series Number (default=1) .HP \fB\-st\fR: Slice thickness [mm] (default=5.0mm) .HP \fB\-stud\fR: Study Description (default=Unknown) .HP \fB\-tcname\fR: Name of transmit coil (default=Unknown) .HP \fB\-te\fR: Time\-to\-echo of the sequence [ms] (default=80.0ms) .HP \fB\-time\fR: Time of scan [hhmmss] (default=165641hhmmss) .HP \fB\-tr\fR: Time between consecutive excitations [ms] (default=1000.0ms) .HP \fB\-cplx\fR: Treat data as complex and extract the given component (options=none abs pha real imag , default=none) .HP \fB\-ds\fR: Dataset index to extract if multiple datasets are read .HP \fB\-filter\fR: Read only those datasets which protocol parameter 'key' contains the string 'value' (given in the format 'key=value') .HP \fB\-fmap\fR: For reduced memory usage, keep filemapping after reading (raw) data, but writing into the array will result in a crash .HP \fB\-jdx\fR: If multiple JDX arrays are present, select this .HP \fB\-rdialect\fR: Read data using given dialect of the format. (default is no dialect) .HP \fB\-rf\fR: Read format, use it to override file extension (options=autodetect 3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect) .HP \fB\-skip\fR: Skip this amount of bytes before reading the raw data (default=0) .SS "File write options:" .HP \fB\-append\fR: Append to existing file, only for raw data .HP \fB\-fnamepar\fR: Space\-separated list of protocol parameters to include when creating unique file names .HP \fB\-split\fR: Force splitting of protocol\-data pairs into separate files. .HP \fB\-type\fR: Image representation type (options=automatic float double s32bit u32bit s16bit u16bit s8bit u8bit , default=automatic) .HP \fB\-wdialect\fR: Write data using given dialect of the format. (default is no dialect) .HP \fB\-wf\fR: Write format, use it to override file extension (options=autodetect 3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect) .HP \fB\-wp\fR: Store the protocol separately to this file. .SS "Filters applied to input file(s):" .HP \fB\-align\fR : Align data to the geometry (voxel locations) of an external file .HP \fB\-automask\fR : Create mask using automatic histogram\-based threshold .HP \fB\-detrend\fR : Remove slow drift over time .HP \fB\-genmask\fR : Create mask including all voxels with value in given range .HP \fB\-isotrop\fR : make image voxels isotrop through interpolation (image geometry will not change) .HP \fB\-lowpass\fR : Lowpass filtering .HP \fB\-max\fR : Clip all values above maximum value .HP \fB\-maxip\fR : Perform maximum intensity projection over given direction .HP \fB\-merge\fR : Merge datasets into a single dataset by expanding the time dimension .HP \fB\-min\fR : Clip all values below mininum value .HP \fB\-minip\fR : Perform minimum intensity projection over given direction .HP \fB\-noNaN\fR : Replaces every NaN by the given value .HP \fB\-pflip\fR : Flip data in phase direction .HP \fB\-prange\fR : Select range in phase direction .HP \fB\-proj\fR : Perform projection over given direction .HP \fB\-quantilmask\fR : Create mask including all voxels above the given fractional threshold .HP \fB\-resample\fR : Temporal resize of image data .HP \fB\-resize\fR : Spatial resize of image data .HP \fB\-reslice\fR : reslices the image to a given orientation .HP \fB\-rflip\fR : Flip data in read direction .HP \fB\-rot\fR : In\-plane rotation .HP \fB\-rrange\fR : Select range in read direction .HP \fB\-scale\fR : Rescale image values .HP \fB\-sflip\fR : Flip data in slice direction .HP \fB\-shift\fR : Shift data spatially .HP \fB\-splice\fR : splices the image in the given direction .HP \fB\-srange\fR : Select range in slice direction .HP \fB\-swapdim\fR <[rps][\-],[rps][\-],[rps][\-]> : swap/reflect dimensions by specifying a direction triple with optional reflection sign appended .HP \fB\-tile\fR : Combine slices into a square 2D image .HP \fB\-trange\fR : Select range in time direction .HP \fB\-typemax\fR : Clip all values above maximum of a specific datatype .HP \fB\-typemin\fR : Clip all values below mininum of a specific datatype .HP \fB\-usemask\fR : Create 1D dataset including all values within mask from file .SS "Other options:" .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information .SS "Supported file extensions(formats):" .TP 3db (Iris3D binary data) .TP asc (ASCII, dialects: tcourse ) .TP coi (JCAMP\-DX data sets) .TP dat (Matlab ascii 2D data matrix) .TP dcm (DICOM, dialects: siemens ) .TP double (double raw data) .TP float (float raw data) .TP gz (GNU\-Zip container for other formats) .TP hdr (NIFTI/ANALYZE, dialects: fsl ) .TP idx (3D\-indices of non\-zeroes in ASCII) .TP ima (DICOM, dialects: siemens ) .TP jdx (JCAMP\-DX image format) .TP mag (DICOM, dialects: siemens ) .TP mhd (MetaImage) .TP nii (NIFTI/ANALYZE, dialects: fsl ) .TP ph (DICOM, dialects: siemens ) .TP png (Portable Network Graphics) .TP pos (x\-y positions of non\-zeroes in ASCII) .TP pro (ODIN measurement protocols) .TP reg (Ansoft HFSS ASCII) .TP s16bit (signed 16 bit raw data) .TP s32bit (signed 32 bit raw data) .TP s8bit (signed 8 bit raw data) .TP smp (JCAMP\-DX data sets) .TP u16bit (unsigned 16 bit raw data) .TP u32bit (unsigned 32 bit raw data) .TP u8bit (unsigned 8 bit raw data) .TP vtk (Visualization Toolkit) odin-1.8.5/cmdline-utils/genmakefile.10000644000175000017500000000121511734623244014506 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH GENMAKEFILE "1" "March 2012" "genmakefile 1.8.5" "User Commands" .SH NAME genmakefile \- Generates a Makefile for ODIN methods .SH SYNOPSIS .B genmakefile [\fIoptions\fR] \fI\fR .SH DESCRIPTION genmakefile: Generates a Makefile for ODIN methods .SH OPTIONS .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information odin-1.8.5/cmdline-utils/miconv.10000644000175000017500000002073611734623245013544 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH MICONV "1" "March 2012" "miconv 1.8.5" "User Commands" .SH NAME miconv \- Converts medical image data between formats. .SH SYNOPSIS .B miconv [\fIoptions\fR] \fI \fR[\fI\fR] .SH DESCRIPTION miconv: Converts medical image data between formats. .IP File formats are automatically identified by their file extension. It expects at least two filenames/directories (for the input and output file) at the end of the command line. An exception is the option '\-l' which requires only one filename/directory to list its content. .SS "General options:" .HP \fB\-l\fR: Lists space\-separated set of protocol parameters and exits. Use '\-l help' to get a list of possible parameters and '\-l all' to list all parameters. The parameter 'output\-file' must be omitted when using this option. .HP \fB\-p\fR: Load this protcol for defaults .SS "Protocol options:" .HP \fB\-date\fR: Date of scan [yyyymmdd] (default=20120328yyyymmdd) .HP \fB\-fp\fR: FOV in phase direction [mm] (default=220.0mm) .HP \fB\-fr\fR: FOV in read direction [mm] (default=220.0mm) .HP \fB\-fs\fR: FOV in slice direction [mm] (default=5.0mm) .HP \fB\-nr\fR: Number of consecutive measurements (default=1) .HP \fB\-nx\fR: Number of points in read direction (default=128) .HP \fB\-ny\fR: Number of points in phase direction (default=128) .HP \fB\-nz\fR: Number of points in slice direction (default=1) .HP \fB\-pbirth\fR: Patients date of birth [yyyymmdd] (default=00000000yyyymmdd) .HP \fB\-pid\fR: Unique patient identifier (default=Unknown) .HP \fB\-pname\fR: Full patient name (default=Unknown) .HP \fB\-psex\fR: Patients sex (options=M F O , default=O) .HP \fB\-pweight\fR: Patients weight [kg] (default=50.0kg) .HP \fB\-scient\fR: Scientist Name (default=Unknown) .HP \fB\-sd\fR: Inter\-slice distance (from center to center) [mm] (default=10.0mm) .HP \fB\-serd\fR: Series Description (default=Unknown) .HP \fB\-serno\fR: Series Number (default=1) .HP \fB\-st\fR: Slice thickness [mm] (default=5.0mm) .HP \fB\-stud\fR: Study Description (default=Unknown) .HP \fB\-tcname\fR: Name of transmit coil (default=Unknown) .HP \fB\-te\fR: Time\-to\-echo of the sequence [ms] (default=80.0ms) .HP \fB\-time\fR: Time of scan [hhmmss] (default=165637hhmmss) .HP \fB\-tr\fR: Time between consecutive excitations [ms] (default=1000.0ms) .SS "File read options:" .HP \fB\-cplx\fR: Treat data as complex and extract the given component (options=none abs pha real imag , default=none) .HP \fB\-ds\fR: Dataset index to extract if multiple datasets are read .HP \fB\-filter\fR: Read only those datasets which protocol parameter 'key' contains the string 'value' (given in the format 'key=value') .HP \fB\-fmap\fR: For reduced memory usage, keep filemapping after reading (raw) data, but writing into the array will result in a crash .HP \fB\-jdx\fR: If multiple JDX arrays are present, select this .HP \fB\-rdialect\fR: Read data using given dialect of the format. (default is no dialect) .HP \fB\-rf\fR: Read format, use it to override file extension (options=autodetect 3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect) .HP \fB\-skip\fR: Skip this amount of bytes before reading the raw data (default=0) .SS "File write options:" .HP \fB\-append\fR: Append to existing file, only for raw data .HP \fB\-fnamepar\fR: Space\-separated list of protocol parameters to include when creating unique file names .HP \fB\-split\fR: Force splitting of protocol\-data pairs into separate files. .HP \fB\-type\fR: Image representation type (options=automatic float double s32bit u32bit s16bit u16bit s8bit u8bit , default=automatic) .HP \fB\-wdialect\fR: Write data using given dialect of the format. (default is no dialect) .HP \fB\-wf\fR: Write format, use it to override file extension (options=autodetect 3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect) .HP \fB\-wp\fR: Store the protocol separately to this file. .SS "Filters:" .HP \fB\-align\fR : Align data to the geometry (voxel locations) of an external file .HP \fB\-automask\fR : Create mask using automatic histogram\-based threshold .HP \fB\-detrend\fR : Remove slow drift over time .HP \fB\-genmask\fR : Create mask including all voxels with value in given range .HP \fB\-isotrop\fR : make image voxels isotrop through interpolation (image geometry will not change) .HP \fB\-lowpass\fR : Lowpass filtering .HP \fB\-max\fR : Clip all values above maximum value .HP \fB\-maxip\fR : Perform maximum intensity projection over given direction .HP \fB\-merge\fR : Merge datasets into a single dataset by expanding the time dimension .HP \fB\-min\fR : Clip all values below mininum value .HP \fB\-minip\fR : Perform minimum intensity projection over given direction .HP \fB\-noNaN\fR : Replaces every NaN by the given value .HP \fB\-pflip\fR : Flip data in phase direction .HP \fB\-prange\fR : Select range in phase direction .HP \fB\-proj\fR : Perform projection over given direction .HP \fB\-quantilmask\fR : Create mask including all voxels above the given fractional threshold .HP \fB\-resample\fR : Temporal resize of image data .HP \fB\-resize\fR : Spatial resize of image data .HP \fB\-reslice\fR : reslices the image to a given orientation .HP \fB\-rflip\fR : Flip data in read direction .HP \fB\-rot\fR : In\-plane rotation .HP \fB\-rrange\fR : Select range in read direction .HP \fB\-scale\fR : Rescale image values .HP \fB\-sflip\fR : Flip data in slice direction .HP \fB\-shift\fR : Shift data spatially .HP \fB\-splice\fR : splices the image in the given direction .HP \fB\-srange\fR : Select range in slice direction .HP \fB\-swapdim\fR <[rps][\-],[rps][\-],[rps][\-]> : swap/reflect dimensions by specifying a direction triple with optional reflection sign appended .HP \fB\-tile\fR : Combine slices into a square 2D image .HP \fB\-trange\fR : Select range in time direction .HP \fB\-typemax\fR : Clip all values above maximum of a specific datatype .HP \fB\-typemin\fR : Clip all values below mininum of a specific datatype .HP \fB\-usemask\fR : Create 1D dataset including all values within mask from file .SS "Other options:" .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information .SS "Supported file extensions(formats):" .TP 3db (Iris3D binary data) .TP asc (ASCII, dialects: tcourse ) .TP coi (JCAMP\-DX data sets) .TP dat (Matlab ascii 2D data matrix) .TP dcm (DICOM, dialects: siemens ) .TP double (double raw data) .TP float (float raw data) .TP gz (GNU\-Zip container for other formats) .TP hdr (NIFTI/ANALYZE, dialects: fsl ) .TP idx (3D\-indices of non\-zeroes in ASCII) .TP ima (DICOM, dialects: siemens ) .TP jdx (JCAMP\-DX image format) .TP mag (DICOM, dialects: siemens ) .TP mhd (MetaImage) .TP nii (NIFTI/ANALYZE, dialects: fsl ) .TP ph (DICOM, dialects: siemens ) .TP png (Portable Network Graphics) .TP pos (x\-y positions of non\-zeroes in ASCII) .TP pro (ODIN measurement protocols) .TP reg (Ansoft HFSS ASCII) .TP s16bit (signed 16 bit raw data) .TP s32bit (signed 32 bit raw data) .TP s8bit (signed 8 bit raw data) .TP smp (JCAMP\-DX data sets) .TP u16bit (unsigned 16 bit raw data) .TP u32bit (unsigned 32 bit raw data) .TP u8bit (unsigned 8 bit raw data) .TP vtk (Visualization Toolkit) odin-1.8.5/cmdline-utils/gencoil.10000644000175000017500000000265511734623247013673 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH GENCOIL "1" "March 2012" "gencoil 1.8.5" "User Commands" .SH NAME gencoil \- Generates a virtual coil suitable for sequence simulation in ODIN .SH DESCRIPTION gencoil: Generates a virtual coil suitable for sequence simulation in ODIN .SS "Usage and options:" .IP Generate a radially inhomogenous coil: .IP gencoil \fB\-rad\fR \fB\-n\fR \fB\-fov\fR \fB\-R\fR \fB\-o\fR .IP Generate an array coil by rotating pre\-existing image file: .IP gencoil \fB\-rot\fR \fB\-n\fR \fB\-fov\fR \fB\-nc\fR \fB\-i\fR \fB\-sl\fR \fB\-o\fR .IP Generate an array coil consisting of simple loops: .TP gencoil \fB\-arr\fR \fB\-n\fR \fB\-nc\fR \fB\-fov\fR \fB\-R\fR \fB\-o\fR .IP Generate coil with a B1 gradient: .IP gencoil \fB\-grad\fR \fB\-n\fR \fB\-fov\fR \fB\-g\fR \fB\-o\fR .SS "Other options:" .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information odin-1.8.5/cmdline-utils/Makefile.am0000644000175000017500000000273411322062353014207 00000000000000if ONLY_LIBS else INCLUDES = $(all_includes) bin_PROGRAMS = odintestsuite gencoil gensample genmakefile miconv micalc swab odintestsuite_SOURCES = odintestsuite.cpp gencoil_SOURCES = gencoil.cpp gensample_SOURCES = gensample.cpp genmakefile_SOURCES = genmakefile.cpp miconv_SOURCES = miconv.cpp micalc_SOURCES = micalc.cpp swab_SOURCES = swab.cpp odintestsuite_LDADD = ../odindata/libodindata.la ../odinseq/libodinseq.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la gencoil_LDADD = ../odindata/libodindata.la ../odinseq/libodinseq.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la gensample_LDADD = ../odindata/libodindata.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la genmakefile_LDADD = 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alloc_JDXcomplexTest(); void alloc_JDXboolTest(); void alloc_JDXenumTest(); void alloc_JDXfileNameTest(); void alloc_CoilSensitivityTest(); void alloc_ProtocolTest(); void alloc_DataUtilsTest(); void alloc_DataTest(); void alloc_ComplexDataTest(); void alloc_FileIOTest(); #ifndef FILEIO_ONLY void alloc_FunctionFitTest(); void alloc_LinAlgTest(); void alloc_FunctionIntegralTest(); void alloc_StatisticsTest(); void alloc_GriddingTest(); #endif //FILEIO_ONLY int main(int argc, char* argv[]) { if(LogBase::set_log_levels(argc,argv)) return 0; if(hasHelpOption(argc,argv)) {STD_cout << "UnitTest of ODIN" << STD_endl; return 0;} #ifdef NO_UNIT_TEST STD_cout << "UnitTest disabled" << STD_endl; return 0; #else alloc_TjToolsTest(); alloc_ComplexTest(); alloc_VectorTest(); alloc_ValListTest(); alloc_ListTest(); alloc_StringTest(); alloc_NumericsTest(); alloc_StlTest(); alloc_NdimTest(); alloc_ArrayTest(); alloc_IndexTest(); alloc_ProcessTest(); alloc_ThreadTest(); alloc_JDXintTest(); alloc_JDXstringTest(); alloc_JDXcomplexTest(); alloc_JDXboolTest(); alloc_JDXenumTest(); alloc_JDXfileNameTest(); alloc_JDXstringArrTest(); alloc_JDXintArrTest(); alloc_JDXcomplexArrTest(); alloc_GeometryTest(); alloc_CoilSensitivityTest(); alloc_ProtocolTest(); alloc_DataUtilsTest(); alloc_DataTest(); alloc_ComplexDataTest(); alloc_FileIOTest(); #ifndef FILEIO_ONLY alloc_FunctionFitTest(); alloc_LinAlgTest(); alloc_FunctionIntegralTest(); alloc_StatisticsTest(); alloc_GriddingTest(); #endif //FILEIO_ONLY int result=UnitTest::check_all(); Static::destroy_all(); // testing StaticHandler return result; #endif } odin-1.8.5/cmdline-utils/genmakefile.cpp0000644000175000017500000000154011322062353015120 00000000000000#include /** * \page genmakefile Generate a Makefile for ODIN sequences * \verbinclude cmdline-utils/genmakefile.usage */ void usage() { STD_cout << "genmakefile: Generates a Makefile for ODIN methods" << STD_endl; STD_cout << "Usage: genmakefile [options] " << STD_endl; STD_cout << "Options:" << STD_endl; STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; } int main(int argc, char* argv[]) { LogBase::set_log_levels(argc,argv); if(hasHelpOption(argc,argv)) {usage(); return 0;} char buff[ODIN_MAXCHAR]; if(argc<=1) {usage(); exit(0);} STD_string methlabel; if(getLastArgument(argc,argv,buff,ODIN_MAXCHAR)) { methlabel=buff; } SeqMakefile mf(methlabel,INSTALL_PREFIX); STD_cout << mf.get_Makefile(".") << STD_endl; return 0; } odin-1.8.5/cmdline-utils/swab.10000644000175000017500000000102711734623244013174 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH SWAB: "1" "March 2012" "swab: Mirrors bytes, in the case of 2, it swaps adjacent bytes" "User Commands" .SH NAME swab: \- Mirrors bytes, in the case of 2, it swaps adjacent bytes .SH SYNOPSIS .B swab \fI \fR .SH DESCRIPTION swab: Mirrors bytes, in the case of 2, it swaps adjacent bytes .PP Usage: swab odin-1.8.5/cmdline-utils/gensample.cpp0000644000175000017500000003771111363773560014653 00000000000000#include #include /** * \page gensample Generate a sample file * \verbinclude cmdline-utils/gensample.usage */ void inplane_reduction(Data& map, int factor) { if(factor>1) { TinyVector newshape=map.shape(); newshape(3)/=factor; newshape(2)/=factor; map.congrid(newshape); } } farray create_map(const Data& inmap) { Range all=Range::all(); TinyVector inshape=inmap.shape(); Data outmap(inshape(0),1,inshape(1),inshape(2),inshape(3)); outmap(all,0,all,all,all)=inmap; return outmap; } ///////////////////////////////////////////////////////////////////////////////////////////////// void usage(const STD_string& missing_arg="") { STD_cout << STD_endl; STD_cout << "gensample: Generates a virtual sample suitable for sequence simulation in ODIN" << STD_endl; STD_cout << STD_endl; STD_cout << "Usage and options:" << STD_endl; STD_cout << " Create a sample from external maps:" << STD_endl; STD_cout << " gensample -fr -fp -fs -s0 [-t1 ] [-t2 ] [-pm ] [-ir ] [-ss ] [-fr ] -o " << STD_endl; STD_cout << " Create a point-spread function:" << STD_endl; STD_cout << " gensample -psf -t1 -t2 [-dc ] -o " << STD_endl; STD_cout << " Create rectangle of uniform spin distribution about origin in all 3 spatial dimensions:" << STD_endl; STD_cout << " gensample -uni -n -f [-t1 ] [-t2 ] -o " << STD_endl; STD_cout << " Create an isochromat distribution:" << STD_endl; STD_cout << " gensample -iso -n -df -t1 -t2 [-dc ] -o " << STD_endl; STD_cout << " Create a homogenous disk with given radius:" << STD_endl; STD_cout << " gensample -dsk -n -f -R [-t1 ] [-t2 ] [-dc ] -o " << STD_endl; STD_cout << " Create coaxial cylinder:" << STD_endl; STD_cout << " gensample -cyl -n -f -Xi -Xo -Ri -Ro [-t1 -t2 -sl ] -o " << STD_endl; STD_cout << "Other options:" << STD_endl; STD_cout << " " << LogBase::get_usage() << STD_endl; STD_cout << " " << helpUsage() << STD_endl; if(missing_arg!="") STD_cout << "Missing argument: -" << missing_arg << STD_endl; } int main(int argc, char* argv[]) { LogBase::set_log_levels(argc,argv); Log odinlog("gensample","main"); if(hasHelpOption(argc,argv)) {usage(); return 0;} Range all=Range::all(); char optval[ODIN_MAXCHAR]; STD_string phantom_fname; if(getCommandlineOption(argc,argv,"-o",optval,ODIN_MAXCHAR)) phantom_fname=optval; else {usage("o");exit(0);} Sample sample("Virtual Sample",false); bool valid_mode=false; ////////////////////////////////////////////////////////////////////////////////////////////////////////// if(isCommandlineOption(argc,argv,"-psf")) { ODINLOG(odinlog,infoLog) << "Creating point spread function" << STD_endl; float t1=0.0; float t2=0.0; float D=0.0; if(getCommandlineOption(argc,argv,"-t1",optval,ODIN_MAXCHAR)) t1=atof(optval); else {usage("t1");exit(0);} if(getCommandlineOption(argc,argv,"-t2",optval,ODIN_MAXCHAR)) t2=atof(optval); else {usage("t2");exit(0);} if(getCommandlineOption(argc,argv,"-dc",optval,ODIN_MAXCHAR)) D=atof(optval); sample.resize(1,1,1,1,1); farray point(sample.get_extent()); point=1.0; sample.set_spinDensity(point); point=t1; sample.set_T1map(point); point=t2; sample.set_T2map(point); point=D; sample.set_DcoeffMap(point); sample.set_FOV(10.0); valid_mode=true; } ////////////////////////////////////////////////////////////////////////////////////////////////////////// if(isCommandlineOption(argc,argv,"-iso")) { ODINLOG(odinlog,infoLog) << "Creating isochromat distribution" << STD_endl; float t1,t2,df; int n; float D=0; if(getCommandlineOption(argc,argv,"-df",optval,ODIN_MAXCHAR)) df=atof(optval); else {usage("df");exit(0);} if(getCommandlineOption(argc,argv,"-t1",optval,ODIN_MAXCHAR)) t1=atof(optval); else {usage("t1");exit(0);} if(getCommandlineOption(argc,argv,"-t2",optval,ODIN_MAXCHAR)) t2=atof(optval); else {usage("t2");exit(0);} if(getCommandlineOption(argc,argv,"-n" ,optval,ODIN_MAXCHAR)) n=atoi(optval); else {usage("n");exit(0);} if(getCommandlineOption(argc,argv,"-dc",optval,ODIN_MAXCHAR)) D=atof(optval); float total_width=4.0*df; sample.resize(1,n,1,1,1); sample.set_freqrange(total_width); farray map(sample.get_extent()); map=t1; sample.set_T1map(map); map=t2; sample.set_T2map(map); map=D; sample.set_DcoeffMap(map); float sum=0.0; for(int i=0; i=0) nz=1; ODINLOG(odinlog,infoLog) << "nx/nz=" << nx << "/" << nz << STD_endl; ODINLOG(odinlog,infoLog) << "Initializing sample ..." << STD_endl; sample.resize(1,1,nz,1,nx); // x-z-plane sample.set_FOV(xAxis, fov); sample.set_FOV(yAxis, 1.0); sample.set_FOV(zAxis, fov); if(sl>=0) sample.set_FOV(zAxis, fov/n); ODINLOG(odinlog,infoLog) << "Initializing maps ..." << STD_endl; farray map(sample.get_extent()); farray sdmap (sample.get_extent()); sdmap=1.0; ODINLOG(odinlog,infoLog) << "Setting T1/T2 maps " << STD_endl; if(t1>0.0) {map=t1; sample.set_T1map(map);} if(t2>0.0) {map=t2; sample.set_T2map(map);} ODINLOG(odinlog,infoLog) << "Calculating sample ..." << STD_endl; map=0.0; ndim ii(n_sampleDim); ii[frameDim]=0; ii[freqDim]=0; ii[yDim]=0; for(int iz=0; iz=0) z=(double(sl)/double(n)-0.5)*fov; float r=norm(x,z); ii[zDim]=iz; ii[xDim]=ix; if(r>=Ri && r<=Ro) { if(Xo==0.0 && Xi==0.0) map(ii)=0.0; else { float factor=0.5*(Xo-Xi)*Ri*Ri; map(ii)=1.0-Xo/6.0 + secureDivision(factor*(x*x-z*z),r*r*r*r); } } else { sdmap(ii)=0.0; } } } ODINLOG(odinlog,infoLog) << "Setting spinDensity/ppmMap maps ..." << STD_endl; sample.set_spinDensity(sdmap); sample.set_ppmMap(map); valid_mode=true; } ////////////////////////////////////////////////////////////////////////////////////////////////////////// if(isCommandlineOption(argc,argv,"-dsk")) { ODINLOG(odinlog,infoLog) << "Creating disk" << STD_endl; float t1=0.0; float t2=0.0; float fov,R; int n; int nz=1; //20; float D=0; if(getCommandlineOption(argc,argv,"-t1",optval,ODIN_MAXCHAR)) t1=atof(optval); if(getCommandlineOption(argc,argv,"-t2",optval,ODIN_MAXCHAR)) t2=atof(optval); if(getCommandlineOption(argc,argv,"-dc",optval,ODIN_MAXCHAR)) D=atof(optval); if(getCommandlineOption(argc,argv,"-n" ,optval,ODIN_MAXCHAR)) n=atoi(optval); else {usage("n");exit(0);} if(getCommandlineOption(argc,argv,"-f" ,optval,ODIN_MAXCHAR)) fov=atof(optval);else {usage("f");exit(0);} if(getCommandlineOption(argc,argv,"-R" ,optval,ODIN_MAXCHAR)) R=atof(optval); else {usage("R");exit(0);} ODINLOG(odinlog,infoLog) << "Initializing sample ..." << STD_endl; sample.resize(1,1,nz,n,n); sample.set_FOV(xAxis, fov); sample.set_FOV(yAxis, fov); sample.set_FOV(zAxis, nz); ODINLOG(odinlog,infoLog) << "Initializing maps ..." << STD_endl; farray sdmap (sample.get_extent()); sdmap=0.0; farray Dmap (sample.get_extent()); Dmap=0.0; ODINLOG(odinlog,infoLog) << "Setting T1/T2 " << STD_endl; if(t1>0.0) {sample.set_T1(t1);} if(t2>0.0) {sample.set_T2(t2);} ODINLOG(odinlog,infoLog) << "Calculating sample ..." << STD_endl; for(int iy=0; iy0.0) {map=t1; sample.set_T1map(map);} if(t2>0.0) {map=t2; sample.set_T2map(map);} if(t2>0.0) {map=1.0; sample.set_spinDensity(map);} valid_mode=true; } ////////////////////////////////////////////////////////////////////////////////////////////////////////// if(!valid_mode) { ODINLOG(odinlog,infoLog) << "Combining arrays" << STD_endl; int inplane_reduction_factor=1; int single_slice=-1; dvector frame_durations; float FOVread; float FOVphase; float FOVslice; STD_string S0map_fname; STD_string T1map_fname; STD_string T2map_fname; STD_string ppmMap_fname; if(getCommandlineOption(argc,argv,"-fr",optval,ODIN_MAXCHAR)) FOVread=atof(optval); else {usage("fr");exit(0);} if(getCommandlineOption(argc,argv,"-fp",optval,ODIN_MAXCHAR)) FOVphase=atof(optval); else {usage("fp");exit(0);} if(getCommandlineOption(argc,argv,"-fs",optval,ODIN_MAXCHAR)) FOVslice=atof(optval); else {usage("fs");exit(0);} if(getCommandlineOption(argc,argv,"-s0",optval,ODIN_MAXCHAR)) S0map_fname=optval; else {usage("s0");exit(0);} if(getCommandlineOption(argc,argv,"-t1",optval,ODIN_MAXCHAR)) T1map_fname=optval; if(getCommandlineOption(argc,argv,"-t2",optval,ODIN_MAXCHAR)) T2map_fname=optval; if(getCommandlineOption(argc,argv,"-pm",optval,ODIN_MAXCHAR)) ppmMap_fname=optval; if(getCommandlineOption(argc,argv,"-ir",optval,ODIN_MAXCHAR)) inplane_reduction_factor=atoi(optval); if(getCommandlineOption(argc,argv,"-ss",optval,ODIN_MAXCHAR)) single_slice=atoi(optval); int nframes_arg=0; if(getCommandlineOption(argc,argv,"-fr",optval,ODIN_MAXCHAR)) { svector toks=tokens(optval,','); nframes_arg=toks.size(); ODINLOG(odinlog,infoLog) << "nframes_arg=" << nframes_arg << STD_endl; frame_durations.resize(nframes_arg); for(unsigned int i=0; i filedata_s0; filedata_s0.autoread(S0map_fname); nframes_max=STD_max(nframes_max, filedata_s0.extent(0)); Data filedata_t1; if(T1map_fname!="") filedata_t1.autoread(T1map_fname); nframes_max=STD_max(nframes_max, filedata_t1.extent(0)); Data filedata_t2; if(T2map_fname!="") filedata_t2.autoread(T2map_fname); nframes_max=STD_max(nframes_max, filedata_t2.extent(0)); Data filedata_ppmmap; if(ppmMap_fname!="") filedata_ppmmap.autoread(ppmMap_fname); nframes_max=STD_max(nframes_max, filedata_ppmmap.extent(0)); ODINLOG(odinlog,infoLog) << "nframes_max=" << nframes_max << STD_endl; if(nframes_max==nframes_arg) { sample.set_frame_durations(frame_durations); } else { ODINLOG(odinlog,infoLog) << "nframes_max(" << nframes_max << ") != nframes_arg(" << nframes_arg << ")" << STD_endl; return -1; } if(single_slice>=0) { FOVslice/=filedata_s0.extent(1); filedata_s0.reference(filedata_s0(all,Range(single_slice,single_slice),all,all)); if(filedata_t1.size()) { filedata_t1.reference(filedata_t1(all,Range(single_slice,single_slice),all,all)); } if(filedata_t2.size()) { filedata_t2.reference(filedata_t2(all,Range(single_slice,single_slice),all,all)); } if(filedata_ppmmap.size()) { filedata_ppmmap.reference(filedata_t2(all,Range(single_slice,single_slice),all,all)); } } /* for(int i=0; i index=filedata_s0.create_index(i); bool valid_voxel=true; if(filedata_s0(index)<=0.0) valid_voxel=false; if(filedata_t1(index)<=0.0) valid_voxel=false; if(filedata_t2(index)<=0.0) valid_voxel=false; if(!valid_voxel) { filedata_s0(index)=0.0; filedata_t1(index)=0.0; filedata_t2(index)=0.0; filedata_ppmmap(index)=0.0; } } */ if(inplane_reduction_factor>1) { inplane_reduction(filedata_s0,inplane_reduction_factor); if(filedata_t1.size()) inplane_reduction(filedata_t1,inplane_reduction_factor); if(filedata_t2.size()) inplane_reduction(filedata_t2,inplane_reduction_factor); if(filedata_ppmmap.size()) inplane_reduction(filedata_ppmmap,inplane_reduction_factor); } TinyVector s0shape=filedata_s0.shape(); sample.resize(s0shape(0),1,s0shape(1),s0shape(2),s0shape(3)); sample.set_FOV(xAxis, FOVread); sample.set_FOV(yAxis, FOVphase); sample.set_FOV(zAxis, FOVslice); sample.set_spinDensity(create_map(filedata_s0)); if(filedata_t1.size()) sample.set_T1map(create_map(filedata_t1)); else sample.set_T1(1000.0); if(filedata_t2.size()) sample.set_T2map(create_map(filedata_t2)); else sample.set_T2(100.0); if(filedata_ppmmap.size()) sample.set_ppmMap(create_map(filedata_ppmmap)); } ODINLOG(odinlog,infoLog) << "sample.get_extent()=" << STD_string(sample.get_extent()) << STD_endl; sample.write(phantom_fname); return 0; } odin-1.8.5/cmdline-utils/gensample.10000644000175000017500000000410011734623245014207 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH GENSAMPLE "1" "March 2012" "gensample 1.8.5" "User Commands" .SH NAME gensample \- Generates a virtual sample suitable for sequence simulation in ODIN .SH DESCRIPTION gensample: Generates a virtual sample suitable for sequence simulation in ODIN .SS "Usage and options:" .IP Create a sample from external maps: .TP gensample \fB\-fr\fR \fB\-fp\fR \fB\-fs\fR \fB\-s0\fR [\-t1 ] [\-t2 ] [\-pm ] [\-ir ] [\-ss ] [\-fr ] \fB\-o\fR .IP Create a point\-spread function: .IP gensample \fB\-psf\fR \fB\-t1\fR \fB\-t2\fR [\-dc ] \fB\-o\fR .IP Create rectangle of uniform spin distribution about origin in all 3 spatial dimensions: .IP gensample \fB\-uni\fR \fB\-n\fR \fB\-f\fR [\-t1 ] [\-t2 ] \fB\-o\fR .IP Create an isochromat distribution: .IP gensample \fB\-iso\fR \fB\-n\fR \fB\-df\fR \fB\-t1\fR \fB\-t2\fR [\-dc ] \fB\-o\fR .IP Create a homogenous disk with given radius: .IP gensample \fB\-dsk\fR \fB\-n\fR \fB\-f\fR \fB\-R\fR [\-t1 ] [\-t2 ] [\-dc ] \fB\-o\fR .IP Create coaxial cylinder: .IP gensample \fB\-cyl\fR \fB\-n\fR \fB\-f\fR \fB\-Xi\fR \fB\-Xo\fR \fB\-Ri\fR \fB\-Ro\fR [\-t1 \fB\-t2\fR \fB\-sl\fR ] \fB\-o\fR .SS "Other options:" .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information odin-1.8.5/configure.in0000644000175000017500000006675111714537614011740 00000000000000dnl Boilerplate AC_INIT(tjutils/tjutils.h) AC_PREREQ(2.57) AM_INIT_AUTOMAKE(odin,1.8.5) AM_CONFIG_HEADER(tjutils/config.h) AC_PREFIX_DEFAULT(/usr/local) if test "x$prefix" = "xNONE"; then prefix=$ac_default_prefix ac_configure_args="$ac_configure_args --prefix $prefix" fi dnl Options AC_ARG_ENABLE([debug], [AC_HELP_STRING([--enable-debug],[Include code for debugging/tracing])], enable_debug=yes ) AC_ARG_ENABLE([stdcpp-replacement], [AC_HELP_STRING([--enable-stdcpp-replacement],[Use built-in replacement for C++ standard library (STL, strings, streams)])], enable_stdcpp_replacement=yes ) AC_ARG_ENABLE([custom-heap], [AC_HELP_STRING([--enable-custom-heap=SIZE],[Use a heap which is a static block of memory (SIZE MB large), useful for real-time systems which do not have a safe new/delete])], enable_custom_heap=yes custom_heap_size=$enableval if test "$enableval" = "yes"; then custom_heap_size=2; fi ) AC_ARG_ENABLE([cmdline], [AC_HELP_STRING([--disable-cmdline],[Disable code for the command line, useful for real-time systems])], enable_cmdline=no, enable_cmdline=yes ) AC_ARG_ENABLE([filehandling], [AC_HELP_STRING([--disable-filehandling],[Disable code for file handling, useful if ODIN is used on a platform without file system])], enable_filehandling=no, enable_filehandling=yes ) AC_ARG_ENABLE([threads], [AC_HELP_STRING([--disable-threads],[Disable multithreading])], enable_threads=no, enable_threads=yes ) AC_ARG_ENABLE([unit-test], [AC_HELP_STRING([--disable-unit-test],[Disable unit test])], enable_unittest=no, enable_unittest=yes ) AC_ARG_ENABLE([gui], [AC_HELP_STRING([--disable-gui],[Disable graphical user interface])], enable_gui=no, enable_gui=yes ) AC_ARG_ENABLE([only-corelibs], [AC_HELP_STRING([--enable-only-corelibs],[Compile only the essential libraries for sequence execution (tjutils/odinpara/odinseq)])], enable_onlylibs=yes ) srcdir_abs=$(cd "$srcdir" && pwd) have_ideaplugin=no have_paravisionplugin=no have_standaloneplugin=no have_epicplugin=no if test -d $srcdir_abs/platforms/IDEA_n4 ; then have_ideaplugin=yes ; fi if test -d $srcdir_abs/platforms/Paravision ; then have_paravisionplugin=yes ; fi if test -d $srcdir_abs/platforms/StandAlone ; then have_standaloneplugin=yes ; fi if test -d $srcdir_abs/platforms/EPIC ; then have_epicplugin=yes ; fi enable_ideaplugin=$have_ideaplugin enable_paravisionplugin=$have_paravisionplugin enable_standaloneplugin=$have_standaloneplugin enable_epicplugin=$have_epicplugin AC_ARG_ENABLE([only-epic-plugin], [AC_HELP_STRING([--enable-only-epic-plugin],[Compile only the plugin for Epic])], enable_ideaplugin=no enable_paravisionplugin=no enable_standaloneplugin=no ) AC_ARG_ENABLE([only-idea-plugin], [AC_HELP_STRING([--enable-only-idea-plugin],[Compile only the plugin for IDEA(Siemens)])], enable_paravisionplugin=no enable_standaloneplugin=no enable_epicplugin=no ) AC_ARG_ENABLE([only-paravision-plugin], [AC_HELP_STRING([--enable-only-paravision-plugin],[Compile only the plugin for Paravision(Bruker)])], enable_ideaplugin=no enable_standaloneplugin=no enable_epicplugin=no ) AC_ARG_ENABLE([only-standalone-plugin], [AC_HELP_STRING([--enable-only-standalone-plugin],[Compile only the plugin for stand-alone mode])], enable_ideaplugin=no enable_paravisionplugin=no enable_epicplugin=no ) dnl disable unavailable plugins if test "x$have_ideaplugin" = "xno" ; then enable_ideaplugin=no ; fi if test "x$have_paravisionplugin" = "xno" ; then enable_paravisionplugin=no ; fi if test "x$have_standaloneplugin" = "xno" ; then enable_standaloneplugin=no ; fi if test "x$have_epicplugin" = "xno" ; then enable_epicplugin=no ; fi AC_ARG_ENABLE([ideasupport], [AC_HELP_STRING([--enable-ideasupport],[Compile against IDEA(Siemens) libraries, implies --enable-only-corelibs and --enable-stdcpp-replacement])], enable_ideasupport=yes enable_onlylibs=yes enable_stdcpp_replacement=yes ) AC_ARG_ENABLE([niftisupport], [AC_HELP_STRING([--enable-niftisupport],[Use libniftiio to read/write NIFTI files])], enable_niftisupport="$enableval" ) AC_ARG_ENABLE([vtksupport], [AC_HELP_STRING([--enable-vtksupport],[Use VTK for input/output and visualization])], enable_vtksupport="$enableval" ) AC_ARG_ENABLE([dcmtksupport], [AC_HELP_STRING([--enable-dcmtksupport],[Use DICOMTK to read/write DICOM files])], enable_dcmtksupport="$enableval" ) AC_ARG_ENABLE([pngsupport], [AC_HELP_STRING([--enable-pngsupport],[Use libpng to write PNG files])], enable_pngsupport="$enableval" ) AC_ARG_WITH([qt-dir], [AC_HELP_STRING([--with-qt-dir=DIR],[Base directory of the Qt library])], with_qtdir=$withval ) AC_ARG_WITH([extra-include-base], [AC_HELP_STRING([--with-extra-include-base=DIR],[Extra base to find includes (default=/usr/include)])], extra_include_base=$withval, extra_include_base="/usr/include" ) AC_ARG_WITH([extra-build-cxxflags], [AC_HELP_STRING([--with-extra-build-cxxflags=FLAGS],[Extra compiler flags during ODIN build (but not during sequence compilation)])], extra_cxxflags=$withval ) AC_ARG_WITH([extra-build-ldflags], [AC_HELP_STRING([--with-extra-build-ldflags=FLAGS],[Extra linker flags during ODIN build (but not during sequence compilation)])], extra_ldflags=$withval ) AC_ARG_WITH([extra-odinseq-include-path], [AC_HELP_STRING([--with-extra-odinseq-include-path=PATH],[Extra include path for odinseq during ODIN build (but not during sequence compilation)])], extra_odinseq_includes=$withval ) AC_ARG_WITH([lapack-libname], [AC_HELP_STRING([--with-lapack-libname=LIBNAME],[Library name of LAPACK (default=lapack)])], lapack_libname=$withval, lapack_libname="lapack" ) AC_ARG_WITH([editor], [AC_HELP_STRING([--with-editor=EDITOR],[Initial settings for editor (default=/usr/bin/sensible-editor)])], initial_editor=$withval, initial_editor="/usr/bin/sensible-editor" ) AC_ARG_WITH([browser], [AC_HELP_STRING([--with-browser=BROWSER],[Initial settings for browser (default=/usr/bin/sensible-browser)])], initial_browser=$withval, initial_browser="/usr/bin/sensible-browser" ) dnl Cache user-supplied compiler flags, but ignore compiler flags of AC_PROG_CXX CXXFLAGS_CACHE="$CXXFLAGS" dnl Set C++ as the programming language and check for C++ compiler AC_LANG(C++) AC_PROG_CXX dnl Add compiler flags in debug/release mode if test "x$enable_debug" = "xyes" ; then dnl Disable debugging symbols and warnings when compiling for VxWorks if test "x$enable_ideasupport" = "xyes" ; then CXXFLAGS="-O2" else CXXFLAGS="-O2 -g -Wall" fi AC_MSG_CHECKING(whether compiler accepts debug flag(s) $CXXFLAGS) AC_COMPILE_IFELSE(int main() {return 0;}, AC_MSG_RESULT(yes); EXTRA_CXXFLAGS="$CXXFLAGS", AC_MSG_RESULT(no)) else dnl work around GCC bug CXXFLAGS="-O3 -fno-tree-vectorize" AC_MSG_CHECKING(whether compiler accepts release flag(s) $CXXFLAGS) AC_COMPILE_IFELSE(int main() {return 0;}, AC_MSG_RESULT(yes); EXTRA_CXXFLAGS="$CXXFLAGS", AC_MSG_RESULT(no)) fi CXXFLAGS="$EXTRA_CXXFLAGS $CXXFLAGS_CACHE" dnl Checks for debugger and xterm to attach debugger AC_CHECK_PROGS(GDB, gdb) AC_CHECK_PROGS(XTERM, xterm) dnl libtool stuff AC_ENABLE_SHARED(yes) AC_ENABLE_STATIC(no) AC_PROG_LIBTOOL dnl cache CXXFLAGS/CPPFLAGS/LDFLAGS for sequence compilation before adding extra_ldflags to exclude absolut pathes and Qt libs on windows CXXFLAGS_EXPORT="$CXXFLAGS" CPPFLAGS_EXPORT="$CPPFLAGS" LDFLAGS_EXPORT="$LDFLAGS" dnl add compiler/linker flags for ODIN build CXXFLAGS="$extra_cxxflags $CXXFLAGS" CPPFLAGS="$extra_cxxflags $CPPFLAGS" LDFLAGS="$extra_ldflags $LDFLAGS" case $host in *apple*) macos=yes ;; esac dnl Checks for libraries. if test "x$enable_onlylibs" = "xyes" ; then AC_MSG_NOTICE([Discarding library linking due to --enable-only-corelibs]) else LIBS_RETAIN="$LIBS" AC_CHECK_LIB(m,sin,LIBS="-lm $LIBS"; BASELIBS="-lm $BASELIBS") valid_dl=yes AC_CHECK_LIB(dl,dlopen,LIBS="-ldl $LIBS"; BASELIBS="-ldl $BASELIBS",valid_dl=no) AC_CHECK_HEADER(dlfcn.h,,valid_dl=no) valid_pthread=yes AC_CHECK_LIB(pthread,pthread_create,LIBS="-lpthread $LIBS"; BASELIBS="-lpthread $BASELIBS",valid_pthread=no) AC_CHECK_HEADER(pthread.h,,valid_pthread=no) valid_libz=yes AC_CHECK_LIB(z,main,LIBS="-lz $LIBS"; DATALIBS="-lz $DATALIBS", valid_libz=no) AC_CHECK_HEADER(zlib.h,,valid_libz=no) dnl GSL is used in tjutils and odindata so we add it to the global LIBS valid_gsl=yes AC_CHECK_LIB(gslcblas,main,LIBS="-lgslcblas $LIBS"; BASELIBS="-lgslcblas $BASELIBS") AC_CHECK_LIB(gsl,gsl_multifit_fdfsolver_iterate,BASELIBS="-lgsl $BASELIBS",valid_gsl=no) AC_CHECK_HEADER(gsl/gsl_multifit_nlin.h,,valid_gsl=no) if test "x$valid_gsl" = "xno" ; then AC_MSG_ERROR([Please install the GNU Scientific Library (There is probably a precompiled package for your UNIX/Linux distribution, otherwise see http://www.gnu.org/software/gsl)]) fi if test "x$macos" = "xyes" ; then AC_MSG_NOTICE([Using vecLib for lapack support]) valid_lapack=yes lapack_libname="vecLib" else dnl Prerequisites for different lapack implementations if test "$lapack_libname" = "lapack" ; then AC_CHECK_LIB(g2c,i_indx,DATALIBS="-lg2c $DATALIBS"; LIBS="-lg2c $LIBS") fi if test "$lapack_libname" = "acml" ; then AC_CHECK_LIB(acml_mv,main,DATALIBS="-lacml_mv $DATALIBS"; LIBS="-lacml_mv $LIBS") AC_CHECK_LIB(gfortran,main,DATALIBS="-lgfortran $DATALIBS"; LIBS="-lgfortran $LIBS") thread_safe_lapack=yes fi valid_lapack=no AC_CHECK_LIB($lapack_libname,cgelss_,DATALIBS="-l${lapack_libname} $DATALIBS"; valid_lapack=yes) if test "x$valid_lapack" = "xno" ; then AC_MSG_WARN([LAPACK not found (using slower GSL linear algebra instead)]) fi fi valid_blitz=yes AC_CHECK_LIB(blitz,main,DATALIBS="-lblitz $DATALIBS",valid_blitz=no) AC_CHECK_HEADER(blitz/array.h,,valid_blitz=no) AC_CHECK_HEADER(blitz/tinyvec-et.h,,valid_blitz=no) if test "x$valid_blitz" = "xno" ; then AC_MSG_ERROR([Please install Blitz++ (Version 0.8 or higher) in order to use the reconstruction library (There is probably a precompiled package for your UNIX/Linux distribution, otherwise see http://www.oonumerics.org/blitz)]) fi dnl optional libraries if test ! "x$enable_niftisupport" = "xno" ; then lib_nifti=yes dnl Hack for Debian if test -d ${extra_include_base}/nifti ; then all_includes="-I${extra_include_base}/nifti $all_includes" fi AC_CHECK_LIB(znz,main,LIBS="-lznz $LIBS"; DATALIBS="-lznz $DATALIBS") AC_CHECK_LIB(niftiio,nifti_image_read,DATALIBS="-lniftiio $DATALIBS",lib_nifti=no) CPPFLAGS_CACHE="$CPPFLAGS" CPPFLAGS="-DHAVE_CONFIG_H $all_includes $CPPFLAGS" AC_CHECK_HEADER(nifti1_io.h,,lib_nifti=no) CPPFLAGS="$CPPFLAGS_CACHE" if test "x$lib_nifti" = "xno" ; then if test "x$enable_niftisupport" = "xyes" ; then AC_MSG_ERROR([libniftiio missing]) else AC_MSG_WARN([NIFTI I/O library not found, NIFTI support will be disabled]) fi fi fi if test ! "x$enable_vtksupport" = "xno" ; then lib_vtk=yes dnl vtk will also be used by Odin GUI so we add an extra variable VTKLIBS AC_CHECK_LIB(vtkIO,main,DATALIBS="-lvtkIO $DATALIBS",lib_vtk=no) AC_CHECK_LIB(vtkRendering,main,VTKLIBS="-lvtkRendering $VTKLIBS",lib_vtk=no) dnl Hack for Debian for vtk_header_dir in vtk vtk-5.0 vtk-5.2 vtk-5.4 ; do if test -d ${extra_include_base}/${vtk_header_dir} ; then all_includes="-I${extra_include_base}/${vtk_header_dir} $all_includes" fi done CPPFLAGS_CACHE="$CPPFLAGS" CPPFLAGS="-DHAVE_CONFIG_H $all_includes $CPPFLAGS" AC_CHECK_HEADERS(vtkStructuredPoints.h vtkArrowSource.h,,lib_vtk=no) CPPFLAGS="$CPPFLAGS_CACHE" if test "x$lib_vtk" = "xno" ; then if test "x$enable_vtksupport" = "xyes" ; then AC_MSG_ERROR([VTK library missing]) else AC_MSG_WARN([VTK library (Version 4.4 or higher) not found, VTK support will be disabled]) fi fi fi if test ! "x$enable_dcmtksupport" = "xno" ; then lib_dcmtk=yes dnl Hack for Debian (dcmtk 3.5.3) if test -d ${extra_include_base}/dcmtk ; then all_includes="-I${extra_include_base}/dcmtk -I${extra_include_base}/dcmtk/dcmdata -I${extra_include_base}/dcmtk/ofstd $all_includes" fi CPPFLAGS_CACHE="$CPPFLAGS" CPPFLAGS="-DHAVE_CONFIG_H $all_includes $CPPFLAGS" AC_CHECK_HEADER(dcmtk/dcmdata/dcdatset.h,,lib_dcmtk=no) AC_CHECK_HEADER(dcmtk/dcmimgle/dcmimage.h,,lib_dcmtk=no) CPPFLAGS="$CPPFLAGS_CACHE" AC_CHECK_LIB(wsock32,main,LIBS="-lwsock32 $LIBS"; DATALIBS="-lwsock32 $DATALIBS") AC_CHECK_LIB(ofstd,main,LIBS="-lofstd $LIBS"; DATALIBS="-lofstd $DATALIBS",lib_dcmtk=no) AC_CHECK_LIB(oflog,main,LIBS="-loflog $LIBS"; DATALIBS="-loflog $DATALIBS") AC_CHECK_LIB(dcmdata,main,LIBS="-ldcmdata $LIBS"; DATALIBS="-ldcmdata $DATALIBS",lib_dcmtk=no) AC_CHECK_LIB(dcmimgle,main,LIBS="-ldcmimgle $LIBS"; DATALIBS="-ldcmimgle $DATALIBS",lib_dcmtk=no) if test "x$lib_dcmtk" = "xno" ; then if test "x$enable_dcmtksupport" = "xyes" ; then AC_MSG_ERROR([DICOMTK library missing]) else AC_MSG_WARN([DICOMTK library not found, DICOM support will be disabled]) fi fi fi if test ! "x$enable_pngsupport" = "xno" ; then lib_png=yes AC_CHECK_HEADER(png.h,,lib_png=no) AC_CHECK_LIB(png, png_create_write_struct, DATALIBS="-lpng $DATALIBS",lib_png=no) if test "x$lib_png" = "xno" ; then if test "x$enable_pngsupport" = "xyes" ; then AC_MSG_ERROR([libpng missing]) else AC_MSG_WARN([PNG library not found, PNG support will be disabled]) fi fi fi LIBS="$LIBS_RETAIN" fi dnl Checks for C/C++ stanard headers headers AC_CHECK_HEADERS(dirent.h unistd.h time.h) AC_CHECK_HEADERS(sys/stat.h sys/types.h sys/wait.h sys/time.h sys/mman.h) AC_CHECK_HEADERS(locale.h ctype.h) AC_CHECK_HEADERS(signal.h setjmp.h) AC_CHECK_HEADERS(typeinfo) dnl Checks for Windows headers have_win32_api=yes AC_CHECK_HEADERS(windows.h direct.h io.h,,have_win32_api=no) dnl get size of integral types AC_DEFUN([AC_COMPILE_CHECK_SIZEOF], [changequote(<<, >>)dnl dnl The name to #define. define(<>, translit(sizeof_$1, [a-z *], [A-Z_P]))dnl dnl The cache variable name. define(<>, translit(ac_cv_sizeof_$1, [ *], [_p]))dnl changequote([, ])dnl AC_MSG_CHECKING(size of $1) AC_CACHE_VAL(AC_CV_NAME, [for ac_size in 4 8 1 2 16 $2 ; do # List sizes in rough order of prevalence. AC_TRY_COMPILE([#include "confdefs.h" #include $2 ], [switch (0) case 0: case (sizeof ($1) == $ac_size):;], AC_CV_NAME=$ac_size) if test x$AC_CV_NAME != x ; then break; fi done ]) if test x$AC_CV_NAME = x ; then AC_MSG_ERROR([cannot determine a size for $1]) fi AC_MSG_RESULT($AC_CV_NAME) AC_DEFINE_UNQUOTED(AC_TYPE_NAME, $AC_CV_NAME, [The number of bytes in type $1]) undefine([AC_TYPE_NAME])dnl undefine([AC_CV_NAME])dnl ]) AC_COMPILE_CHECK_SIZEOF(char) AC_COMPILE_CHECK_SIZEOF(short) AC_COMPILE_CHECK_SIZEOF(int) AC_COMPILE_CHECK_SIZEOF(long) AC_DEFUN([AC_C_LONG_LONG], [AC_CACHE_CHECK(for long long int, ac_cv_c_long_long, [if test "$GCC" = yes; then ac_cv_c_long_long=yes else AC_TRY_COMPILE(,[long long int i;], ac_cv_c_long_long=yes, ac_cv_c_long_long=no) fi]) if test $ac_cv_c_long_long = yes; then AC_DEFINE(HAVE_LONG_LONG, 1, [compiler understands long long]) fi ]) AC_C_LONG_LONG dnl Checks for library functions. AC_CHECK_FUNCS([j1 snprintf erfc acosh gettimeofday nanosleep srand read stat sysconf stat64 fopen64 open64 fseeko fseeko64 ftello ftello64 mmap64 strftime strptime]) dnl Add configured LIBS and all_includes to exported compiler/linker flags CXXFLAGS_EXPORT="$CXXFLAGS_EXPORT $all_includes" CPPFLAGS_EXPORT="$CPPFLAGS_EXPORT $all_includes" LDFLAGS_EXPORT="$LDFLAGS_EXPORT $LIBS" dnl Find location of GUI libraries, they will NOT get exported to sequence compilation if test "x$enable_onlylibs" = "xyes" ; then AC_MSG_NOTICE([Discarding Qt linking due to --enable-only-corelibs]) enable_gui=no fi if test "x$enable_gui" = "xyes" ; then if test -z $with_qtdir ; then CONF_QTDIR="$QTDIR" else CONF_QTDIR="$with_qtdir" fi AC_PATH_X if test "$x_includes" = "" ; then x_includes="." fi if test "$x_libraries" = "" ; then x_libraries="." fi if ! test "$x_includes" = "NONE" ; then all_includes="-I$x_includes $all_includes" fi dnl Add X11 libraries which might be necessary for Qt dnl if ! test "$x_libraries" = "NONE" ; then dnl LDFLAGS="-L$x_libraries $LDFLAGS" dnl for xlib in X11 Xext ICE SM Xi Xrender Xfixes Xinerama Xrandr Xcursor Xft ; do dnl AC_CHECK_LIB($xlib,main,GUILIBS="-l${xlib} $GUILIBS") dnl done dnl fi dnl Trying to detect QTDIR if not provided if test -z $CONF_QTDIR ; then AC_MSG_NOTICE([Environment variable QTDIR not specified, searching for Qt:]) qtdir_found=no for qtdir in /usr/share/qt3 /usr/share/qt4 ; do for subdir in "" "QtCore/" ; do if test "x$qtdir_found" = "xno" ; then AC_CHECK_FILE($qtdir/include/${subdir}qglobal.h, qtdir_found=yes; CONF_QTDIR=$qtdir) fi done done if test "x$qtdir_found" = "xno" ; then AC_MSG_ERROR([Qt headers not found]); exit -1 fi fi dnl Detect Qt version, start with Qt3 AC_CHECK_FILE($CONF_QTDIR/include/qglobal.h, QTVERSION="3") AC_CHECK_FILE($CONF_QTDIR/include/QtCore/qglobal.h, QTVERSION="4") if test -z $QTVERSION ; then AC_MSG_ERROR([Cannot detect Qt version]); exit -1 fi dnl Add QTDIR to include path all_includes="-I$CONF_QTDIR/include $all_includes" dnl Add QTDIR to lib path if test ! -z $CONF_QTDIR ; then for extra_qt_libdir in lib lib64 ; do if test -d $CONF_QTDIR/$extra_qt_libdir ; then LDFLAGS="-L$CONF_QTDIR/$extra_qt_libdir $LDFLAGS" fi done fi lib_qt=no if test "$QTVERSION" = "3" ; then if test "x$lib_qt" = "xno" ; then AC_CHECK_LIB(qt-mt,main,GUILIBS="-lqt-mt $GUILIBS"; lib_qt=yes; CXXFLAGS="-DQT_THREAD_SUPPORT $CXXFLAGS") fi if test "x$lib_qt" = "xno" ; then AC_CHECK_LIB(qt,main,GUILIBS="-lqt $GUILIBS"; lib_qt=yes) fi fi if test "$QTVERSION" = "4" ; then AC_MSG_NOTICE([Searching for Qt4 subdirs:]) AC_CHECK_FILE($CONF_QTDIR/include/QtCore/QPointF, all_includes="-I$CONF_QTDIR/include/QtCore $all_includes") AC_CHECK_FILE($CONF_QTDIR/include/QtGui/QPolygonF, all_includes="-I$CONF_QTDIR/include/QtGui $all_includes") for qt4_extension in "" "4" ; do if test "x$lib_qt" = "xno" ; then AC_CHECK_LIB(QtCore${qt4_extension},main,GUILIBS="-lQtCore${qt4_extension} $GUILIBS"; lib_qtcore=yes) if test "x$lib_qtcore" = "xyes" ; then AC_CHECK_LIB(QtGui${qt4_extension},main,GUILIBS="-lQtGui${qt4_extension} $GUILIBS"; lib_qt=yes) fi fi done fi if test "x$lib_qt" = "xno" ; then if test -z "$extra_ldflags"; then AC_MSG_ERROR([Qt library not found]); exit -1 else AC_MSG_NOTICE([Assuming that Qt library was specified by --extra-build-ldflags=$extra_ldflags]) fi fi AC_CHECK_FILE($CONF_QTDIR/bin/moc, QTMOC=$CONF_QTDIR/bin/moc) if test -z $QTMOC ; then AC_MSG_ERROR([Qt moc not found]); exit -1 fi QWT_ERROR_STR="Qwt Widget Library not found. There is probably a precompiled package for your UNIX/Linux distribution, otherwise see http://qwt.sourceforge.net" qwt_lib=no if test "$QTVERSION" = "3" ; then AC_CHECK_LIB(qwt,main,GUILIBS="-lqwt $GUILIBS"; qwt_lib=yes) fi if test "$QTVERSION" = "4" ; then for qwt_extension in "-qt4" "" ; do if test "x$qwt_lib" = "xno" ; then AC_CHECK_LIB(qwt${qwt_extension},main,GUILIBS="-lqwt${qwt_extension} $GUILIBS"; qwt_lib=yes) fi done fi if test "x$qwt_lib" = "xno" ; then AC_MSG_ERROR($QWT_ERROR_STR); exit -1 fi dnl Check for Qwt headers CPPFLAGS_CACHE="$CPPFLAGS" CPPFLAGS="$all_includes $CPPFLAGS" dnl Shell expansion does not work in AC_CHECK_HEADERS, therefore, we unroll the loop over header locations qwt_headers=no if test "$QTVERSION" = "4" ; then if test "x$qwt_headers" = "xno" ; then dnl for Debian AC_CHECK_HEADERS(qwt-qt4/qwt_global.h,qwt_headers=yes) fi fi if test "x$qwt_headers" = "xno" ; then AC_CHECK_HEADERS(qwt/qwt_global.h,qwt_headers=yes) fi CPPFLAGS="$CPPFLAGS_CACHE" if test "x$qwt_headers" = "xno" ; then AC_MSG_ERROR($QWT_ERROR_STR); exit -1 fi fi dnl Checks for typedefs, structures, and compiler characteristics. AC_MSG_CHECKING(whether compiler accepts empty template list) AC_COMPILE_IFELSE(template class TC{static int s;}; template<> int TC::s; int main() {return 0;}, AC_MSG_RESULT(yes); empty_templ_list=yes, AC_MSG_RESULT(no); empty_templ_list=no) AC_MSG_CHECKING(whether compiler accepts/needs self-friend classes) AC_COMPILE_IFELSE(class C{friend class C;}; int main() {return 0;}, AC_MSG_RESULT(yes); self_friend_class=yes, AC_MSG_RESULT(no); self_friend_class=no) dnl Create Defines AC_MSG_NOTICE([------------ Custom ODIN Configuration ------------]) AC_MSG_NOTICE([host=$host]) if test "x$macos" = "xyes" ; then AC_DEFINE(MACOS,,"MacOS support") fi if test "x$GXX" = "xyes" ; then AC_MSG_NOTICE([Using the GNU compiler collection]) AC_DEFINE(USING_GCC,,"Using the GNU compiler collection") fi if test "x$enable_debug" = "xyes" ; then AC_MSG_NOTICE([Debug compilation]) AC_DEFINE(ODIN_DEBUG,,"Debug compilation") fi if test "x$enable_stdcpp_replacement" = "xyes" ; then AC_MSG_NOTICE([Using built-in C++ standard library]) AC_DEFINE(STL_REPLACEMENT,,"Using STL replacement") AC_DEFINE(STRING_REPLACEMENT,,"Using string replacement") AC_DEFINE(STREAM_REPLACEMENT,,"Using stream replacement") fi if test "x$enable_custom_heap" = "xyes" ; then AC_MSG_NOTICE([Using custom heap of size $custom_heap_size MB]) AC_DEFINE(CUSTOM_HEAP,,"Using custom heap") AC_DEFINE_UNQUOTED(CUSTOM_HEAP_SIZE,$custom_heap_size,[Size of Custom Heap in MB]) fi if test "x$enable_cmdline" = "xno" ; then AC_MSG_NOTICE([Not using command line]) AC_DEFINE(NO_CMDLINE,,"Not using command line") fi if test "x$enable_filehandling" = "xno" ; then AC_MSG_NOTICE([No file handling]) AC_DEFINE(NO_FILEHANDLING,,"No file handling") fi if test "x$enable_ideasupport" = "xyes" ; then AC_MSG_NOTICE([IDEA support]) AC_DEFINE(ODIN4IDEA,,"IDEA support") fi if test "x$have_win32_api" = "xyes" ; then AC_MSG_NOTICE([Using Win32-API]) AC_DEFINE(USING_WIN32,,"Using Win32-API") fi if test "x$enable_onlylibs" = "xyes" ; then AC_MSG_NOTICE([Only essential libraries]) fi AM_CONDITIONAL(ONLY_LIBS, test "x$enable_onlylibs" = "xyes") if test "x$enable_gui" = "xyes" ; then AC_DEFINE(GUISUPPORT,,"Graphical User Interface enabled") AC_MSG_NOTICE([Graphical User Interface enabled]) AC_MSG_NOTICE([QTDIR:QTVERSION=${CONF_QTDIR}:${QTVERSION}]) fi AM_CONDITIONAL(GUI_ENABLED, test "x$enable_gui" = "xyes") if test "x$enable_ideaplugin" = "xyes" ; then AC_MSG_NOTICE([Compiling IDEA drivers]) PLUGIN_LIBS="$PLUGIN_LIBS odinseq_idea" AC_DEFINE(IDEA_PLUGIN,,"Compile IDEA drivers") PLATFORMS="$PLATFORMS IDEA_n4" fi AM_CONDITIONAL(IDEA_PLUGIN, test "x$enable_ideaplugin" = "xyes") if test "x$enable_paravisionplugin" = "xyes" ; then AC_MSG_NOTICE([Compiling Paravision drivers]) PLUGIN_LIBS="$PLUGIN_LIBS odinseq_paravision" AC_DEFINE(PARAVISION_PLUGIN,,"Compile Paravision drivers") PLATFORMS="$PLATFORMS Paravision" fi AM_CONDITIONAL(PARAVISION_PLUGIN, test "x$enable_paravisionplugin" = "xyes") if test "x$enable_standaloneplugin" = "xyes" ; then AC_MSG_NOTICE([Compiling Standalone drivers]) PLUGIN_LIBS="$PLUGIN_LIBS odinseq_standalone" AC_DEFINE(STANDALONE_PLUGIN,,"Compile Standalone drivers") PLATFORMS="$PLATFORMS StandAlone" fi AM_CONDITIONAL(STANDALONE_PLUGIN, test "x$enable_standaloneplugin" = "xyes") if test "x$enable_epicplugin" = "xyes" ; then AC_MSG_NOTICE([Compiling EPIC drivers]) PLUGIN_LIBS="$PLUGIN_LIBS odinseq_epic" AC_DEFINE(EPIC_PLUGIN,,"Compile EPIC drivers") PLATFORMS="$PLATFORMS EPIC" fi AM_CONDITIONAL(EPIC_PLUGIN, test "x$enable_epicplugin" = "xyes") if test "x$enable_unittest" = "xno" ; then AC_MSG_NOTICE([Unit test disabled]) AC_DEFINE(NO_UNIT_TEST,,"Unit test disabled") fi if test "x$enable_threads" = "xno" ; then AC_MSG_NOTICE([Multithreading disabled]) AC_DEFINE(NO_THREADS,,"Multithreading disabled") fi if test "x$valid_dl" = "xyes" ; then AC_MSG_NOTICE([Using dynamic linking loader]) AC_DEFINE(HAVE_DL,,"Using dynamic linking loader") fi if test "x$valid_pthread" = "xyes" ; then AC_MSG_NOTICE([Using POSIX threads]) AC_DEFINE(HAVE_PTHREAD,,"Using POSIX threads") fi if test "x$valid_lapack" = "xyes" ; then if test "x$thread_safe_lapack" = "xyes" ; then AC_DEFINE(HAVE_THREADSAFE_LAPACK,,"Thread-safe LAPACK") tsmessage=" thread-safe" fi AC_MSG_NOTICE([Using${tsmessage} LAPACK($lapack_libname)]) AC_DEFINE(HAVE_LAPACK,,"Using LAPACK") fi if test "x$valid_libz" = "xyes" ; then AC_DEFINE(HAVE_LIBZ,,"libz support") fi if test "x$valid_gsl" = "xyes" ; then AC_DEFINE(HAVE_LIBGSL,,"GSL support") fi if test "x$lib_vista" = "xyes" ; then AC_MSG_NOTICE([Vista support]) AC_DEFINE(VISTASUPPORT,,"Vista support") fi if test "x$lib_nifti" = "xyes" ; then AC_MSG_NOTICE([NIFTI support]) AC_DEFINE(NIFTISUPPORT,,"NIFTI support") fi if test "x$lib_vtk" = "xyes" ; then AC_MSG_NOTICE([VTK support]) AC_DEFINE(VTKSUPPORT,,"VTK support") fi if test "x$lib_dcmtk" = "xyes" ; then AC_MSG_NOTICE([DICOM support]) AC_DEFINE(DICOMSUPPORT,,"DICOM support") fi if test "x$lib_png" = "xyes" ; then AC_MSG_NOTICE([PNG support]) AC_DEFINE(PNGSUPPORT,,"PNG support") fi if test "x$empty_templ_list" = "xyes" ; then AC_DEFINE(EMPTY_TEMPL_LIST,template<>,"empty template list") else AC_DEFINE(EMPTY_TEMPL_LIST,,define for empty template list) fi if test "x$self_friend_class" = "xyes" ; then AC_DEFINE(SELF_FRIEND_CLASS,,"self-friend class possible/required") fi if test ! -z "$GDB" -a ! -z "$XTERM" ; then AC_MSG_NOTICE([Using gdb/xterm to attach debugger]) AC_DEFINE(HAVE_GDB_XTERM,,"Using gdb/xterm") fi AC_MSG_NOTICE([INSTALL_PREFIX=$prefix]) AC_MSG_NOTICE([---------------------------------------------------]) AC_SUBST(PLATFORMS,$PLATFORMS) dnl Common generation command for manpages AC_SUBST(HELP2MAN,"help2man -N") AC_SUBST(MOC,$QTMOC) AC_SUBST(BASELIBS) AC_SUBST(GUILIBS) AC_SUBST(DATALIBS) AC_SUBST(VTKLIBS) AC_SUBST(ODINSEQ_INCLUDES,$extra_odinseq_includes) dnl Make sure top-level source and build dir are in the include path all_includes="-I.. -I$srcdir_abs $all_includes" AC_SUBST(all_includes) AC_DEFINE_UNQUOTED(BASELIBS,"$BASELIBS",[Third-party libraries used by all ODIN components]) AC_DEFINE_UNQUOTED(CXXFLAGS,"$CXXFLAGS_EXPORT",[Compiler flags]) AC_DEFINE_UNQUOTED(CPPFLAGS,"$CPPFLAGS_EXPORT",[Preprocessor flags]) AC_DEFINE_UNQUOTED(LDFLAGS,"$LDFLAGS_EXPORT",[Linker flags]) AC_DEFINE_UNQUOTED(CXX,"$CXX",[Compiler]) AC_DEFINE_UNQUOTED(LD,"$LD",[Linker]) AC_DEFINE_UNQUOTED(PLUGIN_LIBS,"$PLUGIN_LIBS",[Plugin-Libraries]) AC_DEFINE_UNQUOTED(DEFAULT_EDITOR,"$initial_editor",[Initial default editor]) AC_DEFINE_UNQUOTED(DEFAULT_BROWSER,"$initial_browser",[Initial default browser]) AC_DEFINE_UNQUOTED(INSTALL_PREFIX,"$prefix",[Installation prefix]) if test ! "$libdir" = '${exec_prefix}/lib' ; then libdir_export="$libdir" fi AC_DEFINE_UNQUOTED(LIBDIR_CONFIGURE,"$libdir_export",[libdir of configure]) dnl Output AC_OUTPUT(Makefile tjutils/Makefile odinpara/Makefile odinseq/Makefile odinqt/Makefile odindata/Makefile \ odin/Makefile pulsar/Makefile geoedit/Makefile miview/Makefile \ odinreco/Makefile cmdline-utils/Makefile sequences/Makefile samples/Makefile coils/Makefile \ docs/Makefile docs/homepage/Makefile docs/tutorials/Makefile replacements/Makefile) odin-1.8.5/config.guess0000755000175000017500000012763711734622601011741 00000000000000#! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. timestamp='2009-12-30' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Per Bothner. Please send patches (context # diff format) to and include a ChangeLog # entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. Otherwise, it exits with 1. # # You can get the latest version of this script from: # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] Output the configuration name of the system \`$me' is run on. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.guess ($timestamp) Originally written by Per Bothner. Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" >&2 exit 1 ;; * ) break ;; esac done if test $# != 0; then echo "$me: too many arguments$help" >&2 exit 1 fi trap 'exit 1' 1 2 15 # CC_FOR_BUILD -- compiler used by this script. Note that the use of a # compiler to aid in system detection is discouraged as it requires # temporary files to be created and, as you can see below, it is a # headache to deal with in a portable fashion. # Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. 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The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[456]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep -q __LP64__ then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) case ${UNAME_MACHINE} in pc98) echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; authenticamd | genuineintel | EM64T) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) echo ia64-unknown-interix${UNAME_RELEASE} exit ;; esac ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; 8664:Windows_NT:*) echo x86_64-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we # UNAME_MACHINE based on the output of uname instead of i386? echo i586-pc-interix exit ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) echo x86_64-unknown-cygwin exit ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; *:GNU:*:*) # the GNU system echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit ;; *:GNU/*:*:*) # other systems with GNU libc and userland echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu exit ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep -q ld.so.1 if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then echo ${UNAME_MACHINE}-unknown-linux-gnu else echo ${UNAME_MACHINE}-unknown-linux-gnueabi fi exit ;; avr32*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; cris:Linux:*:*) echo cris-axis-linux-gnu exit ;; crisv32:Linux:*:*) echo crisv32-axis-linux-gnu exit ;; frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; i*86:Linux:*:*) LIBC=gnu eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __dietlibc__ LIBC=dietlibc #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` echo "${UNAME_MACHINE}-pc-linux-${LIBC}" exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m32r*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; mips:Linux:*:* | mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef ${UNAME_MACHINE} #undef ${UNAME_MACHINE}el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=${UNAME_MACHINE}el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=${UNAME_MACHINE} #else CPU= #endif #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'` test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; padre:Linux:*:*) echo sparc-unknown-linux-gnu exit ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) echo hppa1.1-unknown-linux-gnu ;; PA8*) echo hppa2.0-unknown-linux-gnu ;; *) echo hppa-unknown-linux-gnu ;; esac exit ;; ppc64:Linux:*:*) echo powerpc64-unknown-linux-gnu exit ;; ppc:Linux:*:*) echo powerpc-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux exit ;; sh64*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sh*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sparc:Linux:*:* | sparc64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; vax:Linux:*:*) echo ${UNAME_MACHINE}-dec-linux-gnu exit ;; x86_64:Linux:*:*) echo x86_64-unknown-linux-gnu exit ;; xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. echo i386-sequent-sysv4 exit ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit ;; i*86:atheos:*:*) echo ${UNAME_MACHINE}-unknown-atheos exit ;; i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ && UNAME_MACHINE=i586 (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ && UNAME_MACHINE=i686 (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 echo ${UNAME_MACHINE}-pc-sco$UNAME_REL else echo ${UNAME_MACHINE}-pc-sysv32 fi exit ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i586. # Note: whatever this is, it MUST be the same as what config.sub # prints for the "djgpp" host, or else GDB configury will decide that # this is a cross-build. echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 exit ;; paragon:*:*:*) echo i860-intel-osf1 exit ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 fi exit ;; mini*:CTIX:SYS*5:*) # "miniframe" echo m68010-convergent-sysv exit ;; mc68k:UNIX:SYSTEM5:3.51m) echo m68k-convergent-sysv exit ;; M680?0:D-NIX:5.3:*) echo m68k-diab-dnix exit ;; M68*:*:R3V[5678]*:*) test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) OS_REL='' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; NCR*:*:4.2:* | MPRAS*:*:4.2:*) OS_REL='.3' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; mc68030:UNIX_System_V:4.*:*) echo m68k-atari-sysv4 exit ;; TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; BePC:Haiku:*:*) # Haiku running on Intel PC compatible. echo i586-pc-haiku exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit ;; SX-7:SUPER-UX:*:*) echo sx7-nec-superux${UNAME_RELEASE} exit ;; SX-8:SUPER-UX:*:*) echo sx8-nec-superux${UNAME_RELEASE} exit ;; SX-8R:SUPER-UX:*:*) echo sx8r-nec-superux${UNAME_RELEASE} exit ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in i386) eval $set_cc_for_build if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then UNAME_PROCESSOR="x86_64" fi fi ;; unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` if test "$UNAME_PROCESSOR" = "x86"; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} exit ;; *:QNX:*:4*) echo i386-pc-qnx exit ;; NSE-?:NONSTOP_KERNEL:*:*) echo nse-tandem-nsk${UNAME_RELEASE} exit ;; NSR-?:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "$cputype" = "386"; then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit ;; *:ITS:*:*) echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; V*) echo vax-dec-vms ; exit ;; esac ;; *:XENIX:*:SysV) echo i386-pc-xenix exit ;; i*86:skyos:*:*) echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' exit ;; i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; i*86:AROS:*:*) echo ${UNAME_MACHINE}-pc-aros exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 #echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 eval $set_cc_for_build cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (__arm) && defined (__acorn) && defined (__unix) printf ("arm-acorn-riscix\n"); exit (0); #endif #if defined (hp300) && !defined (hpux) printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) # if !defined (ultrix) # include # if defined (BSD) # if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); # else # if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); # else printf ("vax-dec-bsd\n"); exit (0); # endif # endif # else printf ("vax-dec-bsd\n"); exit (0); # endif # else printf ("vax-dec-ultrix\n"); exit (0); # endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } # Convex versions that predate uname can use getsysinfo(1) if [ -x /usr/convex/getsysinfo ] then case `getsysinfo -f cpu_type` in c1*) echo c1-convex-bsd exit ;; c2*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; c34*) echo c34-convex-bsd exit ;; c38*) echo c38-convex-bsd exit ;; c4*) echo c4-convex-bsd exit ;; esac fi cat >&2 < in order to provide the needed information to handle your system. config.guess timestamp = $timestamp uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = ${UNAME_MACHINE} UNAME_RELEASE = ${UNAME_RELEASE} UNAME_SYSTEM = ${UNAME_SYSTEM} UNAME_VERSION = ${UNAME_VERSION} EOF exit 1 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: odin-1.8.5/install-sh0000755000175000017500000003253711734622601011417 00000000000000#!/bin/sh # install - install a program, script, or datafile scriptversion=2009-04-28.21; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- # TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # # Except as contained in this notice, the name of the X Consortium shall not # be used in advertising or otherwise to promote the sale, use or other deal- # ings in this Software without prior written authorization from the X Consor- # tium. # # # FSF changes to this file are in the public domain. # # Calling this script install-sh is preferred over install.sh, to prevent # `make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. nl=' ' IFS=" "" $nl" # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit=${DOITPROG-} if test -z "$doit"; then doit_exec=exec else doit_exec=$doit fi # Put in absolute file names if you don't have them in your path; # or use environment vars. chgrpprog=${CHGRPPROG-chgrp} chmodprog=${CHMODPROG-chmod} chownprog=${CHOWNPROG-chown} cmpprog=${CMPPROG-cmp} cpprog=${CPPROG-cp} mkdirprog=${MKDIRPROG-mkdir} mvprog=${MVPROG-mv} rmprog=${RMPROG-rm} stripprog=${STRIPPROG-strip} posix_glob='?' initialize_posix_glob=' test "$posix_glob" != "?" || { if (set -f) 2>/dev/null; then posix_glob= else posix_glob=: fi } ' posix_mkdir= # Desired mode of installed file. mode=0755 chgrpcmd= chmodcmd=$chmodprog chowncmd= mvcmd=$mvprog rmcmd="$rmprog -f" stripcmd= src= dst= dir_arg= dst_arg= copy_on_change=false no_target_directory= usage="\ Usage: $0 [OPTION]... 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It does not imply ALL GNU software can. # # This file is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . Submit a context # diff and a properly formatted GNU ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # You can get the latest version of this script from: # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. 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-sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5v6*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ | mips64r5900 | mips64r5900el \ | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | moxie \ | mt \ | msp430 \ | nios | nios2 \ | ns16k | ns32k \ | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | rx \ | score \ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ | ubicom32 \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ | z8k | z80) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12 | picochip) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; ms1) basic_machine=mt-unknown ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ | mips64r5900-* | mips64r5900el-* \ | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ | nios-* | nios2-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* | rx-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tile-* | tilegx-* \ | tron-* \ | ubicom32-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) basic_machine=$basic_machine-unknown ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aros) basic_machine=i386-pc os=-aros ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; blackfin) basic_machine=bfin-unknown os=-linux ;; blackfin-*) basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; bluegene*) basic_machine=powerpc-ibm os=-cnk ;; c90) basic_machine=c90-cray os=-unicos ;; cegcc) basic_machine=arm-unknown os=-cegcc ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | j90) basic_machine=j90-cray os=-unicos ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16) basic_machine=cr16-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; dicos) basic_machine=i686-pc os=-dicos ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. 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Grab either from any GNU archive site." # The file to touch is that specified with -o ... file=`echo "$*" | sed -n "$sed_output"` test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"` if test -z "$file"; then # ... or it is the one specified with @setfilename ... infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'` file=`sed -n ' /^@setfilename/{ s/.* \([^ ]*\) *$/\1/ p q }' $infile` # ... or it is derived from the source name (dir/f.texi becomes f.info) test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info fi # If the file does not exist, the user really needs makeinfo; # let's fail without touching anything. test -f $file || exit 1 touch $file ;; tar*) shift # We have already tried tar in the generic part. # Look for gnutar/gtar before invocation to avoid ugly error # messages. if (gnutar --version > /dev/null 2>&1); then gnutar "$@" && exit 0 fi if (gtar --version > /dev/null 2>&1); then gtar "$@" && exit 0 fi firstarg="$1" if shift; then case $firstarg in *o*) firstarg=`echo "$firstarg" | sed s/o//` tar "$firstarg" "$@" && exit 0 ;; esac case $firstarg in *h*) firstarg=`echo "$firstarg" | sed s/h//` tar "$firstarg" "$@" && exit 0 ;; esac fi echo 1>&2 "\ WARNING: I can't seem to be able to run \`tar' with the given arguments. You may want to install GNU tar or Free paxutils, or check the command line arguments." exit 1 ;; *) echo 1>&2 "\ WARNING: \`$1' is needed, and is $msg. You might have modified some files without having the proper tools for further handling them. Check the \`README' file, it often tells you about the needed prerequisites for installing this package. You may also peek at any GNU archive site, in case some other package would contain this missing \`$1' program." exit 1 ;; esac exit 0 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-time-zone: "UTC" # time-stamp-end: "; # UTC" # End: odin-1.8.5/tjutils/0000755000175000017500000000000011735135550011162 500000000000000odin-1.8.5/tjutils/tjlog_code.h0000644000175000017500000000361211322062342013354 00000000000000#include template void Log::register_comp() { if(!registered) { // retry until LogBase:global is initialized registered=register_component(C::get_compName(),&(Log::set_log_level)); if(registered) { const char* env=getenv(C::get_compName()); if(env) set_log_level(logPriority(atoi(env))); } } if(!registered) { // global may not be initialized yet // Disable tracing until global becomes available logLevel=noLog; constrLevel=noLog; } } template Log::Log(const char* objectLabel, const char* functionName, logPriority level) : LogBase(C::get_compName(),objectLabel,0,functionName), constrLevel(level) { register_comp(); ODINLOG(*this,constrLevel) << "START" << STD_endl; } template Log::Log(const Labeled* labeledObject, const char* functionName, logPriority level) : LogBase(C::get_compName(),0,labeledObject,functionName), constrLevel(level) { register_comp(); ODINLOG(*this,constrLevel) << "START" << STD_endl; } template Log::~Log() { ODINLOG(*this,constrLevel) << "END" << STD_endl; } template logPriority Log::set_log_level(logPriority level) { if(level!=ignoreArgument) logLevel=level; return logLevel; } ///////////////////////////////////////////////////////////////////////////////////////////////////////// // unregister logging component by local static object if shared library is unloaded template class LogUnregister { public: LogUnregister() {} ~LogUnregister() {LogBase::unregister_component(C::get_compName());} }; #define LOGGROUNDWORK(COMPONENT) \ template class Log; \ EMPTY_TEMPL_LIST logPriority Log::logLevel=RELEASE_LOG_LEVEL; \ EMPTY_TEMPL_LIST bool Log::registered=false; \ static LogUnregister COMPONENT ## _unregister; odin-1.8.5/tjutils/tjstring.cpp0000644000175000017500000003275111322062342013450 00000000000000#include "tjstring.h" #include "tjarray.h" #include "tjtools.h" #include "tjlist.h" #include "tjlog.h" #include "tjcstd.h" #include "tjtest.h" #include "tjlog_code.h" const char* StringComp::get_compName() {return "string";} LOGGROUNDWORK(StringComp) /////////////////////////////////////////////////////////////////////////////////////////////// STD_string replaceStr(const STD_string& s, const STD_string& searchstring,const STD_string& replacement,whichOccurences mode) { Log odinlog("","replaceStr"); if(searchstring=="") return s; STD_string::size_type pos=0; int times=0; STD_string concat; STD_string result(s); ODINLOG(odinlog,normalDebug) << "trying to replace >" << searchstring << "< with >" << replacement << "< with mode " << mode << STD_endl; while( (pos=result.find(searchstring,pos)) != STD_string::npos) { concat = result.substr(0,pos); concat += replacement; unsigned int remainingstart=pos+searchstring.length(); unsigned int length2end=result.length()-remainingstart; ODINLOG(odinlog,normalDebug) << "pos/remainingstart/length2end=" << pos << "/" << remainingstart << "/" << length2end << STD_endl; concat += result.substr(remainingstart,length2end); result=concat; // re-feed temporary result into this loop ODINLOG(odinlog,normalDebug) << "result(" << times << ")=" << result << STD_endl; pos+=replacement.length(); // Set to new position: Right after replacement times++; if(pos>=result.length()) break; if(mode==firstOccurence) break; } ODINLOG(odinlog,normalDebug) << "replacing " << times << " time(s) successful" << STD_endl; return result; } //////////////////////////////////////// STD_string extract(const STD_string& s, const STD_string& blockbegin,const STD_string& blockend,bool hierachical,int beginpos) { Log odinlog("","extract"); int startpos,nextbegin,nextend,nocc,tmppos; STD_string tt; if(blockbegin=="") { startpos=beginpos; nextbegin=startpos+1; } else { STD_string::size_type startpos_st = s.find(blockbegin,beginpos); STD_string::size_type nextbegin_st= s.find(blockbegin,beginpos+1); if(startpos_st==STD_string::npos) startpos=-1; else startpos= startpos_st; if(nextbegin_st==STD_string::npos) nextbegin=-1; else nextbegin=nextbegin_st; } if(blockend=="") nextend=s.length(); else { STD_string::size_type nextend_st=s.find(blockend,startpos+1); if(nextend_st==STD_string::npos) nextend=-1; else nextend=nextend_st; } ODINLOG(odinlog,normalDebug) << "startpos/nextbegin/nextend=" << startpos << "/" << nextbegin << "/" << nextend << STD_endl; if (hierachical) { unsigned int remainingstart=startpos+blockbegin.length(); tt=s.substr(remainingstart,nextend-remainingstart); nocc=noccur(tt,blockbegin); while(nocc>0) { tmppos=nextend; for(int i=0;imin && absval odinlog("","justificate"); STD_string result; if(indention>=linewidth) { ODINLOG(odinlog,errorLog) << "indention>=linewidth !" << STD_endl; return result; } STD_string blank(" "); svector tokenvector=tokens(s); STD_list linetokens; unsigned int linesize=0; unsigned int linewidthindent=linewidth-indention; bool firstline=true; for(unsigned int itoken=0; itoken linewidthindent ) { int rest=linewidthindent-linesize; ivector blankvector; if(ntokens>1) { blankvector.resize(ntokens-1); while(rest>0) { for(unsigned int i=0; i<(ntokens-1); i++) { if(rest>0) blankvector[i]++; rest--; } } } if(firstline) { if(!ignore_firstline) result+=n_times(blank,indention); firstline=false; } else result+=n_times(blank,indention); unsigned int iblank=0; for(STD_list::iterator it=linetokens.begin(); it!=linetokens.end(); ++it) { result+=(*it); if(iblank<(ntokens-1)) result+=n_times(blank,blankvector[iblank]); iblank++; } result+="\n"; linetokens.erase(linetokens.begin(),linetokens.end()); linetokens.push_back(tokenvector[itoken]); linesize=tokenlength; } else { linetokens.push_back(tokenvector[itoken]); linesize+=tokenlength; } } if(linetokens.size()) { if(firstline) { if(!ignore_firstline) result+=n_times(blank,indention); } else result+=n_times(blank,indention); for(STD_list::iterator it=linetokens.begin(); it!=linetokens.end(); ++it) { result+=(*it); result+=blank; } result+="\n"; } return result; } //////////////////////////////////////// int textbegin(const STD_string& s, int startpos, const char custom_separator) { // Log odinlog("","textbegin"); int n=s.length(); int pos=startpos; if( startpos<0 || startpos>=n) { // ODINLOG(odinlog,normalDebug) << "index(" << startpos << ") out of range(" << n << ")" << STD_endl; return -1; } else { if(custom_separator) { while(pos odinlog("","sepbegin"); int n=s.length(); int pos=startpos; if( startpos<0 || startpos>=n) { // ODINLOG(odinlog,normalDebug) << "index(" << startpos << ") out of range(" << n << ")" << STD_endl; return -1; } else { if(custom_separator) { while(pos odinlog("","load"); #ifndef NO_FILEHANDLING LONGEST_INT file_size=filesize(filename.c_str()); if(file_size<=0) { ODINLOG(odinlog,warningLog) << "file >" << filename << "< not found or is empty" << STD_endl; return -1; } FILE* file_ptr=FOPEN(filename.c_str(),modestring(readMode)); if(file_ptr==NULL) { ODINLOG(odinlog,errorLog) << "unable to open file >" << filename << "< - " << lasterr() << STD_endl; return -1; } char* s = new char [file_size+1]; int i=fread(s,1,file_size,file_ptr); s[i]='\0'; str=STD_string((const char*)s); if(file_ptr!=NULL) fclose(file_ptr); if(s) delete[] s; #endif return 0; } //////////////////////////////////////// int write(const STD_string& str, const STD_string& filename, fopenMode mode) { Log odinlog("","write"); #ifndef NO_FILEHANDLING FILE* file_ptr=FOPEN(filename.c_str(),modestring(mode)); if(file_ptr==NULL) { ODINLOG(odinlog,errorLog) << "unable to create file: >" << filename << "< - " << lasterr() << STD_endl; return -1; } fwrite(str.c_str(),sizeof(char),str.length(),file_ptr); if(file_ptr!=NULL) fclose(file_ptr); #endif return 0; } ///////////////////////////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class StringTest : public UnitTest { public: StringTest() : UnitTest(StringComp::get_compName()) {} private: bool check() const { Log odinlog(this,"check"); STD_string printed, expected; expected="a"; printed=replaceStr("abb","b",""); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "replaceStr failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } expected="a"; printed=shrink("\n\n \n\ta "); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "shrink failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } expected="00123"; printed=itos(123,10000); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "itos(1) failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } printed=itos(123,99999); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "itos(2) failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } expected="bb"; printed=extract("aaa[bb]cc", "[", "]"); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "extract failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } expected="a(b)c"; printed=extract("g(a(b)c)", "(", ")", true); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "extract(hierachical) failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } return true; } }; void alloc_StringTest() {new StringTest();} // create test instance #endif odin-1.8.5/tjutils/tjheap.cpp0000644000175000017500000001614111322062342013052 00000000000000#include "tjheap.h" #include "tjstring.h" // for ftos #ifdef CUSTOM_HEAP #define MYHEAP_SIZE CUSTOM_HEAP_SIZE*0x100000 void custom_heap_error(const char* txt) { if(Heap::tracefunc) Heap::tracefunc(txt); else fprintf(stderr,"%s\n",txt); abort(); } //#define USE_TRIVIAL_ALGORITM #ifdef USE_TRIVIAL_ALGORITM //////////////////////////////////// START of Trivial Algoritm ///////////////////////////// #define TRIVIAL_HEAP_SIZE 100*MYHEAP_SIZE // Use large heap since it is never freed static char myheap[TRIVIAL_HEAP_SIZE]; static unsigned int heapcount=0; void* trivial_alloc(size_t size) { if((heapcount+size)>=TRIVIAL_HEAP_SIZE) { custom_heap_error("Out of memory"); } void* result=myheap+heapcount; heapcount+=size; return result; } //#ifndef STL_REPLACEMENT //void* operator new(size_t size) throw (std::bad_alloc) {return trivial_alloc(size);} //#else void* operator new(size_t size) {return trivial_alloc(size);} //#endif //void* operator new(size_t size) {return qf_malloc(size);} void* operator new[](size_t size) {return trivial_alloc(size);} void operator delete(void* mptr) {} void operator delete[](void* mptr) {} //////////////////////////////////// END of Trivial Algoritm ///////////////////////////// #else // USE_TRIVIAL_ALGORITM /////////////////////////////////// START of List Allocator Algoritm ///////////////////// #define ALIGNMENT 8 static char la_heap[MYHEAP_SIZE]; static bool la_init_done=false; inline size_t la_downalign(size_t ptr) { return (ptr/ALIGNMENT)*ALIGNMENT; } inline size_t la_upalign(size_t ptr) { if(ptr%ALIGNMENT) return (ptr/ALIGNMENT+1)*ALIGNMENT; return (ptr/ALIGNMENT)*ALIGNMENT; } struct la_cell { inline void set_used() {next=(la_cell*)((size_t)next | 1);} // Set least significant bit inline void set_unused() {next=(la_cell*)((size_t)next & ~1);} // Clear least significant bit inline bool is_used() const { return (size_t)next & 1; // Read least significant bit } inline size_t size() const { if(nextaligned_next(); la_cell* prev=cell->aligned_prev(); // Exclude from check if(next==la_begin || next==la_end) return; if(prev==la_begin || prev==la_end) return; if(cell==la_begin || cell==la_end) return; if(prev>=cell) {fprintf(stderr,"%s: prev>=cell\n",caller); custom_heap_error("check_integrity failed");} if(cell>=next) {fprintf(stderr,"%s: cell>=next\n",caller); custom_heap_error("check_integrity failed");} } void la_dump() { la_cell* iter=la_begin; while(1) { fprintf(stdout,"size(%p)=%i\t\t prev=%p\t\t next=%p\t\t used=%i\n",iter,iter->size(),iter->aligned_prev(),iter->aligned_next(),iter->is_used()); iter=iter->aligned_next(); if(iter==la_begin) { break; } } } */ inline void la_init() { // some checks for implicit assumptions if(la_upalign(sizeof(la_cell))!=sizeof(la_cell)) custom_heap_error("la_cell does not align"); if(sizeof(la_cell)!=(2*sizeof(la_cell*))) custom_heap_error("sizeof(la_cell) exceeds"); // Place begin cell la_begin=(la_cell*)la_upalign((size_t)la_heap); // Place end cell char* offset=la_heap+MYHEAP_SIZE-2*(ALIGNMENT+sizeof(la_cell)); // leave enough space for un-aligned memory and both cells la_end=(la_cell*)la_downalign((size_t)offset); // Connect both cells cyclically la_begin->prev=la_begin->next=la_end; la_end->prev=la_end->next=la_begin; la_begin->set_unused(); // This will hold all of the free memory upon startup la_end->set_used(); // So last cell will never be modified la_rovptr=la_begin; // set to begin of list la_init_done=true; } inline void* list_alloc(size_t size) { if(!la_init_done) la_init(); size=la_upalign(size); // Iterate to next free cell la_cell* iter=la_rovptr; while(iter->is_used() || iter->size()aligned_next(); if(iter==la_rovptr) { // la_dump(); custom_heap_error("Out of memory"); } } // To split a cell is only useful if it can accomodate // some data (i.e. ALIGNMENT) plus one extra cell header bool split_cell = ( iter->size() >= (size+ALIGNMENT+sizeof(la_cell)) ); if(split_cell) { la_cell* next=iter->aligned_next(); // Create new header to hold remainder of cell la_cell* remainder= (la_cell*)( (size_t)iter + sizeof(la_cell) + size ); // Connect cells remainder->next=next; remainder->prev=iter; next->prev=remainder; iter->next=remainder; remainder->set_unused(); iter->set_used(); la_rovptr=remainder; // Set to the (free) remainder return iter->memptr(); } else { // Use entire cell iter->set_used(); la_rovptr=iter->aligned_next(); // Set to the cell after the exact match return iter->memptr(); } } inline void delete_cell(la_cell* cell) { // check_integrity("delete_cell:cell",cell); la_cell* next=cell->aligned_next(); la_cell* prev=cell->aligned_prev(); // Connect ends prev->next=next; next->prev=prev; // Alternative: Just jump to freed space if sufficiently large // However, this seems to have a somewhat arbitray maximum in // performance depending on the threshold, so we will not use it // if(prev->size()>16*ALIGNMENT) la_rovptr=prev; // else la_rovptr=next; la_rovptr=prev; // Set roving pointer to free space. (Found out empirically that this gives a great performance boost) } inline void list_free(void *ptr) { // Convert pointer to header la_cell* freecell = (la_cell*) ( (size_t)ptr - sizeof(la_cell) ); // Try to join with next la_cell* nextcell=freecell->aligned_next(); if(!nextcell->is_used()) delete_cell(nextcell); // Try to join with previous if(!freecell->aligned_prev()->is_used()) delete_cell(freecell); else freecell->set_unused(); // Otherwise, just reset used bit } //#ifndef STL_REPLACEMENT //void* operator new(size_t size) throw (std::bad_alloc) {return list_alloc(size);} //#else void* operator new(size_t size) {return list_alloc(size);} //#endif //void* operator new(size_t size) {return qf_malloc(size);} void* operator new[](size_t size) {return list_alloc(size);} void operator delete(void* mptr) {list_free(mptr);} void operator delete[](void* mptr) {list_free(mptr);} /////////////////////////////////// END of List Allocator Algoritm ///////////////////// #endif // USE_TRIVIAL_ALGORITM #endif // CUSTOM_HEAP heaptracefunction Heap::tracefunc=0; void Heap::malloc_stats() { #ifdef CUSTOM_HEAP #ifndef USE_TRIVIAL_ALGORITM if(la_end) { float used_mb=float(MYHEAP_SIZE-la_end->aligned_prev()->size())/float(0x100000); // Estimate by size of last cell if(Heap::tracefunc) Heap::tracefunc(("Memory used: "+ftos(used_mb)+"/"+ftos(CUSTOM_HEAP_SIZE)+" MB").c_str()); } #endif #endif // CUSTOM_HEAP } odin-1.8.5/tjutils/tjtest.h0000644000175000017500000000332211322062342012556 00000000000000/*************************************************************************** tjtest.h - description ------------------- begin : Mon Dec 12 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJTEST_H #define TJTEST_H #include #include /** * @addtogroup tjutils * @{ */ #ifndef NO_UNIT_TEST /** * Base class for unit tests. Derive from this, implement * the check() function and place a static instanve in the * source file to register it for the test run. */ class UnitTest : public StaticHandler, public Labeled { public: static int check_all(); static void init_static(); static void destroy_static(); static const char* get_compName(); protected: UnitTest(const char* label); virtual ~UnitTest() {} private: virtual bool check() const = 0; static STD_list* tests; }; #endif /** @} */ #endif odin-1.8.5/tjutils/tjhandler.h0000644000175000017500000001267511322062342013227 00000000000000/*************************************************************************** tjhandler.h - description ------------------- begin : Mon Aug 19 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJHANDLER_H #define TJHANDLER_H #include #include /** * @addtogroup tjutils * @{ */ class HandlerComponent { public: static const char* get_compName(); }; ////////////////////////////////////////////////////////////// template class Handled; // forawrd declaration ///////////////////////////////////////////// template class Handler { public: Handler(); Handler(const Handler& handler); Handler& operator = (const Handler& handler); ~Handler(); const Handler& clear_handledobj() const; const Handler& set_handled(I handled) const; I get_handled() const; private: friend class Handled; const Handler& handled_remove(Handled* handled) const; mutable I handledobj; }; ///////////////////////////////////////////// template class Handled { public: Handled(); ~Handled(); bool is_handled() const {return bool(handlers.size());} private: friend class Handler; const Handled& set_handler(const Handler& handler) const; const Handled& erase_handler(const Handler& handler) const; mutable STD_list< const Handler* > handlers; }; //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// class SingletonBase; // forward declaration // mapping between singletons and labels typedef STD_map SingletonMap; class SingletonBase { public: virtual void* get_ptr() const = 0; static SingletonMap* get_singleton_map(); static void set_singleton_map_external(SingletonMap* extmap); protected: SingletonBase(); virtual ~SingletonBase() {} static STD_string get_singleton_label(SingletonBase* sing_ptr); static void* get_external_map_ptr(const STD_string& sing_label); static SingletonMap* singleton_map; static SingletonMap* singleton_map_external; }; //////////////////////////////////////////////////////////////////// /** * Helper class to enable locking of resources while accessing them with pointer-like syntax. */ template class LockProxy { public: LockProxy(volatile T* r, Mutex* m) : presource(const_cast(r)), pmutex(m) {if(pmutex) pmutex->lock();} ~LockProxy() {if(pmutex) pmutex->unlock();} T* operator -> () {return presource;} private: T* presource; Mutex* pmutex; }; //////////////////////////////////////////////////////////////////// /** * Template class to manage singleton objects of type T, * i.e. those objects which are exist only once in the * program. The instantiation must be a static field of * of a certain class. The init/destroy member functions * are used to create/destroy the singleton. * If 'thread_safe' is set to 'true', use a mutex to manage multi-threaded * access to the singleton object. * * Its main purpose is to * share singletons across DLL boundaries on Windows * and/or thread-safe access to global resources. * This class has an pointer-to-T-like interface. */ template // VxWorks does not support default-template args class SingletonHandler : public SingletonBase { public: SingletonHandler() { // do nothing because members are already initialized by init() } /** * Initialize the singleton with the unique identifier 'unique_label'. * The singleton object will be allocated if it does not already exist * somewhere in the program. */ void init (const char* unique_label); /** * Deletes the singleton */ void destroy (); /** * Copies this to 'destination' */ void copy(T& destination) const; /** * Returns unlocked ptr to object (know what you are doing) */ T* unlocked_ptr() {return get_map_ptr();} // emulate pointer syntax: /** * Returns mutex-locked pointer to handled singleton */ LockProxy operator -> () {return LockProxy(get_map_ptr(),mutex);} /** * Returns read-only pointer to handled singleton */ const T* operator -> () const {return get_map_ptr();} /** * Returns whether singleton is already initialized */ operator bool () const {return (bool)get_map_ptr();} private: // implement virtual function of SingletonBase void* get_ptr() const {return ptr;} T* get_map_ptr() const; // Use pointers to avoid the need for static initialization mutable T* ptr; STD_string* singleton_label; Mutex* mutex; }; /** @} */ #endif odin-1.8.5/tjutils/tjprocess.h0000644000175000017500000000671611322062342013267 00000000000000/*************************************************************************** tjprocess.h - description ------------------- begin : Sat May 5 2007 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJPROCESS_H #define TJPROCESS_H #include #include /** * @addtogroup tjutils * @{ */ //////////////////////////////////////////////////////////////////// // for debugging class ProcessComponent { public: static const char* get_compName(); }; //////////////////////////////////////////////////////////////////// /** * Class to for process abstraction. */ class Process { public: /** * Create non-running process. */ Process() {reset();} /** * Start new process with by executing 'cmdline'. If 'block_till_finished' is true, * return only after process has terminated. * If 'log_std_streams' is true, the output of stdout/stderr is catched and can * be queried later by finished(). * Returns 'true' if no error occured. */ bool start(const STD_string& cmdline, bool block_till_finished=false, bool log_std_streams=true); /** * Return whether process has terminated, returns return value and stdout/stderr * output in 'proc_return_value' and 'stdout_result/stderr_result', respectively. * If 'block_till_finished' is true return only after process has terminated. */ bool finished(int& proc_return_value, STD_string& stdout_result, STD_string& stderr_result, bool block_till_finished=false); /** * Return whether process has terminated, returns return value in 'proc_return_value'. * Writes stdout/stderr of child process to the log. * If 'block_till_finished' is true return only after process has terminated. */ bool finished(int& proc_return_value, bool block_till_finished=false); /** * Kill process. Additionlly, kill child processes whose program name is in 'extra_kill'. */ bool kill(const svector& extra_kill=svector()); /** * Start process by executing 'cmdline'. Return after process has terminated with * stdout/stderr output in 'stdout_result/stderr_result'. Returns return code of the process. */ static int system(const STD_string& cmdline, STD_string& stdout_result, STD_string& stderr_result); // Comparison operators for list of processes with STL replacement bool operator == (const Process& op) const {return pid==op.pid;} bool operator < (const Process& op) const {return pid!=op.pid;} bool operator != (const Process& op) const {return !(*this==op);} private: static bool read_pipe(int fd, STD_string& result); void reset() {pid=0; stdout_child=-1; stderr_child=-1;} int pid; int stdout_child; int stderr_child; }; /** @} */ #endif odin-1.8.5/tjutils/tjtypes.h0000644000175000017500000001027111322062342012744 00000000000000/*************************************************************************** tjtypes.h - description ------------------- begin : Thu Jul 24 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJTYPES_H #define TJTYPES_H #include #include /** * @addtogroup tjutils * @{ */ // Get appropriate data types for signed/unsigned 8, 16 and 32 bit data on this platform #if SIZEOF_CHAR == 1 typedef char s8bit; typedef unsigned char u8bit; #else #error "sizeof(char)!=1" #endif #if SIZEOF_SHORT == 2 typedef short s16bit; typedef unsigned short u16bit; #else #error "sizeof(short)!=2" #endif #if SIZEOF_INT == 4 typedef int s32bit; typedef unsigned int u32bit; #else #if SIZEOF_LONG == 4 typedef long s32bit; typedef unsigned long u32bit; #else #error "sizeof(int)!=4 and sizeof(long)!=4" #endif #endif /** * Class to manage string conversions and properties of * simple (i.e. atomic) types. To be used in higher level * template classes to dispatch functionality according * to type. */ class TypeTraits { public: // Convert a type's value to a string static STD_string type2string(s8bit v) {return itos(v);} static STD_string type2string(u8bit v) {return itos(v);} static STD_string type2string(s16bit v) {return itos(v);} static STD_string type2string(u16bit v) {return itos(v);} static STD_string type2string(s32bit v) {return itos(v);} static STD_string type2string(u32bit v) {return itos(v);} static STD_string type2string(float v) {return ftos(v);} static STD_string type2string(double v) {return ftos(float(v));} static STD_string type2string(const STD_complex& v) {return ctos(v);} static STD_string type2string(const STD_string& v) {return v;} // Parses type's value from string static void string2type(const STD_string& s, s8bit& v) {v=(s8bit)atoi(s.c_str());} static void string2type(const STD_string& s, u8bit& v) {v=(u8bit)atoi(s.c_str());} static void string2type(const STD_string& s, s16bit& v) {v=(s16bit)atoi(s.c_str());} static void string2type(const STD_string& s, u16bit& v) {v=(u16bit)atoi(s.c_str());} static void string2type(const STD_string& s, s32bit& v) {v=(s32bit)atoi(s.c_str());} static void string2type(const STD_string& s, u32bit& v) {v=(u32bit)atoi(s.c_str());} static void string2type(const STD_string& s, float& v) {v=(float)atof(s.c_str());} static void string2type(const STD_string& s, double& v) {v=atof(s.c_str());} static void string2type(const STD_string& s, STD_complex& v) {v=stoc(s);} static void string2type(const STD_string& s, STD_string& v) {v=s;} // Type label (identifier) as string static const char* type2label(s8bit) {return "s8bit";} static const char* type2label(u8bit) {return "u8bit";} static const char* type2label(s16bit) {return "s16bit";} static const char* type2label(u16bit) {return "u16bit";} static const char* type2label(s32bit) {return "s32bit";} static const char* type2label(u32bit) {return "u32bit";} static const char* type2label(float) {return "float";} static const char* type2label(double) {return "double";} static const char* type2label(const STD_complex&) {return "complex";} static const char* type2label(const STD_string&) {return "string";} /** * Returns size of data type */ static unsigned int typesize(const STD_string& typelabel); }; /** @} */ #endif odin-1.8.5/tjutils/tjstream.h0000644000175000017500000001451011322062342013073 00000000000000/*************************************************************************** tjstream.h - description ------------------- begin : Sun Jun 13 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJSTREAM_H #define TJSTREAM_H #include // Macros, includes and typedefs are handled in tjstd.h to avoid circular dependencies typedef STD_ostream& (*streammanipulator)(STD_ostream&); /** * @addtogroup tjutils * @{ */ #ifdef STREAM_REPLACEMENT class tjstd_ostream { public: tjstd_ostream() {} virtual ~tjstd_ostream() {} inline tjstd_ostream& operator<<(char v) {append2buff(STD_string(1,v)); return *this;} inline tjstd_ostream& operator<<(unsigned char v) {append2buff(STD_string(1,v)); return *this;} inline tjstd_ostream& operator<<(signed char v) {append2buff(STD_string(1,v)); return *this;} inline tjstd_ostream& operator<<(const char* v) {append2buff(v); return *this;} inline tjstd_ostream& operator<<(int v) {buff_int(v); return *this;} inline tjstd_ostream& operator<<(unsigned int v) {buff_int(v); return *this;} inline tjstd_ostream& operator<<(long v) {buff_int(v); return *this;} inline tjstd_ostream& operator<<(unsigned long v) {buff_int(v); return *this;} #ifdef HAVE_LONG_LONG inline tjstd_ostream& operator<<(long long v) {buff_int(v); return *this;} #endif inline tjstd_ostream& operator<<(short v) {buff_int(v); return *this;} inline tjstd_ostream& operator<<(unsigned short v){buff_int(v); return *this;} inline tjstd_ostream& operator<<(bool v) {if(v) append2buff("true"); else append2buff("false"); return *this;} inline tjstd_ostream& operator<<(double v) {buff_float(v); return *this;} inline tjstd_ostream& operator<<(float v) {buff_float(v); return *this;} inline tjstd_ostream& operator<<(streammanipulator v) {v(*this); return *this;} private: // disable copying tjstd_ostream(const tjstd_ostream&) {} tjstd_ostream& operator = (const tjstd_ostream&) {return *this;} virtual void append2buff(const STD_string& str) {} // do nothing by default, i.e. for cout/cerr void buff_float(float f); void buff_int(int i); }; //////////////////////////////////////////////////////////////////////////// class tjstd_ostringstream : public tjstd_ostream { public: tjstd_ostringstream() {} ~tjstd_ostringstream() {} const STD_string& str() const {return buff;} private: // disable copying tjstd_ostringstream(const tjstd_ostringstream&) {} tjstd_ostringstream& operator = (const tjstd_ostringstream&) {return *this;} // overloaded from tjstd_ostream void append2buff(const STD_string& str) {buff+=str;} STD_string buff; }; //////////////////////////////////////////////////////////////////////////// class tjstd_ofstream : public tjstd_ostream { public: tjstd_ofstream(const char* filename=""); ~tjstd_ofstream() {close();} void close(); bool bad() {return !file_ptr;} private: // disable default construction and copying tjstd_ofstream(const tjstd_ofstream&) {} tjstd_ofstream& operator = (const tjstd_ofstream&) {return *this;} // overloaded from tjstd_ostream void append2buff(const STD_string& str); void* file_ptr; }; //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////// class tjstd_istream { public: tjstd_istream() {} inline tjstd_istream& operator>>(char) {return *this;} inline tjstd_istream& operator>>(unsigned char) {return *this;} inline tjstd_istream& operator>>(signed char) {return *this;} inline tjstd_istream& operator>>(const char *) {return *this;} inline tjstd_istream& operator>>(int) {return *this;} inline tjstd_istream& operator>>(unsigned int) {return *this;} inline tjstd_istream& operator>>(long) {return *this;} inline tjstd_istream& operator>>(unsigned long) {return *this;} #ifdef HAVE_LONG_LONG inline tjstd_istream& operator>>(long long) {return *this;} #endif inline tjstd_istream& operator>>(short) {return *this;} inline tjstd_istream& operator>>(unsigned short){return *this;} inline tjstd_istream& operator>>(bool) {return *this;} inline tjstd_istream& operator>>(double) {return *this;} inline tjstd_istream& operator>>(float) {return *this;} inline tjstd_istream& get(char&) {return *this;} inline tjstd_istream& putback(char) {return *this;} operator void* () const {return 0;} // stream is always empty }; inline tjstd_istream& tjstd_getline(tjstd_istream& is, STD_string&) {return is;} //////////////////////////////////////////////////////////////////////////// class tjstd_ifstream : public tjstd_istream { public: tjstd_ifstream(const char* ="") {} void close() {} bool bad() {return false;} }; //////////////////////////////////////////////////////////////////////////// static tjstd_ostream tjstd_cout; static tjstd_ostream tjstd_cerr; static tjstd_istream tjstd_cin; inline STD_ostream& tjstd_endl(STD_ostream& os) {return os << "\n";} inline STD_ostream& tjstd_flush(STD_ostream& os) {return os;} inline const char* tjstd_setprecision(unsigned int) {return "";} #endif /** @} */ #endif odin-1.8.5/tjutils/tjprocess.cpp0000644000175000017500000002767611322062342013632 00000000000000#include "tjprocess.h" #include "tjtest.h" #include "tjlog_code.h" #ifdef USING_WIN32 // Win-style process handling #include #include #include #include #else #if defined(HAVE_SYS_WAIT_H) && defined(HAVE_SYS_TYPES_H) && defined(HAVE_UNISTD_H) && defined(HAVE_SIGNAL_H) // Unix-style process handling #include #include #include #include #define USING_UNIX_PROCESSES #else #warning "no process handling style selected" #endif #endif /////////////////////////////////////////////////////////// const char* ProcessComponent::get_compName() {return "Process";} LOGGROUNDWORK(ProcessComponent) /////////////////////////////////////////////////////////// // quick hack to kill pending cc1plus process void kill_additional_procs(const svector& extra_kill) { Log odinlog("","kill_additional_procs"); #ifdef USING_UNIX_PROCESSES if(!extra_kill.size()) return; STD_string pslist; STD_string stderrstr; Process ps; if(!ps.start("ps")) return; int retval; if(!ps.finished(retval, pslist, stderrstr, true)) return; ODINLOG(odinlog,normalDebug) << "pslist=" << pslist << STD_endl; svector toks(tokens(pslist)); if(toks.size()<8) return; for(unsigned int i=4; i odinlog("Process","start"); svector cmdtoks(tokens(cmdline)); unsigned int ntoks=cmdtoks.size(); if(!ntoks) { ODINLOG(odinlog,errorLog) << "empty cmdline" << STD_endl; return false; } // kill previously started process kill(); // will reset pid, stdout/stderr_child #ifndef HAVE_READ if(log_std_streams) { ODINLOG(odinlog,errorLog) << "Cannot log_std_streams without read" << STD_endl; return false; } #endif int pipefd_stdout[2]; // pair of file descriptors for stdout pipe int pipefd_stderr[2]; // pair of file descriptors for stderr pipe if(log_std_streams) { bool pipeerror=false; #ifdef USING_UNIX_PROCESSES if(pipe(pipefd_stdout)==-1) pipeerror=true; if(pipe(pipefd_stderr)==-1) pipeerror=true; #endif #ifdef USING_WIN32 if(_pipe( pipefd_stdout, 10000, O_NOINHERIT | O_BINARY)==-1) pipeerror=true; if(_pipe( pipefd_stderr, 10000, O_NOINHERIT | O_BINARY)==-1) pipeerror=true; #endif if(pipeerror) { ODINLOG(odinlog,errorLog) << "pipe: " << lasterr() << STD_endl; return false; } } #ifdef USING_UNIX_PROCESSES pid = ::fork(); #endif #ifdef USING_WIN32 const char* args[100]; if(ntoks>=100) { ODINLOG(odinlog,errorLog) << "too many args" << STD_endl; return false; } STD_string prog(replaceStr(cmdtoks[0],"\"","")); ODINLOG(odinlog,normalDebug) << "prog=" << prog << STD_endl; for(unsigned int itok=0; itok odinlog("Process","finished"); bool console_log= ( stdout_child==-1 || stderr_child==-1 ); // Check before calling finish() STD_string coutstr; STD_string cerrstr; bool result=Process::finished(proc_return_value,coutstr,cerrstr,block_till_finished); if(console_log) { // We are logging directly to the console STD_cout << coutstr; STD_cerr << cerrstr; } else { if(coutstr.length()) ODINLOG(odinlog,infoLog) << coutstr; // dump stdout result of child process if(cerrstr.length()) ODINLOG(odinlog,errorLog) << cerrstr; // dump stderr result of child process } return result; } bool Process::read_pipe(int fd, STD_string& result) { Log odinlog("Process","read_pipe"); char buff[ODIN_MAXCHAR+1]; result=""; while(true) { int nbytes=0; #ifdef HAVE_READ nbytes=read(fd, (void*)buff, ODIN_MAXCHAR); #else ODINLOG(odinlog,errorLog) << "read missing"<< STD_endl; return false; #endif if(nbytes<0) { ODINLOG(odinlog,errorLog) << "read: " << lasterr() << STD_endl; return false; } if(!nbytes) break; buff[nbytes]='\0'; result+=buff; } #if defined(USING_UNIX_PROCESSES) || defined(USING_WIN32) close(fd); #endif return true; } bool Process::kill(const svector& extra_kill) { Log odinlog("Process","kill"); ODINLOG(odinlog,normalDebug) << "pid=" << pid << STD_endl; if(pid) { ODINLOG(odinlog,normalDebug) << "Sending SIGKILL to process " << pid << STD_endl; #ifdef USING_UNIX_PROCESSES ::kill(pid,SIGKILL); #endif #ifdef USING_WIN32 TerminateProcess((HANDLE)int(pid),0); #endif } kill_additional_procs(extra_kill); reset(); return true; } int Process::system(const STD_string& cmdline, STD_string& stdout_result, STD_string& stderr_result) { Process proc; if(!proc.start(cmdline)) return -1; int proc_return_value=-1; if(!proc.finished(proc_return_value, stdout_result, stderr_result, true)) return -1; return proc_return_value; } //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class ProcessTest : public UnitTest { public: ProcessTest() : UnitTest("process") {} private: bool check() const { Log odinlog(this,"check"); //#ifdef USING_UNIX_PROCESSES // stdout_result not implemented yet for win32 Process proc; // STD_string cmd("ping -c 1 localhost"); STD_string cmd("echo teststring"); #ifdef USING_WIN32 // cmd=STD_string(secure_getenv("WINDIR"))+SEPARATOR_STR+"system32"+SEPARATOR_STR+"ping.exe -n 1 localhost"; cmd=STD_string(secure_getenv("WINDIR"))+SEPARATOR_STR+"system32"+SEPARATOR_STR+"cmd.exe /C \"echo teststring\""; #endif if(!proc.start(cmd)) { ODINLOG(odinlog,errorLog) << "start failed, cmd=" << cmd << STD_endl; return false; } int proc_return_value; STD_string stdout_result; STD_string stderr_result; if(!proc.finished(proc_return_value, stdout_result, stderr_result, true)) { ODINLOG(odinlog,errorLog) << "finished failed" << STD_endl; return false; } if(proc_return_value) { ODINLOG(odinlog,errorLog) << "proc_return_value=" << proc_return_value << STD_endl; return false; } // if(stdout_result.find("127.0.0.1")==STD_string::npos) { if(stdout_result.find("teststring")==STD_string::npos) { ODINLOG(odinlog,errorLog) << "stdout_result=>" << stdout_result << "<"; return false; } //#endif return true; } }; void alloc_ProcessTest() {new ProcessTest();} // create test instance #endif odin-1.8.5/tjutils/tjstring.h0000644000175000017500000001467211322062342013117 00000000000000/*************************************************************************** tjstring.h - description ------------------- begin : Mon Mar 10 2003 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJSTRING_H #define TJSTRING_H #include //#include #include /** * @addtogroup tjutils * @{ */ #define _DEFAULT_DIGITS_ 5 #define _DEFAULT_LINEWIDTH_ 74 #ifdef USING_WIN32 #define SEPARATOR_STR "\\" #define SEPARATOR_CHAR '\\' #else #define SEPARATOR_STR "/" #define SEPARATOR_CHAR '/' #endif ////////////////////////////////////////////////////////////// // class for debugging string component class StringComp { public: static const char* get_compName(); }; ////////////////////////////////////////////////////////////// /** * Enum to flag replacement policy: * - allOccurences: All occurences will be replaced * - firstOccurence: Only the first occurence is replaced */ enum whichOccurences {allOccurences,firstOccurence}; /////////////////////////////////////////////////////////////////////////////// // String helper functions /** * * Returns a string where occurences of 'searchstring' are replaced by 'replacement' in s. * The 'mode' parameter determines whether only the first or all occurences should be replaced. */ STD_string replaceStr(const STD_string& s, const STD_string& searchstring, const STD_string& replacement, whichOccurences mode=allOccurences); /** * * returns a block of characters within s that is enclosed by 'blockbegin' and * 'blockend'; the delimiters itself are not returned; If hierachical * is true the nesting is considered, e.g. extract("(a(b)c)", "(", ")", true) * will return "a(b)c" and not "a(b" ; beginpos is the position * to start searching; * If 'blockbegin' is a zero-length string, extraction will start at the beginning of the string; * If 'blockend' is a zero-length string, extraction will stop at the end of the string; */ STD_string extract(const STD_string& s, const STD_string& blockbegin, const STD_string& blockend, bool hierachical=false, int beginpos=0); /** * * Returns s whereby a block of characters that is enclosed by 'blockbegin' and * 'blockend' is removed; the flags rmbegin/rmend specify whether the delimiters * itself should be removed. * If 'rmall' is true, the last possible end delimiter will be used, otherwise the first. * If 'hierachical' is true the nesting is considered, e.g. extract("(",")",true) applied * to "(a(b)c)" will return "a(b)c" and not "a(b" */ STD_string rmblock(const STD_string& s, const STD_string& blockbegin, const STD_string& blockend, bool rmbegin=true, bool rmend=true, bool rmall=true, bool hierachical=false); /** * * returns s, but with all lowercase characters transformed to uppercase */ STD_string toupperstr(const STD_string& s); /** * * returns s, but with all uppercase characters transformed to lowercase */ STD_string tolowerstr(const STD_string& s); /** * Enum to flag exponential printing of floating point numbers: * - autoExp: Automatic * - alwaysExp: Always use exponential format * - neverExp: Never use exponential format */ enum expFormat {autoExp, alwaysExp, neverExp}; /** * * returns a string that contains the formatted floating point number 'f' with precision 'digits' and exponential usage 'eformat' */ STD_string ftos (float f,unsigned int digits=_DEFAULT_DIGITS_, expFormat eformat=autoExp); /** * * returns a string that contains the formatted integer 'i'. * If 'maxabs' is non-zero, the string will be formatted to * have the same number of (possibly zero-padded) digits as 'maxabs'. */ STD_string itos (int i, unsigned int maxabs=0); /** * * returns a string that contains the address of pointer 'p' */ STD_string ptos (const void* p); /** * * Returns n times s, e.g. n_times("3",3) ---> "333" */ STD_string n_times(const STD_string& s, unsigned int n); /** * * returns a justification of s with the specified indention and linewidth */ STD_string justificate(const STD_string& s, unsigned int indention=0,bool ignore_firstline=false, unsigned int linewidth=_DEFAULT_LINEWIDTH_); /** * * Gives the position of the first non-speparator character in s. * Search starts at 'startpos'. * Blanks, tabs and newlines or 'custom_separator' if non-zero are considered as separators. */ int textbegin(const STD_string& s, int startpos=0, const char custom_separator=0); /** * * Gives the position of the first speparator character in s. * Search starts at 'startpos'. * Blanks, tabs and newlines or 'custom_separator' if non-zero are considered as separators. */ int sepbegin(const STD_string& s, int startpos=0, const char custom_separator=0); /** * * Remove all blanks, tabs and newlines from the string s */ STD_string shrink(const STD_string& s); /** * * searches for number of occurences of 'searchstring' in s, returns number of matches * otherwise 0 */ int noccur(const STD_string& s, const STD_string& searchstring); /** * * Replaces all '0d0a' sequences by '0a' in the string */ STD_string dos2unix(const STD_string& s); /** * * Loads 'str' from the ASCII-file 'filename'. * Returns 0 on success, -1 otherwise. */ int load (STD_string& str, const STD_string& filename); /** * * Writes 'str' to the ASCII-file 'filename', the 'mode' determines * whether data will be appended/overwritten if the file already exists. * Returns 0 on success, -1 otherwise. */ int write (const STD_string& str, const STD_string& filename, fopenMode mode=overwriteMode); /** @} */ #endif odin-1.8.5/tjutils/tjstate.cpp0000644000175000017500000000021211322062342013245 00000000000000#include "tjstate.h" #include "tjlog_code.h" const char* StateComponent::get_compName() {return "State";} LOGGROUNDWORK(StateComponent) odin-1.8.5/tjutils/tjutils.h0000644000175000017500000000253211322062342012741 00000000000000/*************************************************************************** tjutils.h - description ------------------- begin : Thu Dec 5 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJUTILS_H #define TJUTILS_H #ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif // boilerplate includes for a clean C++ environment #include #include #include //////////////////////////////////////////////////////////////////////////// #endif odin-1.8.5/tjutils/tjarray.h0000644000175000017500000002312511322062342012720 00000000000000 /*************************************************************************** tjvector.h - description ------------------- begin : Thu Feb 22 2001 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJARRAY_H #define TJARRAY_H #include #include /** * @addtogroup tjutils * @{ */ /** * * This class is an extent vector for arrays, i.e. it is used to hold * dimension information of multidimensional arrays. * It is a vector of integer numbers which describe the extent of the * array in each direction/dimension. * It can also be used to index a certain element in the multidimensional array. */ class ndim : public STD_vector { public: /** * * Constructs an extent vector of size 'd'. */ ndim (unsigned long d=0); /** * * Copy constructor. */ ndim (const ndim& mm) : STD_vector(mm) {} /** * * Constructs an extent vector by parsing the string 's'. The string * must have the syntax (i,j,...) e.g. (3,2,5) to describe a 3-dimensional array. */ ndim (const STD_string& s); /** * * The number of dimensions, i.e. the length of the extent vector. */ unsigned long dim() const {return size();} /** * * Returns the extent vector as a formatted string, e.g. (3,2,5). */ operator STD_string () const; /** * Stream operator */ friend STD_ostream& operator << (STD_ostream& s,const ndim& nn) { return s << STD_string(nn);} /** * * Prefix -- operator: Strips of the first dimension/index. */ ndim& operator -- ( ); /** * * Postfix -- operator: Strips of the last dimension/index. */ ndim& operator -- (int); /** * * Add new dimension with extent 'e' either as last * or first dim, depending on 'first' */ ndim& add_dim ( unsigned long e, bool first=false ); /** * * Returns the total product of the vector. */ unsigned long total() const; /** * * Converts an index vector to the linear index in the array. */ unsigned long extent2index(const ndim& mm) const; /** * * Converts the linear index in the array to an index vector. */ ndim index2extent(unsigned long index) const; /** * * Returns true if nn and this are equal, otherwise false. */ bool operator == (const ndim& nn) const; /** * * Returns true if nn and this are unequal, otherwise false. */ bool operator != (const ndim& nn) const; /** * * Reduce to dimension dim, e.g. ( 3, 4, 7).reduce(2) -> ( 12, 7 ) */ ndim& reduce ( unsigned long dim ); /** * * Resize to essential dims, e.g. ( 1, 3, 1, 7).autosize() -> ( 3, 7 ) */ ndim& autosize (); }; ///////////////////////////////////////////////////////////////////////////// /** * * This class represents a multidimensional array. * It is implemented by deriving it from a one dimensional * vector which holds the data and adding a member of type 'ndim' * that contains the information about the extent in each dimension. */ template class tjarray : public V { public: /** * * default constructor */ tjarray (); /** * * constructs an array of dimensionality 'dim' and allocates memory for i,j,... values */ tjarray (unsigned long n1); tjarray (unsigned long n1, unsigned long n2); tjarray (unsigned long n1, unsigned long n2, unsigned long n3); tjarray (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4); tjarray (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5); /** * * copy constructor */ tjarray (const tjarray &ta); /** * * conversion from fvector to 1-dim array */ tjarray (const V& sv); /** * * constructs an array according to an extent 'nn' */ tjarray (const ndim &nn); /** * Copy assignment */ tjarray& operator = (const tjarray& ta); /** * * assigns 'value' to all elements */ tjarray& operator = (const T& value); /** * * Resize the array, that is create a 1-dim array with the given new size (virtual) */ V& resize(unsigned int newsize); /** * * Redimensionalize and resize the array according to the given extent vector. * If the total number of values does not change, the array is simply reshaped * but the values are preserved. */ tjarray& redim (const ndim &nn); /** * * Redimensionalize and resize the array according to the given extent vector * If the total number of values does not change, the array is simply reshaped * but the values are preserved. */ tjarray& redim (unsigned long n1); tjarray& redim (unsigned long n1, unsigned long n2); tjarray& redim (unsigned long n1, unsigned long n2, unsigned long n3); tjarray& redim (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4); tjarray& redim (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5); /** * * Remove all dimensions with a size of 1 from the extent vector */ tjarray& autosize () {extent.autosize(); return *this;} /** * * Get the extent vector, i.e. the information about the dimensions */ const ndim& get_extent () const; /** * * returns the element indexed by the extent vector ii */ T& operator () (const ndim& ii); /** * * returns the readonly element indexed by the extent vector ii */ const T& operator () (const ndim& ii) const; /** * * returns the element with index firstIndex,... */ T& operator () (unsigned long n1); T& operator () (unsigned long n1, unsigned long n2); T& operator () (unsigned long n1, unsigned long n2, unsigned long n3); T& operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4); T& operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5); /** * * returns the readonly element with index firstIndex,... */ const T& operator () (unsigned long n1) const; const T& operator () (unsigned long n1, unsigned long n2) const; const T& operator () (unsigned long n1, unsigned long n2, unsigned long n3) const; const T& operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4) const; const T& operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5) const; /** * * returns the dimensionality */ unsigned long dim() const; /** * * returns the extent in the i'th dimension */ unsigned long size(unsigned long i) const; /** * * returns the total number of elements */ unsigned long total() const; /** * * returns the total number of elements */ unsigned long length() const; /** * * returns the size of each element in bytes */ unsigned int elementsize() const; /** * * If the size of the given array 'ta' matches this object, all values from 'ta' will be assigned to this */ tjarray& assignValues(const tjarray &ta) ; /** * * The array will be resized to the size of ta and all values from 'ta' will be assigned to this */ tjarray& copy(const tjarray &ta) ; /** * * returns the elements of the array as a formatted string */ STD_string printbody() const; /** * * Converts a linear index to a tuple of indices in the array */ ndim create_index(unsigned long index) const; protected: STD_ostream& printbody2stream(STD_ostream& s) const; // required for JDX arrays private: static ndim create_extent(unsigned long n1); static ndim create_extent(unsigned long n1,unsigned long n2); static ndim create_extent(unsigned long n1,unsigned long n2,unsigned long n3); static ndim create_extent(unsigned long n1,unsigned long n2,unsigned long n3,unsigned long n4); static ndim create_extent(unsigned long n1,unsigned long n2,unsigned long n3,unsigned long n4,unsigned long n5); ndim extent; T element_dummy; }; ///////////////////////////////////////////////////////////////////////////// // Aliases: /** * An array of floating point numbers */ typedef tjarray farray; /** * An array of double precision floating point numbers */ typedef tjarray darray; /** * An array of integer numbers */ typedef tjarray iarray; /** * An array of complex numbers */ typedef tjarray carray; /** * An array of strings */ typedef tjarray sarray; ///////////////////////////////////////////////////////////////////////////// // Helper functions: /** * * Prints the 2-dimensional array 'table' (rows x cols) with the column widths * adjusted to the maximum width (string length) in each column. */ STD_string print_table(const sarray& table); /** * * Parses the string 'str' as a table and returns result as a 2-dim array (rows x cols). */ sarray parse_table(const STD_string& str); /** @} */ #endif odin-1.8.5/tjutils/tjlist.cpp0000644000175000017500000000372111322062342013110 00000000000000#include "tjlist.h" #include "tjlist_code.h" #include "tjtest.h" #include "tjlog_code.h" const char* ListComponent::get_compName() {return "List";} LOGGROUNDWORK(ListComponent) #ifndef NO_UNIT_TEST class ListTest : public UnitTest { public: ListTest() : UnitTest(ListComponent::get_compName()) {} private: class StrItem : public ListItem, public STD_string {}; typedef List StrList; bool check() const { Log odinlog(this,"check"); StrItem* item0=new StrItem; item0->STD_string::operator = ("item0"); StrItem* item1=new StrItem; item1->STD_string::operator = ("item1"); StrItem* item2=new StrItem; item2->STD_string::operator = ("item2"); StrList* slist=new StrList; slist->append(*item0); slist->append(*item1); slist->append(*item2); if(slist->size()!=3) { ODINLOG(odinlog,errorLog) << "size()!=3" << STD_endl; return false; } int index=0; for(StrList::constiter it=slist->get_const_begin(); it!=slist->get_const_end(); ++it) { STD_string expected="item"+itos(index); if((**it)!=expected) { ODINLOG(odinlog,errorLog) << "expected=" << expected << STD_endl; return false; } index++; } delete item0; if(slist->size()!=2) { ODINLOG(odinlog,errorLog) << "size()!=2" << STD_endl; return false; } delete item1; if(slist->size()!=1) { ODINLOG(odinlog,errorLog) << "size()!=1" << STD_endl; return false; } if(item2->numof_references()!=1) { ODINLOG(odinlog,errorLog) << "references(pre)=" << item2->numof_references() << STD_endl; return false; } delete slist; if(item2->numof_references()!=0) { ODINLOG(odinlog,errorLog) << "references(post)=" << item2->numof_references() << STD_endl; return false; } delete item2; return true; } }; void alloc_ListTest() {new ListTest();} // create test instance #endif odin-1.8.5/tjutils/tjstream.cpp0000644000175000017500000000146311322062342013431 00000000000000#include "tjstream.h" #include "tjstring.h" #ifdef STREAM_REPLACEMENT void tjstd_ostream::buff_float(float f) {append2buff(ftos(f));} void tjstd_ostream::buff_int(int i) {append2buff(itos(i));} //////////////////////////////////////////////////////////////// tjstd_ofstream::tjstd_ofstream(const char* filename) : file_ptr(0) { #ifndef NO_FILEHANDLING if(STD_string(filename)!="") { FILE* fp=FOPEN(filename, modestring(overwriteMode)); if(fp!=NULL) { file_ptr=(void*)fp; } } #endif } void tjstd_ofstream::close() { #ifndef NO_FILEHANDLING if(file_ptr) fclose((FILE*)file_ptr); file_ptr=0; #endif } void tjstd_ofstream::append2buff(const STD_string& str) { #ifndef NO_FILEHANDLING if(file_ptr) fwrite(str.c_str(), sizeof(char), str.length(), (FILE*)file_ptr); #endif } #endif odin-1.8.5/tjutils/tjstatic.cpp0000644000175000017500000000117511322062342013425 00000000000000#include "tjstatic.h" void Static::append_to_destructor_list(Static* sp) { if(!destructor_list) { destructor_list=new STD_list; } destructor_list->push_front(sp); } void Static::destroy_all() { if(destructor_list) { for(STD_list::iterator it=destructor_list->begin(); it!=destructor_list->end(); ++it) { // STD_cout << "Static::destroy_all(): destructing " << typeid(*(*it)).name() << "<" << STD_endl; delete *it; // STD_cout << "Static::destroy_all(): done" << STD_endl; } delete destructor_list; } destructor_list=0; } STD_list* Static::destructor_list=0; odin-1.8.5/tjutils/tjfeedback.h0000644000175000017500000000664311322062342013334 00000000000000/*************************************************************************** tjfeedback.h - description ------------------- begin : Fri Jun 6 2003 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJFEEDBACK_H #define TJFEEDBACK_H #include #include /** * @addtogroup tjutils * @{ */ /** * * Base class for all display drivers of a progress, e.g. console, widget, ... */ class ProgressDisplayDriver { public: virtual ~ProgressDisplayDriver() {} /** * Initializes the driver to display to expect 'nsteps' calls to 'increase()'. * The message 'txt' will be displayed prior to the progress report. */ virtual void init(unsigned int nsteps, const char* txt) = 0; /** * Increments progress display. * The message 'subj', if non-null, will be displayed. */ virtual void increase(const char* subj) = 0; /** * Refreshes display without increasing progress. * Returns true if cancel is requested by the driver. */ virtual bool refresh() = 0; }; ////////////////////////////////////////////////////// /** * * Class to preset the progress of an operation to the user. * The implementation is thread-safe. */ class ProgressMeter { public: /** * Creates progress meter using display driver 'disp' which should * exist for the whole life time of the progress meter. */ ProgressMeter(ProgressDisplayDriver& disp) : display(&disp) {} /** * Initialize new task with 'total_steps' increments. * The message 'txt' will be displayed prior to the progress report. */ ProgressMeter& new_task(unsigned int total_steps, const char* txt = 0); /** * Increments progress display. * The message 'subj', if non-null, will be displayed. */ bool increase_counter(const char* subj = 0); /** * Refreshes display without increasing progress. * Returns true if cancel is requested by the driver. */ bool refresh_display(); private: // disable copy construction and copying ProgressMeter(const ProgressMeter&) {} ProgressMeter& operator = (const ProgressMeter&) {return *this;} ProgressDisplayDriver* display; Mutex mutex; }; ////////////////////////////////////////////////////// #ifndef NO_CMDLINE class ProgressDisplayConsole : public virtual ProgressDisplayDriver { public: ProgressDisplayConsole() : counter(0), nsteps_cache(0), done(false) {} // Implementing virtual functions of ProgressDisplayDriver void init(unsigned int nsteps, const char* txt); void increase(const char*); bool refresh() {return false;} private: unsigned int counter, nsteps_cache, old_perc; bool done; }; #endif /** @} */ #endif odin-1.8.5/tjutils/tjnumeric.cpp0000644000175000017500000001205511735132611013604 00000000000000#include "tjnumeric.h" #include "tjvector.h" #include "tjtest.h" #include "tjlog_code.h" class NumericsComp { public: static const char* get_compName() {return "numerics";} }; LOGGROUNDWORK(NumericsComp) /////////////////////////////////////////////////////////////////// // copy & pasted from the GSL library int solve_cubic (double a, double b, double c, double *x0, double *x1, double *x2) { double q = (a * a - 3 * b); double r = (2 * a * a * a - 9 * a * b + 27 * c); double Q = q / 9; double R = r / 54; double Q3 = Q * Q * Q; double R2 = R * R; double CR2 = 729 * r * r; double CQ3 = 2916 * q * q * q; if (R == 0 && Q == 0) { *x0 = - a / 3 ; *x1 = - a / 3 ; *x2 = - a / 3 ; return 3 ; } else if (CR2 == CQ3) { /* this test is actually R2 == Q3, written in a form suitable for exact computation with integers */ /* Due to finite precision some double roots may be missed, and considered to be a pair of complex roots z = x +/- epsilon i close to the real axis. */ double sqrtQ = sqrt (Q); if (R > 0) { *x0 = -2 * sqrtQ - a / 3; *x1 = sqrtQ - a / 3; *x2 = sqrtQ - a / 3; } else { *x0 = - sqrtQ - a / 3; *x1 = - sqrtQ - a / 3; *x2 = 2 * sqrtQ - a / 3; } return 3 ; } else if (CR2 < CQ3) /* equivalent to R2 < Q3 */ { double sqrtQ = sqrt (Q); double sqrtQ3 = sqrtQ * sqrtQ * sqrtQ; double theta = acos (R / sqrtQ3); double norm = -2 * sqrtQ; *x0 = norm * cos (theta / 3) - a / 3; *x1 = norm * cos ((theta + 2.0 * PII) / 3) - a / 3; *x2 = norm * cos ((theta - 2.0 * PII) / 3) - a / 3; /* Sort *x0, *x1, *x2 into increasing order */ if (*x0 > *x1) STD_swap(*x0, *x1) ; if (*x1 > *x2) { STD_swap(*x1, *x2) ; if (*x0 > *x1) STD_swap(*x0, *x1) ; } return 3; } else { double sgnR = (R >= 0 ? 1 : -1); double A = -sgnR * pow (fabs (R) + sqrt (R2 - Q3), 1.0/3.0); double B = Q / A ; *x0 = A + B - a / 3; return 1; } } //////////////////////////////////////////////////////////////////////////////////////// #ifdef HAVE_LIBGSL #include #include #endif RandomDist::RandomDist() { #ifdef HAVE_LIBGSL rng = (gsl_rng*)gsl_rng_alloc(gsl_rng_tt800); // rng = (gsl_rng*)gsl_rng_alloc(gsl_rng_default); gsl_rng_set ((gsl_rng*)rng, time(NULL)); #endif } RandomDist::~RandomDist() { #ifdef HAVE_LIBGSL gsl_rng_free((gsl_rng*)rng); #endif } double RandomDist::gaussian(double stdev) const { #ifdef HAVE_LIBGSL return gsl_ran_gaussian ((gsl_rng*)rng, stdev); #else STD_cerr << "ERROR: RandomDist::gaussian: libgsl missing" << STD_endl; return 0.0; #endif } double RandomDist::uniform() const { #ifdef HAVE_LIBGSL return gsl_rng_uniform ((gsl_rng*)rng); #else STD_cerr << "ERROR: RandomDist::uniform: libgsl missing" << STD_endl; return 0.0; #endif } //////////////////////////////////////////////////////////////////////////////////////// fvector bruteforce_minimize1d(const MinimizationFunction& f, float low, float upp) { Log odinlog("","bruteforce_minimize1d"); if(f.numof_fitpars()!=1) { ODINLOG(odinlog,errorLog) << "rank of minimization function != 1" << STD_endl; return 0.0; } int nvals=10; int niter=10; fvector xvals(nvals); fvector yvals(nvals); fvector funcarg(1); for(int iter=0; iter odinlog(this,"check"); MinimizationTestFunction mtf; float min=bruteforce_minimize1d(mtf, -12.45, 9.77)[0]; float expected=2.0; if( fabs(expected-min)>1.0e-3 ) { ODINLOG(odinlog,errorLog) << "minimize failed, got " << min << " but expected " << expected << STD_endl; return false; } return true; } }; void alloc_NumericsTest() {new NumericsTest();} // create test instance #endif odin-1.8.5/tjutils/tjcstd.cpp0000644000175000017500000000722611322062342013076 00000000000000#include "tjcstd.h" #include "tjutils.h" #include "tjstring.h" #ifdef USING_WIN32 #include #include #include #endif #ifndef HAVE_CTYPE_H int isdigit (int c) { if(c>='0' && c<='9') return true; else return false; } int isspace (int c) { if(c==' ' || c=='\n' || c=='\r' || c=='\t') return true; else return false; } int islower (int c) { return (c>='a' && c<='z'); } int tolower (int c) { if(isupper(c)) c+=32; return c; } int isupper (int c) { return (c>='A' && c<='Z'); } int toupper (int c) { if(islower(c)) c-=32; return c; } #endif #ifndef HAVE_J1 double j1(double x) { double xa=fabs(x); double result=0.0; static double a1[] = { 0.1171875, -0.1441955566406250, 0.6765925884246826, -6.883914268109947, 1.215978918765359e2, -3.302272294480852e3, 1.276412726461746e5, -6.656367718817688e6, 4.502786003050393e8, -3.833857520742790e10, 4.011838599133198e12, -5.060568503314727e14, 7.572616461117958e16, -1.326257285320556e19}; static double b1[] = { -0.1025390625, 0.2775764465332031, -1.993531733751297, 2.724882731126854e1, -6.038440767050702e2, 1.971837591223663e4, -8.902978767070678e5, 5.310411010968522e7, -4.043620325107754e9, 3.827011346598605e11, -4.406481417852278e13, 6.065091351222699e15, -9.833883876590679e17, 1.855045211579828e20}; if(xa==0.0) return result; double x2=xa*xa; if(xa<=12.0) { // simple series expansion for small numbers result=1.0; double r=1.0; for(int i=1;i<=30;i++) { r *= -0.25*x2/(i*(i+1)); result += r; if (fabs(r) < fabs(result)*1e-15) break; } result *= 0.5*xa; } else { int n; if (xa >= 50.0) n = 8; else if (xa >= 35.0) n = 10; else n = 12; double t2 = xa-0.75*PII; double p1 = 1.0; double q1 = 0.375/xa; for (int i=0; i 1.0 / GSL_SQRT_DBL_EPSILON) { return log (x) + GSL_M_LN2; } else if (x > 2) { return log (2 * x - 1 / (sqrt (x * x - 1) + x)); } else if (x > 1) { double t = x - 1; return gsl_log1p (t + sqrt (2 * t + t * t)); } else if (x == 1) { return 0; } else { return 0; // GSL_NAN; } } #endif #ifdef VXWORKS double exp4vxworks(double x) { if(x<-50.0) return 0.0; // otherwise the C-library on VxWorks throws an exception (no comment ;-) #undef exp else return exp(x); #define exp exp4vxworks } #endif //////////////////////////////////////////////////////////////////// #ifndef HAVE_DL void *dlopen (const char *filename, int flag) { #ifdef USING_WIN32 HINSTANCE inst=LoadLibraryA(filename); return (void*)inst; #else return 0; #endif } const char *dlerror(void) { return lasterr(); } void *dlsym(void *handle, char *symbol) { #ifdef USING_WIN32 FARPROC fp=GetProcAddress((HMODULE)handle,symbol); return (void*)fp; #else return 0; #endif } int dlclose (void *handle) { #ifdef USING_WIN32 BOOL b=FreeLibrary((HMODULE)handle); return (int)!b; #else return 0; #endif } #endif odin-1.8.5/tjutils/tjindex.h0000644000175000017500000000751711322062342012720 00000000000000/*************************************************************************** tjindex.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJINDEX_H #define TJINDEX_H #include #include #include #include /** * @addtogroup tjutils * @{ */ class Index { public: static const char* get_compName(); }; ////////////////////////////////////////////////////////// // mapping between UniquIndex types and typenames struct UniqueIndexMap : public STD_map >, public Labeled { unsigned int get_index(STD_list::iterator& index, const STD_string& type, unsigned int max_instances); void remove_index(const STD_list::iterator& index, const STD_string& type); private: bool contiguous; // cache whether list of indices is contiguous for fast assignment of indices unsigned int assign_index(STD_list::iterator& index, const STD_string& type); // Get the next lowest index which is available }; ////////////////////////////////////////////////////////// // keeps track of all index lists class UniqueIndexBase : public StaticHandler { public: // for StaticHandler static void init_static() {indices_map.init("indices_map");} static void destroy_static() {indices_map.destroy();} protected: UniqueIndexBase() {} // Use only as base class static SingletonHandler indices_map; // global lists of indices }; ////////////////////////////////////////////////////////// /** * This template class provides a unique index, i.e. an unique * unsigned integer number for all instances of the (derived) class. * A new index for the object is created whenever a call to 'get_index()' * is issued the first time. The assigned index is removed from the list * of assigned indices if the object is destroyed. * Please note that the index of temporary objects is deleted from * the list of indices, even it is assigned to another object. * The class T must have two static member functions, 'get_typename()' * and 'get_max_instances()' to return a unique label and the * maximum number of instances per class, respectively. */ template class UniqueIndex : public UniqueIndexBase { public: UniqueIndex() {init();} UniqueIndex(const UniqueIndex&) {init();} UniqueIndex& operator = (const UniqueIndex&) {erase(); init(); return *this;} ~UniqueIndex() {erase();} /** * Returns a unique index for this object. */ unsigned int get_index() const { return indices_map->get_index(index, T::get_typename(), T::get_max_instances()); } private: void init() { // Start with unassigned index (pointing to end()) index=indices_map->operator[](T::get_typename()).end(); } void erase() { // Remove index indices_map->remove_index(index, T::get_typename()); } mutable STD_list::iterator index; }; /** @} */ #endif odin-1.8.5/tjutils/tjnumeric.h0000644000175000017500000000517211735132611013253 00000000000000/*************************************************************************** tjnumeric.h - description ------------------- begin : Mon May 5 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJNUMERIC_H #define TJNUMERIC_H #include #include /** * @addtogroup tjutils * @{ */ /** * * Solve cubic equation x^3 + a x^2 + b x + c = 0 , copied from the GSL-lib */ int solve_cubic (double a, double b, double c, double *x0, double *x1, double *x2); //////////////////////////////////////////////////////////////////////////////////////// /** * Calculate random number distributions, the generator is seeded once upon construction * using the system time. */ class RandomDist { public: RandomDist(); ~RandomDist(); /** * Calculate Gaussian distribution with given standard deviation, uses GSL random number generator */ double gaussian(double stdev) const; /** * Calculate uniformly distributed random number in range [0,1), uses GSL random number generator */ double uniform() const; private: void* rng; }; //////////////////////////////////////////////////////////////////////////////////////// /** * Function which is used for optimization */ class MinimizationFunction { public: /** * Returns the number of independent fitting parameters */ virtual unsigned int numof_fitpars() const = 0; /** * Multi-dimensional function to be minimized */ virtual float evaluate(const fvector&) const = 0; }; //////////////////////////////////////////////////////////////////////////////////////// /** * one-dimensional brute-force minimizer in given interval [low,upp]. * Returns coordinates of minimum. */ fvector bruteforce_minimize1d(const MinimizationFunction& f, float low, float upp); /** @} */ #endif odin-1.8.5/tjutils/tjcomplex.cpp0000644000175000017500000000426411322062342013607 00000000000000#include "tjcomplex.h" #include "tjtest.h" #include "tjlog.h" STD_string ctos (const STD_complex& z) { STD_string s; s=ftos(z.real()); if(z.imag()>=0.0) s+="+"; s+=ftos(z.imag())+"i"; return s; } STD_complex stoc(const STD_string& s) { char value[250]; unsigned int index=0,i=0; STD_string tt(s); tt=replaceStr(tt,"e-","m"); tt=replaceStr(tt,"E-","m"); tt=replaceStr(tt,"e+","p"); tt=replaceStr(tt,"E+","p"); tt=replaceStr(tt,"e","p"); tt=replaceStr(tt,"E","p"); while(index<249 && tt[index] != '+' && tt[index] != '-' && tt[index] != '.' && (tt[index] < '0' || tt[index] > '9') ) index++; if (tt[index] == '+' || tt[index] == '-') { value[0]=tt[index]; i=1;index++; } else i=0; while(tt[index] != '+' && tt[index] != '-' && index<249) { value[i]=tt[index]; index++; i++; } value[i]='\0'; STD_string valstr_re(value); valstr_re=replaceStr(valstr_re,"m","e-"); valstr_re=replaceStr(valstr_re,"p","e+"); float val_re=atof(valstr_re.c_str()); i=0; while(tt[index] != 'i' && tt[index] != 'I' && index<249) { value[i]=tt[index]; index++; i++; } value[i]='\0'; STD_string valstr_im(value); valstr_im=replaceStr(valstr_im,"m","e-"); valstr_im=replaceStr(valstr_im,"p","e+"); float val_im=atof(valstr_im.c_str()); i=0; return STD_complex(val_re,val_im); } #ifndef NO_UNIT_TEST class ComplexTest : public UnitTest { public: ComplexTest() : UnitTest("complex") {} private: bool check() const { Log odinlog(this,"check"); // making sure complex type contains only re/im member int expected_size=2*sizeof(float); int complex_size=sizeof(STD_complex); if(expected_size!=complex_size) { ODINLOG(odinlog,errorLog) << "complex type has NOT twice the size of float" << STD_endl; return false; } // check memory alignment float re=1.2; float im=3.4; STD_complex c(re,im); float* f=(float*)&c; if(f[0]!=re || f[1]!=im) { ODINLOG(odinlog,errorLog) << "wrong alignment of complex type" << STD_endl; return false; } return true; } }; void alloc_ComplexTest() {new ComplexTest();} // create test instance #endif odin-1.8.5/tjutils/tjprofiler.cpp0000644000175000017500000000470511322062342013762 00000000000000#include "tjprofiler.h" #include "tjstring.h" #include "tjtools.h" #include "tjarray.h" #include "tjhandler_code.h" #include "tjlog_code.h" #ifdef HAVE_UNISTD_H #include #endif //#ifdef ODIN_DEBUG #define ENABLE_PROFILER //#endif const char* Profiler::get_compName() {return "Prof";} LOGGROUNDWORK(Profiler) Profiler::Profiler(const STD_string& func_name) : func_label(func_name) { #ifdef ENABLE_PROFILER starttime=current_time_s(); #endif } Profiler::~Profiler() { #ifdef ENABLE_PROFILER func_map->operator [] (func_label).time_spent+=(current_time_s()-starttime); #endif } void Profiler::reset() { #ifdef ENABLE_PROFILER if(func_map) func_map->clear(); #endif } void Profiler::dump_final_result() { #ifdef ENABLE_PROFILER Log odinlog("Profiler","dump_final_result"); if(!func_map) return; if(!func_map->size()) return; unsigned int maxlen=0; STD_map::const_iterator it; for(it=func_map->begin(); it!=func_map->end(); ++it) maxlen=STD_max(maxlen,(unsigned int)it->first.length()); for(it=func_map->begin(); it!=func_map->end(); ++it) { ODINLOG(odinlog,infoLog) << it->first << ": " << STD_string(maxlen-it->first.length(),' ') << it->second.time_spent << STD_endl; } reset(); #endif } STD_string Profiler::get_memory_usage() { STD_string result; #ifdef ENABLE_PROFILER #ifndef NO_FILEHANDLING FILE* file_ptr=FOPEN("/proc/self/statm",modestring(readMode)); if(file_ptr==NULL) { return "Profiler::get_memory_usage: Memory usage not available"; } char* cstr = new char [ODIN_MAXCHAR+1]; int i=fread(cstr,1,ODIN_MAXCHAR,file_ptr); if(i<=ODIN_MAXCHAR) cstr[i]='\0'; fclose(file_ptr); svector toks=tokens(cstr); delete[] cstr; if(toks.size()!=7) return result; float psize_mb=1.0; #ifdef HAVE_UNISTD_H // MinGW does not have getpagesize #ifndef USING_WIN32 psize_mb=float(getpagesize())/1048576.0; #endif #endif float total=atof(toks[0].c_str())*psize_mb; float shared=atof(toks[2].c_str())*psize_mb; float ram=total-shared; result+="total="+ftos(total)+"MB "; result+="shared="+ftos(shared)+"MB "; result+="ram="+ftos(ram)+"MB"; #endif #endif return result; } void Profiler::init_static() {func_map.init("func_map");} void Profiler::destroy_static() {func_map.destroy();} template class SingletonHandler; SingletonHandler Profiler::func_map; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/tjutils/tjlog.h0000644000175000017500000002070111322062342012360 00000000000000/*************************************************************************** tjlog.h - description ------------------- begin : Fri Aug 2 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJLOG_H #define TJLOG_H #ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif #include #include #include #include #include #include #include /** * @addtogroup tjutils * @{ */ #define MAX_COMPONENT_SIZE 10 #define MAX_LOG_STRINGSIZE 25 /** * This enum is used to assign a priority to the log messages * If a given logging level is selected by the user (via GUI or command * line argument), all messages with an equal or lesser priority are * shown. */ enum logPriority { noLog=0, errorLog, warningLog, infoLog, significantDebug, normalDebug, verboseDebug, numof_log_priorities, ignoreArgument}; static const char* logPriorityLabel[]={"noLog", "errorLog", "warningLog", "infoLog", "significantDebug", "normalDebug", "verboseDebug"}; ////////////////////////////////////////////////////////////////////////////////////// /** * Message token which is passed to the trace function */ struct LogMessage { /** * The priority level of the message */ logPriority level; /** * Component, i.e. subsystem, from which message originates */ STD_string comp; /** * Object (label) from which message originates */ STD_string obj; /** * Function (name) from which message originates */ STD_string func; /** * Message text */ STD_string txt; /** * Produce single string from message with at most 'maxwidth' characters * including the component label if 'include_comp' is 'true'. * If 'maxwidth' is zero, the length is unlimited. */ STD_string str(unsigned int maxwidth=0, bool include_comp=true) const; }; ////////////////////////////////////////////////////////////////////////////////////// /** * Trace function signature */ typedef void (*tracefunction)(const LogMessage& msg); /** * Default trace function */ void default_tracefunction(const LogMessage& msg); ////////////////////////////////////////////////////////////////////////////////////// // function pointer to get/set log levels in global map of logLevels typedef logPriority (*log_component_fptr) (logPriority); ////////////////////////////////////////////////////////////////////////////////////// /** * Base class for all Log-component types which manages global settings */ class LogBase : public virtual StaticHandler { public: LogBase() {} // for LogBaseoc LogBase(const char* component, const char* object, const Labeled* labeledObject, const char* function) : compLabel(component), objLabel(object), namedObj(labeledObject), funcName(function) {} /** * Set the log output level of component 'compname' to 'level' */ static void set_log_level(const char* compname, logPriority level); /** * Set uniform log output level for all components */ static void set_uniform_log_level(logPriority level); #ifndef NO_CMDLINE /** * Set log levels from command line */ static bool set_log_levels(int argc, char *argv[], bool trigger_error=true); #endif /** * Get command line usage for setting log levels */ static STD_string get_usage(); // Functions to used by Log-component types static bool register_component(const char*,log_component_fptr); static void unregister_component(const char*); /** * Serialize log-level settings to string */ static const char* get_levels(); /** * Set log levels from string */ static void set_levels(const char* str); /** * Set trace function */ static void set_log_output_function(tracefunction func); // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); protected: friend class LogOneLine; // Cache only plain pointers for efficiency const char* compLabel; const char* objLabel; // Cache either the string const Labeled* namedObj; // or the object to retrieve the label from const char* funcName; void flush_oneline(const STD_string& txt, logPriority level); #ifndef NO_CMDLINE static void parse_log_cmdline_options(int argc, char *argv[], const char* opt, logPriority base); #endif // global (singleton) data struct Global : public Labeled { Global() : tracefunc(default_tracefunction), uniform_init_level(ignoreArgument) {} tracefunction tracefunc; STD_map components; STD_map init_level; logPriority uniform_init_level; }; static SingletonHandler global; // Thread-safe singleton for global data private: friend class DebugDialog; }; ////////////////////////////////////////////////////////////////////////////////////// /** * Logging class to store logging information of the current scope (object, function, ...). * The template parameter specifies the component in which * logging is placed, e.g. Log for tracing sequence code. */ template class Log : public virtual LogBase { public: /** * Constructs a logging stream for object 'objectLabel' and function 'functionName'. * Both strings will precede the actual message in the log. The third argument specifies * a uniform logging priority for the constructor and destructor. * This constructor will automatically generate a START tag in the log for the function * it is used in. */ Log(const char* objectLabel, const char* functionName, logPriority level=verboseDebug); /** * Constructs a logging stream for labeled object 'labeledObject' and function 'functionName'. * Both the label and the function name will precede the actual message in the log. The third argument specifies * a uniform logging priority for the constructor and destructor. * This constructor will automatically generate a START tag in the log for the function * it is used in. */ Log(const Labeled* labeledObject, const char* functionName, logPriority level=verboseDebug); /** * This destructor will automatically generate an END tag in the log for the function * its object is used in. */ ~Log(); static logPriority set_log_level(logPriority level); // to be called via log_component_fptr function pointer inline static logPriority get_log_level() {return logLevel;} // to be used by LogOneLine private: logPriority constrLevel; void register_comp(); static logPriority logLevel; static bool registered; // call register_component only in 1st constructor }; ////////////////////////////////////////////////////////////////////////////////////// // Temporary object to log one line via ostringstream // This ingenious technique was presented by Petru Marginean in Dr.Dobb's under the title 'Logging in C++' struct LogOneLine { public: LogOneLine(LogBase& logobj, logPriority level) : log(logobj), lev(level) {} ~LogOneLine() {log.flush_oneline(oss.str(),lev);} STD_ostream& get_stream() {return oss;} private: LogBase& log; logPriority lev; STD_ostringstream oss; }; ////////////////////////////////////////////////////////////////////////////////////// // Min level which is included in release compilation #define RELEASE_LOG_LEVEL infoLog #ifdef ODIN_DEBUG #define ODINLOG(logobj,level) \ if ((level) > (logobj).get_log_level()) ; \ else LogOneLine(logobj,level).get_stream() #else #define ODINLOG(logobj,level) \ if ((level) > RELEASE_LOG_LEVEL) ; \ else if ((level) > (logobj).get_log_level()) ; \ else LogOneLine(logobj,level).get_stream() #endif /** @} */ #endif odin-1.8.5/tjutils/tjstd.h0000644000175000017500000005603611322062342012403 00000000000000/*************************************************************************** tjstd.h - description ------------------- begin : Thu Dec 5 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJSTD_H #define TJSTD_H ///////////////////////////////////////////////////////////////// #ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif #include // memory management #include // C standard lib ///////////////////////////////////////////////////////////////// // Macros for stream replacement // Must be placed here to avoid circular dependencies #ifdef STREAM_REPLACEMENT #define STD_ostream tjstd_ostream #define STD_istream tjstd_istream #define STD_ostringstream tjstd_ostringstream #define STD_ofstream tjstd_ofstream #define STD_ifstream tjstd_ifstream #define STD_cout tjstd_cout #define STD_cerr tjstd_cerr #define STD_cin tjstd_cin #define STD_endl tjstd_endl #define STD_flush tjstd_flush #define STD_setprecision tjstd_setprecision #define STD_getline tjstd_getline #define STD_make_pair tjstd_make_pair class tjstd_ostream; // forward declaration class tjstd_istream; // forward declaration class tjstd_string; // forward declaration #else #define STD_ostream std::ostream #define STD_istream std::istream #define STD_ostringstream std::ostringstream #define STD_ofstream std::ofstream #define STD_ifstream std::ifstream #define STD_cout std::cout #define STD_cerr std::cerr #define STD_cin std::cin #define STD_endl std::endl #define STD_flush std::flush #define STD_setprecision std::setprecision #define STD_getline std::getline #define STD_make_pair std::make_pair #include #include #include #endif // STREAM_REPLACEMENT ///////////////////////////////////////////////////////////////// #ifdef STL_REPLACEMENT #define STD_list tjstd_list #define STD_find tjstd_find #define STD_pair tjstd_pair #define STD_map tjstd_map #define STD_vector tjstd_vector #define STD_complex tjstd_complex #define STD_back_inserter tjstd_back_inserter #define STD_unique_copy tjstd_unique_copy #define STD_swap tjstd_swap #define STD_max tjstd_max #define STD_min tjstd_min // complex math funcs #define STD_abs tjstd_abs #define STD_arg tjstd_arg #define STD_log tjstd_log #define STD_exp tjstd_exp #define STD_conj tjstd_conj #else // STL_REPLACEMENT #include #include #include #include #include #include #include #include // For Visual Studio 2005 #define STD_list std::list #define STD_find std::find #define STD_pair std::pair #define STD_map std::map #define STD_vector std::vector #define STD_complex std::complex #define STD_back_inserter std::back_inserter #define STD_unique_copy std::unique_copy #define STD_swap std::swap #define STD_max std::max #define STD_min std::min // complex math funcs #define STD_abs std::abs #define STD_arg std::arg #define STD_log std::log #define STD_exp std::exp #define STD_conj std::conj #endif // STL_REPLACEMENT /////////////////////////////////////////////// #ifdef STRING_REPLACEMENT #define STD_string tjstd_string #else // STRING_REPLACEMENT #include #define STD_string std::string #endif // STRING_REPLACEMENT /** * @addtogroup tjutils * @{ */ ///////////////////// STL replacement follows ///////////////////////////// #ifdef STL_REPLACEMENT template class tjnode { public: tjnode() : value(0), next(0), prev(0) {} tjnode (const I& newval) : value(new I(newval)), next(0), prev(0) {} ~tjnode() {if(value) delete value;} I* value; tjnode* next; tjnode* prev; private: // make these member functions private to prevent their usage tjnode(const tjnode&) {} tjnode& operator = (const tjnode&) {return *this;} }; ///////////////////////// template class tjiterator { public: tjiterator(tjnode* itemptr=0) : current(itemptr) {} operator I* () { if(current) return (current->value); else return 0; } operator const I* () const { if(current) return (current->value); else return 0; } I& operator * () {return *(operator I* ());} const I& operator * () const {return *(operator const I* ());} I* operator -> () {return operator I* ();} const I* operator -> () const {return operator const I* ();} tjiterator operator ++ () { if(current && current->next) current=current->next; return *this; } tjiterator operator ++ (int) { // postfix tjnode* old=current; if(current && current->next) current=current->next; return tjiterator(old); } tjiterator operator -- () { if(current && current->prev) current=current->prev; return *this; } tjiterator operator -- (int) { // postfix tjnode* old=current; if(current && current->prev) current=current->prev; return tjiterator(old); } bool operator == (const tjiterator& i2) const { return (current==i2.current); } bool operator != (const tjiterator& i2) const { return (current!=i2.current); } tjnode* current; }; //////////////////////////// template class tjstd_list { public: typedef tjiterator iterator; typedef tjiterator const_iterator; tjstd_list() : first(&end_node), size_cache(0) {} tjstd_list(unsigned int n, const I& value) : first(&end_node), size_cache(0) { for(unsigned int i=0; i begin() {return tjiterator(first);} tjiterator end() {return tjiterator(&end_node);} tjiterator begin() const {return tjiterator(first);} tjiterator end() const {return tjiterator(&end_node);} tjiterator push_back(const I& newval) { check("push_back(pre)"); tjnode* newnode=new tjnode(newval); push_back_node(newnode); check("push_back(post)"); return tjiterator(newnode); } tjiterator push_front(const I& newval) { check("push_front(pre)"); tjnode* newnode=new tjnode(newval); push_front_node(newnode); check("push_front(post)"); return tjiterator(newnode); } tjiterator insert(const tjiterator& pos, const I& newval) { check("insert(pre)"); tjnode* newnode=new tjnode(newval); insert_node(pos.current, newnode); return tjiterator(newnode); } void remove(const I& remval) { check("remove(pre)"); I value2Bremoved(remval); //create copy in the case it is an element of the list itself iterator it=begin(); while(it!=end()) { if((*it)==value2Bremoved) { tjnode* toberemoved=it.current; ++it; remove_node(toberemoved); delete toberemoved; } else ++it; } check("remove(post)"); } tjiterator erase(const tjiterator& b,const tjiterator& e) { check("erase2(pre)"); iterator it=b; while(it!=e) { tjnode* toberemoved=it.current; it.current=toberemoved->next; // iterate to next node remove_node(toberemoved); delete toberemoved; } check("erase2(post)"); return e; } tjiterator erase(const tjiterator& p) { check("erase1(pre)"); tjiterator result=p; result++; tjnode* toberemoved=p.current; remove_node(toberemoved); delete toberemoved; check("erase1(post)"); return result; } void clear() {erase(begin(),end());} unsigned int size() const {return size_cache;} bool empty() const {return !size_cache;} void sort() { check("sort(pre)"); // make list_unsrt a shallow copy of this tjstd_list list_unsrt; if(first!=(&end_node)) { list_unsrt.first=first; list_unsrt.end_node.prev=end_node.prev; list_unsrt.end_node.prev->next=&(list_unsrt.end_node); list_unsrt.size_cache=size_cache; } // reset me first=&end_node; end_node.prev=0; size_cache=0; while(list_unsrt.begin()!=list_unsrt.end()) { tjnode* node2sort=list_unsrt.first; list_unsrt.remove_node(node2sort); iterator it=begin(); while(it!=end() && (*it)<(*(node2sort->value))) ++it; insert_node(it.current,node2sort); } list_unsrt.check("sort::list_unsrt"); check("sort(post)"); } void unique() { check("unique(pre)"); for(iterator it=begin(); it!=end(); ++it) { while(it.current->next && it.current->next->value && (*(it.current->value))==(*(it.current->next->value)) ) { tjnode* toberemoved=it.current->next; remove_node(toberemoved); delete toberemoved; } } check("unique(post)"); } private: void push_back_node(tjnode* newnode) { check("push_back_node(pre)"); newnode->next=0; newnode->prev=0; if(first==(&end_node)) { first=end_node.prev=newnode; newnode->next=&end_node; } else { end_node.prev->next=newnode; newnode->prev=end_node.prev; end_node.prev=newnode; newnode->next=&end_node; } size_cache++; check("push_back_node(post)"); } void push_front_node(tjnode* newnode) { check("push_front_node(pre)"); newnode->next=0; newnode->prev=0; if(first==(&end_node)) { first=end_node.prev=newnode; newnode->next=&end_node; } else { first->prev=newnode; newnode->next=first; first=newnode; } size_cache++; check("push_front_node(post)"); } void remove_node(tjnode* toberemoved) { check("remove_node(pre)"); if(toberemoved->prev) toberemoved->prev->next=toberemoved->next; if(toberemoved->next) toberemoved->next->prev=toberemoved->prev; if(toberemoved==first) first=toberemoved->next; if(toberemoved==end_node.prev) end_node.prev= toberemoved->prev; toberemoved->next=0; toberemoved->prev=0; size_cache--; check("remove_node(post)"); } // Insert before posnode void insert_node(tjnode* posnode, tjnode* newnode) { check("insert_node(pre)"); newnode->next=0; newnode->prev=0; if(posnode==(&end_node)) { push_back_node(newnode); } else { if(posnode==first) push_front_node(newnode); else { // in the following the order is important posnode->prev->next=newnode; newnode->prev=posnode->prev; newnode->next=posnode; posnode->prev=newnode; size_cache++; } } check("insert_node(post)"); } void check(const char* /*caller*/) const { #ifdef ODIN_DEBUG /* if(!first) STD_cerr << "ERROR: tjstd_list::" << caller << " !first " << STD_endl; int size=0; for(const_iterator it=begin(); it!=end(); ++it) size++; if(size!=size_cache) STD_cerr << "ERROR: tjstd_list::" << caller << " size(" << size << ") != size_cache(" << size_cache << ")" << STD_endl; */ #endif } tjnode* first; mutable tjnode end_node; int size_cache; }; template tjiterator tjstd_find(const tjiterator& b,const tjiterator& e, const I& findval) { tjiterator it=b; while(it!=e) { if((*it)==findval) return it; ++it; } return e; } //////////////////////////////////////////////////////////////////////////// template class tjstd_pair { public: tjstd_pair() {} tjstd_pair(const K& key, const V& value) : first(key), second(value) {} bool operator == (const tjstd_pair& i2) const { // do not use == operator of K, otherwise it has to be defined if( (first& i2) const { return (first tjstd_pair tjstd_make_pair(const K& k, const V& v) { return tjstd_pair(k,v); } ////////////////////////////// template class tjstd_map : public tjstd_list< tjstd_pair > { public: V& operator [] (const K& key) { typename tjstd_map::iterator it=find(key); if(it==tjstd_list< tjstd_pair >::end()) { it=push_back(tjstd_pair(key,V())); tjstd_list< tjstd_pair >::sort(); } return it->second; } typename tjstd_map::iterator find(const K& key) { for(typename tjstd_map::iterator it=tjstd_list< tjstd_pair >::begin(); it!=tjstd_list< tjstd_pair >::end(); ++it) { if( !( (key<(it->first)) || ((it->first) >::end(); } typename tjstd_map::iterator find(const K& key) const { for(typename tjstd_map::const_iterator it=tjstd_list< tjstd_pair >::begin(); it!=tjstd_list< tjstd_pair >::end(); ++it) { if( !( (key<(it->first)) || ((it->first) >::end(); } void insert(const tjstd_pair& pair) { if(find(pair.first)==tjstd_list< tjstd_pair >::end()) { (*this)[pair.first]=pair.second; } } typename tjstd_map::iterator insert(typename tjstd_map::iterator, const tjstd_pair& pair) { if(find(pair.first)==tjstd_list< tjstd_pair >::end()) { (*this)[pair.first]=pair.second; } return find(pair.first); } }; //////////////////////////////////////////////////////////////////////////// // Extra type for vector size to avoid type-conversion problems in arithmetic expressions on VxWorks // which occur if a simple 'unsigned int' is used in the constructor of tjstd_vector struct tjstd_vector_size { tjstd_vector_size(unsigned int size) : s(size) {} unsigned int s; }; template class tjstd_vector { public: tjstd_vector() : data(0), nelements(0), cap(0) {} tjstd_vector(tjstd_vector_size size, const E& initval=E()) : data(0), nelements(0), cap(0) { resize(size.s); for(unsigned int i=0; i& v) : data(0), nelements(0), cap(0) { tjstd_vector::operator = (v); } ~tjstd_vector() { if(data) delete[] data; } tjstd_vector& operator = (const tjstd_vector& v) { if(data) delete[] data; nelements=cap=v.nelements; data=new E[nelements]; for(unsigned int i=0; i=nelements) { // STD_cerr << "ERROR: tjstd_vector: operator[" << i << "] exceeds size=" << nelements << STD_endl; return retdummy; } else return data[i]; } const E& operator [] (unsigned long i) const { if(i>=nelements) { // STD_cerr << "ERROR: tjstd_vector: operator[" << i << "] exceeds size=" << nelements << STD_endl; return retdummy; } else return data[i]; } void clear() { resize(0);} void resize(unsigned long newsize) { if(newsize>cap) { cap=newsize*2; E* newdata=new E[cap]; if(data) { for(unsigned int i=0; icap) { cap=newcap; E* newdata=new E[cap]; if(data) { for(unsigned int i=0; i bool operator == (const tjstd_vector& v1, const tjstd_vector& v2) { if(v1.size()!=v2.size()) return false; bool result=true; for(unsigned int i=0; i bool operator != (const tjstd_vector& v1, const tjstd_vector& v2) { return !(v1==v2); } template bool operator < (const tjstd_vector& v1, const tjstd_vector& v2) { unsigned int v1size=v1.size(); unsigned int v2size=v2.size(); if(v1size!=v2size) return (v1size void tjstd_swap(T& a1, T& a2){ T temp=a1; a1=a2; a2=temp; } template T tjstd_max(const T& a1, const T& a2){ if(a1>a2) return a1; else return a2; } template T tjstd_min(const T& a1, const T& a2){ if(a1 (const tjstd_string& s, const tjstd_string& t); friend STD_ostream& operator << (STD_ostream& s,const tjstd_string& t); friend STD_istream& operator >> (STD_istream& s, tjstd_string& t); tjstd_string substr(unsigned int begin,unsigned int sublength) const; void erase(unsigned int begin,unsigned int end); unsigned int find(const tjstd_string& searchstring, int startpos=0) const; typedef unsigned int size_type; static unsigned int npos; private: void concat2strings(const tjstd_string& srcstring1, const tjstd_string& srcstring2); static bool compare2strings(const char* str1, const char* str2); char* sdata; unsigned int length_cache; static char nullchar; }; #endif // STRING_REPLACEMENT //////////////////////////////////////////////////////////////////////////// /** @} */ #endif odin-1.8.5/tjutils/tjvallist.cpp0000644000175000017500000003035111455553536013633 00000000000000#include "tjvallist.h" #include "tjlog.h" #include "tjtypes.h" #include "tjtest.h" template ValList::ValList(const STD_string& object_label, unsigned int repetitions) : Labeled(), data(new ValListData) { set_label(object_label); data->times=repetitions; data->references=1; } template ValList::ValList(T value) : Labeled(), data(new ValListData) { data->val=new T(value); data->elements_size_cache=1; data->references=1; } template ValList::ValList(const ValList& svl) : Labeled(svl), data(svl.data) { data->references++; } template ValList::~ValList() { clear(); data->references--; if(!(data->references)) delete data; } template ValList& ValList::operator = (const ValList& svl) { Labeled::operator = (svl); set_label(svl.get_label()); data->references--; if(!(data->references)) delete data; data=svl.data; data->references++; return *this; } template bool ValList::operator == (const ValList& vl) const { return ( (get_elements_flat()==vl.get_elements_flat()) && (data->times==vl.data->times) ); } template bool ValList::operator < (const ValList& vl) const { bool result=true; if(! (get_elements_flat()timestimes) ) result=false; return result; } template bool ValList::equalelements (const ValList& svl) const { Log odinlog(this,"equalelements"); ODINLOG(odinlog,normalDebug) << "comparing with " << svl.get_label() << STD_endl; unsigned int thissize=data->elements_size_cache; unsigned int svlsize=svl.data->elements_size_cache; ODINLOG(odinlog,normalDebug) << "thissize/svlsize=" << thissize << "/" << svlsize << STD_endl; if(thissize!=svlsize) return false; if(thissize==0 && svlsize==0) return false; ODINLOG(odinlog,normalDebug) << "getting elements of this" << STD_endl; STD_vector thiselements=get_elements_flat(); ODINLOG(odinlog,normalDebug) << "getting elements of " << svl.get_label() << STD_endl; STD_vector svlelements=svl.get_elements_flat(); ODINLOG(odinlog,normalDebug) << "comparing vectors" << STD_endl; if(thiselements.size()==0 && svlelements.size()==0) return false; return (thiselements==svlelements); } template ValList& ValList::set_value(T value) { copy_on_write(); if(data->sublists) delete data->sublists; data->sublists=0; if(data->val) *(data->val)=value; else data->val=new T(value); data->elements_size_cache=1; return *this; } template ValList& ValList::add_sublist(const ValList& svl) { Log odinlog(this,"add_sublist"); copy_on_write(); if( !(svl.data->val || svl.data->sublists) ) { ODINLOG(odinlog,normalDebug) << "discarding empty list" << STD_endl; return *this; } ODINLOG(odinlog,normalDebug) << "checking for equal elements" << STD_endl; if(equalelements(svl)) { increment_repetitions(svl.get_repetitions()); ODINLOG(odinlog,normalDebug) << "incrementing repetitions" << STD_endl; return *this; } if(data->sublists && data->val) { ODINLOG(odinlog,errorLog) << "sublists and value allocated" << STD_endl; return *this; } if(!data->sublists && !data->val) { ODINLOG(odinlog,normalDebug) << "assigning" << STD_endl; if(svl.data->val) ODINLOG(odinlog,normalDebug) << "svl has val" << STD_endl; if(svl.data->sublists) ODINLOG(odinlog,normalDebug) << "svl has sublists" << STD_endl; STD_string label_cache(get_label()); (*this)=svl; set_label(label_cache); return *this; } if(!data->sublists && data->val) { ODINLOG(odinlog,normalDebug) << "allocating new sublists" << STD_endl; data->sublists=new STD_list< ValList >; for(unsigned int i=0; itimes; i++) data->sublists->push_back(ValList(*data->val)); // add element by element data->elements_size_cache=data->times; delete data->val; data->val=0; data->times=1; data->sublists->push_back(svl); data->elements_size_cache+=svl.size(); return *this; } if(data->sublists && !data->val) { ODINLOG(odinlog,normalDebug) << "appending" << STD_endl; if(data->times!=1) flatten_sublists(); data->sublists->push_back(svl); data->elements_size_cache+=svl.size(); return *this; } return *this; } template void ValList::flatten_sublists() { Log odinlog(this,"flatten_sublists"); copy_on_write(); STD_vector vals_flat=get_values_flat(); if(data->sublists) data->sublists->clear(); else data->sublists=new STD_list< ValList >; for(unsigned int i=0; isublists->push_back(ValList(vals_flat[i])); data->times=1; data->elements_size_cache=vals_flat.size(); } template STD_vector ValList::get_elements_flat() const { STD_list vallist; if(data->val) vallist.push_back(*data->val); if(data->sublists) { for(typename STD_list< ValList >::const_iterator it=data->sublists->begin(); it!=data->sublists->end(); ++it) { STD_vector subelements=it->get_values_flat(); for(unsigned int i=0; i result; result.resize(listsize); unsigned int index=0; for(typename STD_list::const_iterator valit=vallist.begin(); valit!=vallist.end(); ++valit) { result[index]=(*valit); index++; } return result; } template STD_vector ValList::get_values_flat() const { STD_vector elements=get_elements_flat(); unsigned int listsize=elements.size(); STD_vector result; result.resize(listsize*data->times); for(unsigned int itimes=0; itimestimes; itimes++) { for(unsigned int i=0; i T ValList::operator [] (unsigned int i) const { if(data->val) { if(i==0) return (*data->val); else i--; } if(data->sublists) { for(unsigned j=0; jtimes; j++) { for(typename STD_list< ValList >::const_iterator it=data->sublists->begin(); it!=data->sublists->end(); ++it) { unsigned int subsize=it->ValList::size(); if(ioperator [] (i); else i-=subsize; } } } return 0; } /* template unsigned int ValList::elements_size() const { unsigned int result=0; if(data->val) result++; if(data->sublists) { for(typename STD_list< ValList >::const_iterator it=data->sublists->begin(); it!=data->sublists->end(); ++it) { result+=it->ValList::size(); } } return result; } */ template STD_string ValList::printvallist() const { Log odinlog(this,"printvallist"); STD_string result; if(data->val) { result+=TypeTraits::type2string(*data->val)+" "; } if(data->sublists) { for(typename STD_list< ValList >::const_iterator it=data->sublists->begin(); it!=data->sublists->end(); ++it) { result+=it->printvallist(); } } if(data->times>1) result="{"+itos(data->times)+"| "+result+"} "; return result; } template STD_ostream& ValList::print2stream(STD_ostream& os) const { if(data->times>1) os << "{" << itos(data->times) << "| "; if(data->val) os << (*data->val) << " "; if(data->sublists) { for(typename STD_list< ValList >::const_iterator it=data->sublists->begin(); it!=data->sublists->end(); ++it) { it->print2stream(os); } } if(data->times>1) os << "} "; return os; } template bool ValList::parsevallist(const STD_string& str) { Log odinlog(this,"parsevallist"); copy_on_write(); svector toks(tokens(str)); unsigned int ntoks=toks.size(); ODINLOG(odinlog,normalDebug) << "ntoks=" << ntoks << STD_endl; unsigned int itok=0; while(itok=1) slist.increment_repetitions(rep-1); } else { T valdummy; TypeTraits::string2type(toks[itok],valdummy); ODINLOG(odinlog,normalDebug) << "valdummy=" << valdummy << STD_endl; slist.set_value(T(valdummy)); itok++; } add_sublist(slist); } return true; } template void ValList::clear() { copy_on_write(); if(data->sublists) delete data->sublists; data->sublists=0; if(data->val) delete data->val; data->val=0; data->elements_size_cache=0; } template void ValList::copy_on_write() { Log odinlog(this,"copy_on_write"); ODINLOG(odinlog,normalDebug) << "references=" << data->references << STD_endl; if(data->references>1) { data->references--; data=new ValListData(*data); data->references++; } } // instantiations reuired for ODIN template class ValList; template class ValList; ///////////////////////////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST typedef ValList ValListInt; class ValListTest : public UnitTest { public: ValListTest() : UnitTest("vallist") {} private: bool check() const { Log odinlog(this,"check"); ValListInt v1(1); ValListInt v2; v2.set_value(2); ValListInt vl; vl.add_sublist(v1); vl.add_sublist(v2); STD_string expected="1 2 "; STD_string printed=vl.printvallist(); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "add_sublist(v1,v2) failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } ///////////////////////////////////////// ValListInt vl2; vl2.add_sublist(vl); vl2.add_sublist(vl); vl2.add_sublist(vl); expected="{3| 1 2 } "; printed=vl2.printvallist(); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "add_sublist(3*vl) failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } expected="1 2 1 2 1 2"; printed=ivector(vl2.get_values_flat()).printbody(); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "get_values_flat failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } expected="3"; printed=itos(vl2.get_repetitions()); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "get_repetitions failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } ///////////////////////////////////////// vl2.clear(); vl.multiply_repetitions(7); vl2.add_sublist(vl); vl.multiply_repetitions(9); vl2.add_sublist(vl); vl2.multiply_repetitions(2); expected="{140| 1 2 } "; // (7 + 7*9)*2=140 printed=vl2.printvallist(); if( expected!=printed ) { ODINLOG(odinlog,errorLog) << "multiply_repetitions failed, got >" << printed << "< but expected >" << expected << "<" << STD_endl; return false; } ///////////////////////////////////////// v1.clear(); v1.parsevallist("{3| 1 2 {3| 4 5 } }"); unsigned int expected_size=24; unsigned int calculated_size=v1.size(); if( expected_size!=calculated_size ) { ODINLOG(odinlog,errorLog) << "size() failed, got >" << calculated_size << "< but expected >" << expected_size << "<" << STD_endl; return false; } v1.clear(); expected_size=0; calculated_size=v1.size(); if( expected_size!=calculated_size ) { ODINLOG(odinlog,errorLog) << "size() failed, got >" << calculated_size << "< but expected >" << expected_size << "<" << STD_endl; return false; } return true; } }; void alloc_ValListTest() {new ValListTest();} // create test instance #endif odin-1.8.5/tjutils/tjhandler_code.h0000644000175000017500000000752011322062342014212 00000000000000#include #include ////////////////////////////////////////////////////////////// template Handled::Handled() {} template Handled::~Handled() { Log odinlog("Handled","~Handled"); for(typename STD_list< const Handler* >::const_iterator it=handlers.begin(); it!=handlers.end(); ++it) { (*it)->handled_remove(this); // do not call L::remove here because it will modify handlers list } } template const Handled& Handled::set_handler(const Handler& handler) const { handlers.push_back(&handler); return *this; } template const Handled& Handled::erase_handler(const Handler& handler) const { handlers.remove(&handler); return *this; } ///////////////////////////////////////////// template Handler::Handler() { handledobj=0; } template Handler::Handler(const Handler& handler) { Handler::operator = (handler); } template Handler& Handler::operator = (const Handler& handler) { clear_handledobj(); I hd=handler.get_handled(); if(hd) set_handled(hd); return *this; } template Handler::~Handler() { Log odinlog("Handler","~Handler"); clear_handledobj(); } template const Handler& Handler::clear_handledobj() const { Log odinlog("Handler","clear_handledobj"); ODINLOG(odinlog,normalDebug) << "handledobj=" << (void*)handledobj << STD_endl; if(handledobj) handledobj->Handled::erase_handler(*this); handledobj=0; return *this; } template const Handler& Handler::set_handled(I handled) const { Log odinlog("Handler","set_handled"); ODINLOG(odinlog,normalDebug) << "handled=" << (void*)handled << STD_endl; clear_handledobj(); handled->Handled::set_handler(*this); handledobj=handled; return *this; } template I Handler::get_handled() const { return handledobj; } template const Handler& Handler::handled_remove(Handled* handled) const { Log odinlog("Handler","handled_remove"); I handledtype=static_cast(handled); ODINLOG(odinlog,normalDebug) << "handledtype=" << (void*)handledtype << STD_endl; if(handledtype) handledobj=0; else ODINLOG(odinlog,errorLog) << "Unable to remove handled!" << STD_endl; return *this; } //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// template void SingletonHandler::init (const char* unique_label) { // NOTE: Debug uses SingletonHandler -> do not use Debug in here singleton_label=new STD_string; mutex=0; if(thread_safe) mutex=new Mutex(); (*singleton_label)=unique_label; if(!get_external_map_ptr(unique_label)) { ptr=new T; ptr->set_label(unique_label); (*get_singleton_map())[unique_label]=this; // make sure singleton_map is allocated } else { ptr=0; } } template void SingletonHandler::destroy () { if(ptr) delete ptr; ptr=0; delete singleton_label; if(mutex) delete mutex; } template void SingletonHandler::copy(T& destination) const { T* p=get_map_ptr(); if(p) destination=(*p); } template T* SingletonHandler::get_map_ptr() const { if(ptr) return ptr; // fast return without touching the map if(singleton_map_external) { T* ext_ptr=(T*)get_external_map_ptr(*singleton_label); if(ext_ptr) ptr=ext_ptr; } return ptr; } odin-1.8.5/tjutils/Makefile.am0000644000175000017500000000253311322062342013127 00000000000000 INCLUDES = $(all_includes) lib_LTLIBRARIES = libtjutils.la libtjutils_la_LDFLAGS = -no-undefined -release $(VERSION) $(BASELIBS) library_includedir=$(includedir)/tjutils library_include_HEADERS = \ tjarray.h \ tjcomplex.h \ tjcstd.h \ tjembed.h \ tjfeedback.h \ tjhandler.h tjhandler_code.h \ tjheap.h \ tjindex.h \ tjlabel.h \ tjlist.h tjlist_code.h \ tjlog.h tjlog_code.h \ tjnumeric.h \ tjprocess.h \ tjprofiler.h \ tjstate.h \ tjstatic.h \ tjstd.h \ tjstream.h \ tjstring.h \ tjtest.h \ tjthread.h tjthread_code.h \ tjtools.h \ tjtypes.h \ tjutils.h \ tjvallist.h \ tjvector.h tjutils_configdir = $(includedir)/tjutils tjutils_config_DATA = config.h libtjutils_la_SOURCES = \ tjarray.h tjarray.cpp \ tjcomplex.h tjcomplex.cpp \ tjcstd.h tjcstd.cpp \ tjlog.h tjlog.cpp tjlog_code.h \ tjembed.h tjembed.cpp \ tjfeedback.h tjfeedback.cpp \ tjhandler.h tjhandler.cpp tjhandler_code.h \ tjheap.h tjheap.cpp \ tjindex.h tjindex.cpp \ tjlabel.h \ tjlist.h tjlist.cpp tjlist_code.h \ tjnumeric.h tjnumeric.cpp \ tjprocess.h tjprocess.cpp \ tjprofiler.h tjprofiler.cpp \ tjstate.h tjstate.cpp \ tjstatic.h tjstatic.cpp \ tjstd.h tjstd.cpp \ tjstream.h tjstream.cpp \ tjstring.h tjstring.cpp \ tjtest.h tjtest.cpp \ tjthread.h tjthread.cpp tjthread_code.h \ tjtools.h tjtools.cpp \ tjtypes.h tjtypes.cpp \ tjutils.h \ tjvallist.h tjvallist.cpp \ tjvector.h tjvector.cpp odin-1.8.5/tjutils/Makefile.in0000644000175000017500000005521611734622602013156 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 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install-man install-pdf \ install-pdf-am install-ps install-ps-am install-strip \ install-tjutils_configDATA installcheck installcheck-am \ installdirs maintainer-clean maintainer-clean-generic \ mostlyclean mostlyclean-compile mostlyclean-generic \ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \ uninstall-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS uninstall-tjutils_configDATA # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/tjutils/tjlist_code.h0000644000175000017500000001012111322062342013537 00000000000000#include #include #ifdef HAVE_TYPEINFO #include #endif template ListItem::~ListItem() { Log odinlog("ListItem","~ListItem"); #ifdef HAVE_TYPEINFO ODINLOG(odinlog,normalDebug) << "deleting object of type >" << typeid(I).name() << "<" << STD_endl; #endif for(STD_list::iterator it=objhandlers.begin(); it!=objhandlers.end(); ++it) { (*it)->objlist_remove(this); } } template const ListItemBase& ListItem::append_objhandler(ListBase& objhandler) const { Log odinlog("ListItem","append_objhandler"); objhandlers.push_back(&objhandler); return *this; } template const ListItemBase& ListItem::remove_objhandler(ListBase& objhandler) const { Log odinlog("ListItem","remove_objhandler"); objhandlers.remove(&objhandler); return *this; } /////////////////////////////////////////////////////////////////////////////////////////// template List::List() { Log odinlog("List","List()"); #ifdef HAVE_TYPEINFO ODINLOG(odinlog,normalDebug) << "constructing list of >" << typeid(I).name() << "<" << STD_endl; #endif } template List::~List() { Log odinlog("List","~List()"); #ifdef HAVE_TYPEINFO ODINLOG(odinlog,normalDebug) << "destructing list of >" << typeid(I).name() << "<" << STD_endl; #endif clear(); } template List& List::operator = (const List& l) { clear(); for(typename STD_list

    ::const_iterator it=l.objlist.begin(); it!=l.objlist.end(); ++it) { append(**it); } return *this; } template List& List::clear() { Log odinlog("List","clear"); #ifdef HAVE_TYPEINFO ODINLOG(odinlog,normalDebug) << "Clearing list of type >" << typeid(I).name() << "<" << STD_endl; #endif for(typename STD_list

    ::iterator it=objlist.begin(); it!=objlist.end(); ++it) { ODINLOG(odinlog,normalDebug) << "Unlinking " << (*it) << STD_endl; unlink_item(*it); ODINLOG(odinlog,normalDebug) << "Unlinking done" << STD_endl; } objlist.erase(objlist.begin(),objlist.end()); return *this; } template List& List::append(R item) { Log odinlog("List","append"); #ifdef HAVE_TYPEINFO ODINLOG(odinlog,normalDebug) << "appending object of type >" << typeid(I).name() << "<" << STD_endl; #endif link_item(&item); objlist.push_back(&item); return *this; } template List& List::remove(R item) { Log odinlog("List","remove"); #ifdef HAVE_TYPEINFO ODINLOG(odinlog,normalDebug) << "removing object of type >" << typeid(I).name() << "<" << STD_endl; #endif unlink_item(&item); objlist.remove(&item); return *this; } template void List::objlist_remove(ListItemBase* item) { Log odinlog("List","objlist_remove"); #ifdef HAVE_TYPEINFO ODINLOG(odinlog,normalDebug) << "deleting object of type >" << typeid(I).name() << "<" << STD_endl; #endif P itemItype=static_cast

    (item); if(itemItype) { objlist.remove(itemItype); } else { ODINLOG(odinlog,errorLog) << "static_cast failed" << STD_endl; } } template void List::link_item(P ptr) { Log odinlog("List","link_item"); const ListItem* item=static_cast*>(ptr); if(item) { item->append_objhandler(*this); } else { ODINLOG(odinlog,errorLog) << "static_cast failed" << STD_endl; } } template void List::unlink_item(P ptr) { Log odinlog("List","unlink_item"); const ListItem* item=static_cast*>(ptr); if(item) { item->remove_objhandler(*this); } else { ODINLOG(odinlog,errorLog) << "static_cast failed" << STD_endl; } } odin-1.8.5/tjutils/tjvector.h0000644000175000017500000003222611322062342013106 00000000000000 /*************************************************************************** tjvector.h - description ------------------- begin : Thu Feb 22 2001 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJVECTOR_H #define TJVECTOR_H #include #include #include #include #include /** * @addtogroup tjutils * @{ */ class VectorComp { public: static const char* get_compName(); }; /** * * This class represents a basic vector which is derived * from the Standard Template Library (STL) vector class. * it adds some useful functionality to the STL base class, * for example element-wise arithmetics and reading/writing. */ template class tjvector : public STD_vector { public: /** * * constructs a vector and allocates memory for n values * which are initialised to zero. */ tjvector(unsigned int n=0); /** * * constructs a vector of length n and gets n values from array * No bounds checking possible, so take care that the pointer array * has memory allocated which is in fact n values long. */ tjvector(const T *array, unsigned int n); /** * * constructs a copy from std::vector */ tjvector(const STD_vector& v); /** * * Copy constructor */ tjvector(const tjvector& tv); /** * * destructor */ virtual ~tjvector(); /** * * assign value to all elements of vector */ tjvector& operator = (const T& value); /** * * assignment from std::vector */ tjvector& operator = (const STD_vector& vec); /** * * copy assignment */ tjvector& operator = (const tjvector& tv); /** * * returns the element-wise sum of two tjvectors */ tjvector operator + (const STD_vector& w) const { tjvector result(*this); for(unsigned int i=0; i operator - (const STD_vector& w) const { tjvector result(*this); for(unsigned int i=0; i operator * (const STD_vector& w) const { tjvector result(*this); for(unsigned int i=0; i operator / (const STD_vector& w) const { tjvector result(*this); for(unsigned int i=0; i operator - () const { tjvector result(*this); for(unsigned int i=0; i operator + (const T& s, const STD_vector& v) { tjvector result(v); for(unsigned int i=0; i operator + (const T& s) const { return s+(*this); } /** * * returns the element-wise difference of a tjvector with a scalar */ friend tjvector operator - (const T& s, const STD_vector& v) { tjvector result(v); for(unsigned int i=0; i operator - (const T& s) const { return -s+(*this); } /** * * returns the element-wise product of a tjvector with a scalar */ friend tjvector operator * (const T& s, const STD_vector& v) { tjvector result(v); for(unsigned int i=0; i operator * (const T& s) const { return s*(*this); } /** * * returns the element-wise division of a tjvector with a scalar */ friend tjvector operator / (const T& s, const STD_vector& v) { tjvector result(v); for(unsigned int i=0; i operator / ( const T& s) const { return (T(1)/s)*(*this); } /** * Equivalent to: this = this + v */ tjvector& operator += ( const STD_vector& v) { (*this)=(*this)+v; return (*this); } /** * Equivalent to: this = this + s */ tjvector& operator += ( const T& s) { (*this)=(*this)+s; return (*this); } /** * Equivalent to: this = this - v */ tjvector& operator -= ( const STD_vector& v) { (*this)=(*this)-v; return (*this); } /** * Equivalent to: this = this - s */ tjvector& operator -= ( const T& s) { (*this)=(*this)-s; return (*this); } /** * Equivalent to: this = this * v */ tjvector& operator *= ( const STD_vector& v) { (*this)=(*this)*v; return (*this); } /** * Equivalent to: this = this * s */ tjvector& operator *= ( const T& s) { (*this)=(*this)*s; return (*this); } /** * Equivalent to: this = this / v */ tjvector& operator /= ( const STD_vector& v) { (*this)=(*this)/v; return (*this); } /** * Equivalent to: this = this / s */ tjvector& operator /= ( const T& s) { (*this)=(*this)/s; return (*this); } /** * * Resizes the vector to 'newsize'. * If the 'newsize' is smaller than the actual size, * the starting values will be preserved in the smaller vector. * If the 'newsize' is larger than the actual size, * the vector will be zero padded. */ virtual tjvector& resize(unsigned int newsize); /** * * returns the length */ unsigned int length () const; /** * * fill the array linearly from value min to value max, return number of fills */ unsigned int fill_linear(const T& min,const T& max); /** * * Returns the sum of all elements */ T sum() const; /** * * Returns the given range of elements starting at startindex and ending at endindex-1 */ tjvector range(unsigned int startindex, unsigned int endindex) const; /** * * Return the greatest value */ T maxvalue() const; /** * * Return the smallest value */ T minvalue() const; /** * * Maximum absolute value */ T maxabs() const; /** * * Returns an allocated C-style array of Ts with the values of this vector. * The array is deleted automatically at the next call of c_array() or if * this vector is destroyed. */ const T* c_array() const; /** * * Gets n values from 'array' (raw memory), no resizing is done * prior to assignment, this has to be manually beforehand. * No bounds checking possible, so take care that the pointer array * has memory allocated which is in fact n values long. */ tjvector& set_c_array(const unsigned char* array, unsigned int n); /** * * Normalize the vector, i.e. make its smallest/largest non-zero value become -1 or 1. * Returns the maximum absolute value which was used to achieve the normalization. */ T normalize(); /** * * interpolate values to new size 'newsize'. Add extra shift 'subpixel_shift' * in units of pixels on the destination grid. */ tjvector& interpolate(unsigned int newsize, float subpixel_shift=0.0); /** * * Loads the values from disk, the file is expected * to contain the same data type as the array. * Returns 0 on success, -1 otherwise. */ int load(const STD_string& fname); /** * * Writes the first 'nelements' values to disk as raw data, the 'mode' determines * whether data will be appended/overwritten if the file already exists. * If 'nelements' is negative, the whole vector will we written. * Returns 0 on success, -1 otherwise. */ int write(const STD_string& fname, fopenMode mode=overwriteMode, LONGEST_INT nelements=-1) const; /** * * returns the elements of the vector as a formatted string */ STD_string printbody() const; /** * * prints v to the stream s */ friend STD_ostream& operator << (STD_ostream& s,const tjvector& v) { return s << "(" << v.size() << ")=" << v.printbody(); } protected: // allocate aligned memory for type T (to avoid bus errors) static T* allocate_memory(unsigned int nelements) {return new T[nelements];} private: mutable T* c_array_cache; }; ///////////////////////////////////////////////////////////////////////////// // Aliases: /** * A vector of floating point numbers */ typedef tjvector fvector; /** * A vector of double precision floating point numbers */ typedef tjvector dvector; /** * A vector of integer numbers */ typedef tjvector ivector; /** * A vector of complex numbers */ typedef tjvector cvector; /** * A vector of strings */ struct svector : public STD_vector { // some extra stuff to be compatible with STD_vector svector() {} svector(const STD_vector& sv) {svector::operator = (sv);} svector& operator = (const STD_vector& sv) {STD_vector::operator = (sv); return *this;} // interface functions for JDXarray unsigned char* c_array() const {return 0;} svector& set_c_array(const unsigned char*, unsigned int) {return *this;} static unsigned char* allocate_memory(unsigned int) {return 0;} // other useful functions, imitating a tjvector STD_string printbody() const; }; ///////////////////////////////////////////////////////////////////////////// // Stuff to re-used in odindata STD_complex* interpolate1D(const STD_complex* data,unsigned int oldsize,unsigned int newsize, float subpixel_shift); float* interpolate1D(const float* olddata,unsigned int oldsize,unsigned int newsize, float subpixel_shift); double* interpolate1D(const double* olddata,unsigned int oldsize,unsigned int newsize, float subpixel_shift); int* interpolate1D(const int* olddata,unsigned int oldsize,unsigned int newsize, float subpixel_shift); ///////////////////////////////////////////////////////////////////////////// // Specialised helper functions: /** * * Converts a list into a vector */ template STD_vector list2vector(const STD_list& src) { STD_vector result; result.resize(src.size()); unsigned int i=0; for(typename STD_list::const_iterator it=src.begin(); it!=src.end(); ++it) { result[i]=(*it); i++; } return result; } /** * * Returns the real portion of a complex array */ fvector real(const cvector& cv); /** * * Returns the imaginary portion of a complex array */ fvector imag(const cvector& cv); /** * * Returns the amplitude of a complex array */ fvector amplitude(const cvector& cv); /** * * Returns the phase of a complex array */ fvector phase(const cvector& cv); /** * * Returns a complex array with 'fv' in the real component */ cvector real2complex(const fvector& fv); /** * * Converts a vector of floats to a vector of doubles */ dvector fvector2dvector(const fvector& fv); /** * * Converts a vector of doubles to a vector of floats */ fvector dvector2fvector(const dvector& dv); /** * * Splits the string into tokens, which are substrings separated by blanks, * tabs and newlines or custom_separator (if custom_separator!=0) and returns them as a vector of strings. * Parts of the string enclosed by 'escape_begin' and 'escape_end' will not be decomposed into tokens. */ svector tokens(const STD_string& tokenstring, char custom_separator=0, char escape_begin='"', char escape_end='"'); /** * * Produces a string with linebreaks if width exceeds 'linewidth' from a vector of single strings. * A 'linewidth' of zero will produce no linebreaks. */ STD_string tokenstring(const svector& tokens,unsigned int linewidth=_DEFAULT_LINEWIDTH_); /** * * Returns all entries in the given directory, if 'only_dirs' is 'true' * only subdirectories will be reported. Files starting with a dot * are discarded when setting 'discard_dotfiles' to 'true'. * The resulting vector is sorted alphanumerically according to the file names. */ svector browse_dir(const STD_string& dirname,bool only_dirs=false, bool discard_dotfiles=false); /** @} */ #endif odin-1.8.5/tjutils/tjtest.cpp0000644000175000017500000000207311322062342013113 00000000000000#include "tjtest.h" #include "tjlog_code.h" #ifndef NO_UNIT_TEST const char* UnitTest::get_compName() {return "UnitTest";} void UnitTest::init_static() { tests=new STD_list; } void UnitTest::destroy_static() { for(STD_list::const_iterator it=tests->begin(); it!=tests->end(); ++it) { delete (*it); } delete tests; } UnitTest::UnitTest(const char* label) { set_label(label); tests->push_back(this); } int UnitTest::check_all() { Log odinlog("","check_all"); if(!tests) return 0; for(STD_list::const_iterator it=tests->begin(); it!=tests->end(); ++it) { ODINLOG(odinlog,infoLog) << "Testing " << (*it)->get_label() << " ..." << STD_endl; if(!(*it)->check()) { ODINLOG(odinlog,errorLog) << "Test of " << (*it)->get_label() << " failed" << STD_endl; return -1; } } ODINLOG(odinlog,infoLog) << "All tests passed" << STD_endl; return 0; } STD_list* UnitTest::tests=0; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; LOGGROUNDWORK(UnitTest) #endif odin-1.8.5/tjutils/config.h.in0000644000175000017500000001547611734622601013137 00000000000000/* tjutils/config.h.in. Generated from configure.in by autoheader. */ /* Third-party libraries used by all ODIN components */ #undef BASELIBS /* Preprocessor flags */ #undef CPPFLAGS /* "Using custom heap" */ #undef CUSTOM_HEAP /* Size of Custom Heap in MB */ #undef CUSTOM_HEAP_SIZE /* Compiler */ #undef CXX /* Compiler flags */ #undef CXXFLAGS /* Initial default browser */ #undef DEFAULT_BROWSER /* Initial default editor */ #undef DEFAULT_EDITOR /* "DICOM support" */ #undef DICOMSUPPORT /* define for empty template list */ #undef EMPTY_TEMPL_LIST /* "Compile EPIC drivers" */ #undef EPIC_PLUGIN /* "Graphical User Interface enabled" */ #undef GUISUPPORT /* Define to 1 if you have the `acosh' function. */ #undef HAVE_ACOSH /* Define to 1 if you have the header file. */ #undef HAVE_CTYPE_H /* Define to 1 if you have the header file. */ #undef HAVE_DIRECT_H /* Define to 1 if you have the header file. */ #undef HAVE_DIRENT_H /* "Using dynamic linking loader" */ #undef HAVE_DL /* Define to 1 if you have the header file. */ #undef HAVE_DLFCN_H /* Define to 1 if you have the `erfc' function. */ #undef HAVE_ERFC /* Define to 1 if you have the `fopen64' function. */ #undef HAVE_FOPEN64 /* Define to 1 if you have the `fseeko' function. */ #undef HAVE_FSEEKO /* Define to 1 if you have the `fseeko64' function. */ #undef HAVE_FSEEKO64 /* Define to 1 if you have the `ftello' function. */ #undef HAVE_FTELLO /* Define to 1 if you have the `ftello64' function. */ #undef HAVE_FTELLO64 /* "Using gdb/xterm" */ #undef HAVE_GDB_XTERM /* Define to 1 if you have the `gettimeofday' function. */ #undef HAVE_GETTIMEOFDAY /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_IO_H /* Define to 1 if you have the `j1' function. */ #undef HAVE_J1 /* "Using LAPACK" */ #undef HAVE_LAPACK /* "GSL support" */ #undef HAVE_LIBGSL /* "libz support" */ #undef HAVE_LIBZ /* Define to 1 if you have the header file. */ #undef HAVE_LOCALE_H /* compiler understands long long */ #undef HAVE_LONG_LONG /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define to 1 if you have the `mmap64' function. */ #undef HAVE_MMAP64 /* Define to 1 if you have the `nanosleep' function. */ #undef HAVE_NANOSLEEP /* Define to 1 if you have the `open64' function. */ #undef HAVE_OPEN64 /* "Using POSIX threads" */ #undef HAVE_PTHREAD /* Define to 1 if you have the header file. */ #undef HAVE_QWT_QT4_QWT_GLOBAL_H /* Define to 1 if you have the header file. */ #undef HAVE_QWT_QWT_GLOBAL_H /* Define to 1 if you have the `read' function. */ #undef HAVE_READ /* Define to 1 if you have the header file. */ #undef HAVE_SETJMP_H /* Define to 1 if you have the header file. */ #undef HAVE_SIGNAL_H /* Define to 1 if you have the `snprintf' function. */ #undef HAVE_SNPRINTF /* Define to 1 if you have the `srand' function. */ #undef HAVE_SRAND /* Define to 1 if you have the `stat' function. */ #undef HAVE_STAT /* Define to 1 if you have the `stat64' function. */ #undef HAVE_STAT64 /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the `strftime' function. */ #undef HAVE_STRFTIME /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the `strptime' function. */ #undef HAVE_STRPTIME /* Define to 1 if you have the `sysconf' function. */ #undef HAVE_SYSCONF /* Define to 1 if you have the header file. */ #undef HAVE_SYS_MMAN_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TIME_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_WAIT_H /* "Thread-safe LAPACK" */ #undef HAVE_THREADSAFE_LAPACK /* Define to 1 if you have the header file. */ #undef HAVE_TIME_H /* Define to 1 if you have the header file. */ #undef HAVE_TYPEINFO /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to 1 if you have the header file. */ #undef HAVE_VTKARROWSOURCE_H /* Define to 1 if you have the header file. */ #undef HAVE_VTKSTRUCTUREDPOINTS_H /* Define to 1 if you have the header file. */ #undef HAVE_WINDOWS_H /* "Compile IDEA drivers" */ #undef IDEA_PLUGIN /* Installation prefix */ #undef INSTALL_PREFIX /* Linker */ #undef LD /* Linker flags */ #undef LDFLAGS /* libdir of configure */ #undef LIBDIR_CONFIGURE /* Define to the sub-directory in which libtool stores uninstalled libraries. */ #undef LT_OBJDIR /* "MacOS support" */ #undef MACOS /* "NIFTI support" */ #undef NIFTISUPPORT /* "Not using command line" */ #undef NO_CMDLINE /* "No file handling" */ #undef NO_FILEHANDLING /* "Multithreading disabled" */ #undef NO_THREADS /* "Unit test disabled" */ #undef NO_UNIT_TEST /* "IDEA support" */ #undef ODIN4IDEA /* "Debug compilation" */ #undef ODIN_DEBUG /* Name of package */ #undef PACKAGE /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* "Compile Paravision drivers" */ #undef PARAVISION_PLUGIN /* Plugin-Libraries */ #undef PLUGIN_LIBS /* "PNG support" */ #undef PNGSUPPORT /* "self-friend class possible/required" */ #undef SELF_FRIEND_CLASS /* The number of bytes in type char */ #undef SIZEOF_CHAR /* The number of bytes in type int */ #undef SIZEOF_INT /* The number of bytes in type long */ #undef SIZEOF_LONG /* The number of bytes in type short */ #undef SIZEOF_SHORT /* "Compile Standalone drivers" */ #undef STANDALONE_PLUGIN /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* "Using STL replacement" */ #undef STL_REPLACEMENT /* "Using stream replacement" */ #undef STREAM_REPLACEMENT /* "Using string replacement" */ #undef STRING_REPLACEMENT /* "Using the GNU compiler collection" */ #undef USING_GCC /* "Using Win32-API" */ #undef USING_WIN32 /* Version number of package */ #undef VERSION /* "Vista support" */ #undef VISTASUPPORT /* "VTK support" */ #undef VTKSUPPORT odin-1.8.5/tjutils/tjthread.cpp0000644000175000017500000003376411712547771013437 00000000000000#include "tjthread.h" #include "tjtools.h" #include "tjtest.h" #include "tjindex.h" #include "tjthread_code.h" #include "tjlog_code.h" #ifndef NO_THREADS #ifdef HAVE_PTHREAD #include #define USE_PTHREADS #endif #ifdef USING_WIN32 #include #define USE_WINTHREADS #endif #endif const char* ThreadComponent::get_compName() {return "Thread";} LOGGROUNDWORK(ThreadComponent) //////////////////////////////////////////////////////////////////// #ifdef USE_PTHREADS const char* pthread_err(int code) { if(code==EAGAIN) return "not enough system resources to create a process for the new thread."; if(code==ESRCH) return "No thread could be found corresponding to that specified by |th|."; if(code==EINVAL) return "The |th| thread has been detached./the mutex has not been properly initialized."; if(code==EINVAL) return "Another thread is already waiting on termination of |th|."; if(code==EDEADLK) return "The |th| argument refers to the calling thread./the mutex is already locked by the calling thread."; if(code==EBUSY) return "the mutex could not be acquired because it was currently locked./some threads are currently waiting on |cond|"; if(code==EPERM) return "the calling thread does not own the mutex."; if(code==ETIMEDOUT) return "the condition variable was not signaled until the timeout specified by |abstime|"; if(code==EINTR) return "!pthread_cond_timedwait! was interrupted by a signal"; if(code==ENOMEM) return "Out of memory"; return "Unknown error"; } #endif //////////////////////////////////////////////////////////////////// Mutex::Mutex() : id(0) { // Do not use Log in here since SingletonHandler uses Mutex #ifdef USE_PTHREADS #ifdef MACOS // the Mac OS way of creating recursive threads pthread_mutexattr_t pma_recursive; int errcode=pthread_mutexattr_init(&pma_recursive); if(errcode) { STD_cerr << "ERROR: Mutex: " << pthread_err(errcode) << STD_endl; return; } errcode=pthread_mutexattr_settype(&pma_recursive, PTHREAD_MUTEX_RECURSIVE); if(errcode) { STD_cerr << "ERROR: Mutex: " << pthread_err(errcode) << STD_endl; return; } id=(void*)new pthread_mutex_t; errcode=pthread_mutex_init((pthread_mutex_t*)id, &pma_recursive); if(errcode) { STD_cerr << "ERROR: Mutex: " << pthread_err(errcode) << STD_endl; return; } #else // the Linux way of creating recursive threads pthread_mutex_t pm_recursive=PTHREAD_RECURSIVE_MUTEX_INITIALIZER_NP; id=(void*)new pthread_mutex_t(pm_recursive); #endif #endif #ifdef USE_WINTHREADS CRITICAL_SECTION* cs=new CRITICAL_SECTION; InitializeCriticalSection(cs); id=(void*)cs; #endif } Mutex::~Mutex() { // Do not use Log in here since SingletonHandler uses Mutex if(id) { #ifdef USE_PTHREADS int errcode=pthread_mutex_destroy((pthread_mutex_t*)id); if(errcode) STD_cerr << "ERROR: ~Mutex: " << pthread_err(errcode) << STD_endl; delete (pthread_mutex_t*)id; #endif #ifdef USE_WINTHREADS DeleteCriticalSection((CRITICAL_SECTION*)id); delete (CRITICAL_SECTION*)id; #endif } } void Mutex::lock() { // Do not use Log in here since SingletonHandler uses Mutex if(id) { #ifdef USE_PTHREADS int errcode=pthread_mutex_lock((pthread_mutex_t*)id); if(errcode) STD_cerr << "ERROR: Mutex::lock: " << pthread_err(errcode) << STD_endl; #endif #ifdef USE_WINTHREADS EnterCriticalSection((CRITICAL_SECTION*)id); #endif } } void Mutex::unlock() { // Do not use Log in here since SingletonHandler uses Mutex if(id) { #ifdef USE_PTHREADS int errcode=pthread_mutex_unlock((pthread_mutex_t*)id); if(errcode) STD_cerr << "ERROR: Mutex::unlock: " << pthread_err(errcode) << STD_endl; #endif #ifdef USE_WINTHREADS LeaveCriticalSection((CRITICAL_SECTION*)id); #endif } } //////////////////////////////////////////////////////////////////// Event::Event() : id(0), active(false) { Log odinlog("Event","Event"); #ifdef USE_PTHREADS pthread_cond_t cond=PTHREAD_COND_INITIALIZER; id=(void*)new pthread_cond_t(cond); #endif #ifdef USE_WINTHREADS id=(void*)new HANDLE; *((HANDLE*)id)=CreateEvent(NULL,TRUE,FALSE,NULL); #endif } Event::~Event() { Log odinlog("Event","~Event"); if(id) { #ifdef USE_PTHREADS int errcode=pthread_cond_destroy((pthread_cond_t*)id); if(errcode) ODINLOG(odinlog,errorLog) << pthread_err(errcode) << STD_endl; delete (pthread_cond_t*)id; #endif #ifdef USE_WINTHREADS CloseHandle(*((HANDLE*)id)); delete (HANDLE*)id; #endif } } void Event::wait() { Log odinlog("Event","wait"); #ifdef USE_PTHREADS MutexLock lock(mutex); while(!active) { int errcode=pthread_cond_wait((pthread_cond_t*)id, (pthread_mutex_t*)(mutex.id)); if(errcode) { ODINLOG(odinlog,errorLog) << pthread_err(errcode) << STD_endl; break; } } #endif #ifdef USE_WINTHREADS WaitForSingleObject(*((HANDLE*)id), INFINITE); #endif } void Event::signal() { Log odinlog("Event","signal"); #ifdef USE_PTHREADS MutexLock lock(mutex); active=true; int errcode=pthread_cond_broadcast((pthread_cond_t*)id); if(errcode) ODINLOG(odinlog,errorLog) << pthread_err(errcode) << STD_endl; #endif #ifdef USE_WINTHREADS SetEvent(*((HANDLE*)id)); #endif } void Event::reset() { Log odinlog("Event","reset"); #ifdef USE_PTHREADS MutexLock lock(mutex); active=false; #endif #ifdef USE_WINTHREADS ResetEvent(*((HANDLE*)id)); #endif } //////////////////////////////////////////////////////////////////// // pthread_t cannot be converted to an integer on all platforms (e.g. Darwin) so we need a separate map #ifdef USE_PTHREADS static STD_map pthreadindexmap; static Mutex pthreadindexmutex; struct ThreadIndex : public UniqueIndex { // functions for UniqueIndex static const char* get_typename() {return "ThreadIndex";} static unsigned int get_max_instances() {return 0;} }; #endif ////////////////////////// #ifdef USE_WINTHREADS DWORD WINAPI start_thread(LPVOID t) { #else void* start_thread(void* t) { #endif ((Thread*)t)->run(); return 0; } ////////////////////////// Thread::Thread() : id(0) { #ifdef USE_PTHREADS index=new ThreadIndex; #endif } Thread::~Thread() { clear_id(); #ifdef USE_PTHREADS delete index; #endif } void Thread::clear_id() { if(id) { #ifdef USE_PTHREADS delete ((pthread_t*)id); #endif #ifdef USE_WINTHREADS delete ((HANDLE*)id); #endif } id=0; } bool Thread::start(unsigned int stack_size) { Log odinlog("Thread","start"); wait(); // will clear id #ifdef USE_PTHREADS id=(void*)new pthread_t; pthread_attr_t pt_attr; int errcode=pthread_attr_init (&pt_attr); if(errcode) { ODINLOG(odinlog,errorLog) << "pthread_attr_init: " << pthread_err(errcode) << STD_endl; return false; } if(stack_size) { errcode=pthread_attr_setstacksize (&pt_attr, stack_size); if(errcode) { ODINLOG(odinlog,errorLog) << "pthread_attr_setstacksize: " << pthread_err(errcode) << STD_endl; return false; } } errcode=pthread_create((pthread_t*)id, &pt_attr, &start_thread, this); if(errcode) { ODINLOG(odinlog,errorLog) << "pthread_create: " << pthread_err(errcode) << STD_endl; #ifdef HAVE_SYSCONF ODINLOG(odinlog,errorLog) << "PTHREAD_THREADS_MAX=" << sysconf(_SC_THREAD_THREADS_MAX) << STD_endl; #endif return false; } pthreadindexmutex.lock(); // lock because other threads might already be running pthreadindexmap[index->get_index()]=*((pthread_t*)id); pthreadindexmutex.unlock(); #else #ifdef USE_WINTHREADS HANDLE* handle=new HANDLE; (*handle)=CreateThread(NULL,stack_size,&start_thread,this,0,NULL); id=(void*)handle; if(*handle==NULL) { ODINLOG(odinlog,errorLog) << "CreateThread: " << lasterr() << STD_endl; return false; } #else this->run(); // no threads #endif #endif return true; } bool Thread::wait() { Log odinlog("Thread","wait"); #ifdef USE_PTHREADS int errcode=0; if(id) { void* returnval; errcode=pthread_join(*((pthread_t*)id), &returnval); ODINLOG(odinlog,normalDebug) << "errcode=" << errcode << STD_endl; } clear_id(); if(errcode) { ODINLOG(odinlog,errorLog) << pthread_err(errcode) << STD_endl; return false; } #endif #ifdef USE_WINTHREADS if(id) { DWORD errcode=WaitForSingleObject(*((HANDLE*)id),INFINITE); clear_id(); if(errcode==WAIT_FAILED) { ODINLOG(odinlog,errorLog) << lasterr() << STD_endl; return false; } } #endif return true; } int Thread::self() { Log odinlog("Thread","self"); int result=-1; // the master thread gets this id #ifdef USE_PTHREADS pthread_t ptself=pthread_self(); pthreadindexmutex.lock(); for(STD_map::const_iterator it=pthreadindexmap.begin(); it!=pthreadindexmap.end(); ++it) { if(pthread_equal(ptself, it->second)) result=it->first; } pthreadindexmutex.unlock(); #endif #ifdef USE_WINTHREADS result=GetCurrentThreadId(); #endif return result; } //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST #include "tjvector.h" #define VECSIZE 256 #define NITER 10000 #define NTHREADS 16 class TestThread : public Thread { public: void init(int* v, Mutex* m) { vec=v; mutex=m; } protected: void run() { for(int i=0; isignal(); } private: double* res; Event* event; int delay; }; ////////////////////////////////////////////// class TestEventThread2 : public Thread { public: void init(double* r, Event* e, int d) { res=r; event=e; delay=d; } protected: void run() { sleep_ms(delay); (*res)=123.4; event->wait(); } private: double* res; Event* event; int delay; }; ////////////////////////////////////////////// class ThreadedLoopTest : public ThreadedLoop { private: bool kernel(const STD_string& in, STD_string& out, int&, unsigned int begin, unsigned int end) { out=""; for(unsigned int i=begin; i odinlog(this,"check"); /////////////////////////////////// // Testing Thread / MutexLock TestThread thread[NTHREADS]; Mutex mutex; int vec[VECSIZE]; for(int ivec=0; ivec /** * @addtogroup tjutils * @{ */ /** * This is the base class for all classes which can have a (unique) label */ class Labeled { public: /** * Constructor with initialization of label */ Labeled(const STD_string& label="unnamed") : objlabel(label) {} /** * Assigns a label to the object */ Labeled& set_label(const STD_string& label) {objlabel=label; return *this;} /** * Returns the label of the object */ const STD_string& get_label() const {return objlabel;} /** * Assignment operator */ Labeled& operator = (const Labeled& l) { objlabel=l.objlabel; return *this; } private: STD_string objlabel; }; /** @} */ #endif odin-1.8.5/tjutils/tjtools.cpp0000644000175000017500000004707611322062342013310 00000000000000#include "tjtools.h" #include "tjutils.h" #include "tjcstd.h" #include "tjlog.h" #include "tjlog_code.h" #include "tjstring.h" #include "tjtest.h" #include "tjvector.h" // for testing browse_dir #include #ifdef HAVE_UNISTD_H #include #include #endif #ifdef HAVE_SYS_STAT_H #include #endif #ifdef HAVE_SYS_TYPES_H #include #endif #ifdef HAVE_DIRENT_H #include #endif #ifdef USING_WIN32 #include #include #include #endif #ifdef HAVE_TIME_H #include #endif #ifdef HAVE_SYS_TIME_H #include #endif // for mmap #ifdef HAVE_SYS_MMAN_H #include #include #endif class TjTools { public: static const char* get_compName() {return "tjtools";} }; LOGGROUNDWORK(TjTools) //////////////////////////////////////////////////////////////////// double norm (double x, double y) { double result; result = sqrt (x * x + y * y); return (result); } ///////////////////////////////////////////////////////////// double norm3 (double x, double y, double z) { double result; result = sqrt (x * x + y * y + z * z); return (result); } ///////////////////////////////////////////////////////////// double maxof3(double f1,double f2,double f3) { double result =0.0; if (f1>=f2) result=f1; else result=f2; if (result>=f3) return(result); else return(f3); } ///////////////////////////////////////////////////////////// double secureDivision(double numerator, double denominator) { if(denominator==0.0) return 0.0; return numerator/denominator; } ///////////////////////////////////////////////////////////// const char* secure_getenv(const char* variable_name) { Log odinlog("","secure_getenv"); const char* result=""; const char* env=getenv(variable_name); if(env) result=env; ODINLOG(odinlog,normalDebug) << "result(" << variable_name << ")=" << result << STD_endl; return result; } ///////////////////////////////////////////////////////////// bool little_endian_byte_order() { int one_bit_set_in_least_significant=1; unsigned char* first_byte=(unsigned char*)&one_bit_set_in_least_significant; return (*first_byte)!=0; } ///////////////////////////////////////////////////////////// unsigned int numof_cores() { unsigned int result=1; #ifdef USING_WIN32 SYSTEM_INFO sysinfo; GetSystemInfo( &sysinfo ); result = sysinfo.dwNumberOfProcessors; #else #if defined(HAVE_UNISTD_H) && defined(HAVE_SYSCONF) #ifdef _SC_NPROCESSORS_ONLN result=sysconf(_SC_NPROCESSORS_ONLN); #endif #endif #endif return result; } ///////////////////////////////////////////////////////////// #ifndef NO_FILEHANDLING const char* modestring(fopenMode mode) { if(mode==readMode) return "rb"; if(mode==overwriteMode) return "w+b"; if(mode==appendMode) return "a+b"; return ""; } LONGEST_INT filesize(const char *filename) { Log odinlog("","filesize"); LONGEST_INT result=-1; #ifdef STAT struct STAT st; if(!STAT(filename, &st)) result=st.st_size; else if(errno!=ENOENT) ODINLOG(odinlog,errorLog) << "stat(" << filename << "): " << lasterr() << STD_endl; #else FILE *file_ptr; file_ptr = FOPEN(filename, modestring(readMode)); if(file_ptr == NULL) { if(errno!=ENOENT) ODINLOG(odinlog,errorLog) << "fopen(" << filename << "): " << lasterr() << STD_endl; return result; } if(fgetc(file_ptr) != EOF) { if(fseek(file_ptr, 0, SEEK_END)) { if(errno!=ENOENT) ODINLOG(odinlog,errorLog) << "fseek(" << filename << "): " << lasterr() << STD_endl; } else result=FTELL(file_ptr); } fclose(file_ptr); #endif return result; } ///////////////////////////////////////////////////////////// char getpwd_buff[ODIN_MAXCHAR]; const char* getpwd() { Log odinlog("","getpwd"); const char* result=""; #ifdef USING_WIN32 result=_getcwd(getpwd_buff,ODIN_MAXCHAR); #else #ifdef HAVE_UNISTD_H result=getcwd(getpwd_buff,ODIN_MAXCHAR); #endif #endif if(result==NULL) ODINLOG(odinlog,errorLog) << lasterr() << STD_endl; return result; } ///////////////////////////////////////////////////////////// int chpwd(const char *dirname) { Log odinlog("","chpwd"); int result=0; #ifdef USING_WIN32 result=_chdir(dirname); // will consider drive letter #else #ifdef HAVE_UNISTD_H result=chdir(dirname); #endif #endif if(result<0) ODINLOG(odinlog,errorLog) << "(" << dirname << ")" << lasterr() << STD_endl; return result; } ///////////////////////////////////////////////////////////// int createdir(const char *dirname) { Log odinlog("","createdir"); int result=0; if(checkdir(dirname)) return result; // already there #ifdef USING_WIN32 result=_mkdir(dirname); ODINLOG(odinlog,normalDebug) << "created USING_WIN32 dir" << dirname << STD_endl; #else #if defined(HAVE_SYS_STAT_H) && defined(HAVE_SYS_TYPES_H) && defined(HAVE_UNISTD_H) result=mkdir(dirname, S_IRWXU | S_IRGRP | S_IXGRP | S_IROTH | S_IXOTH); // permission: 0755 #endif #endif if(result<0) ODINLOG(odinlog,errorLog) << "(" << dirname << ") " << lasterr() << STD_endl; return result; } ///////////////////////////////////////////////////////////// bool checkdir(const char *dirname) { Log odinlog("","checkdir"); #ifdef USING_WIN32 _finddata_t fileinfo; STD_string dirmatch=STD_string(dirname)+"\\*"; long findhandle=_findfirst(dirmatch.c_str(), &fileinfo ); if(findhandle!=-1) { _findclose(findhandle); return true; } else { ODINLOG(odinlog,normalDebug) << "(" << dirname << ") " << lasterr() << STD_endl; } #else #ifdef HAVE_DIRENT_H DIR* dp = opendir(dirname); if (dp != NULL) { closedir(dp); return true; } #endif #endif return false; } ///////////////////////////////////////////////////////////// int movefile(const char *src, const char* dst) { int result=0; #ifdef USING_WIN32 result=rename(src,dst); #else result=system((STD_string("mv ")+src+" "+dst).c_str()); // rename() does not work across filesystems #endif return result; } ///////////////////////////////////////////////////////////// int copyfile(const char *src, const char* dst) { Log odinlog("","copyfile"); int result=0; #ifdef USING_WIN32 if(!CopyFileA(src,dst,FALSE)) result=-1; #else result=system((STD_string("cp ")+src+" "+dst).c_str()); #endif if(result<0) ODINLOG(odinlog,errorLog) << "(" << src << "," << dst << ") " << lasterr() << STD_endl; return result; } ///////////////////////////////////////////////////////////// int rmfile(const char *fname) { Log odinlog("","rmfile"); int result=0; if(filesize(fname)<0) return 0; #ifdef USING_WIN32 if(checkdir(fname)) { result=_rmdir(fname); if(result<0) ODINLOG(odinlog,errorLog) << "_rmdir(" << fname << ") " << lasterr() << STD_endl; } else { result=remove(fname); if(result<0) ODINLOG(odinlog,errorLog) << "remove(" << fname << ") " << lasterr() << STD_endl; } #else result=remove(fname); // Works for both, files and directories if(result<0) ODINLOG(odinlog,errorLog) << "(" << fname << ") " << lasterr() << STD_endl; #endif return result; } ///////////////////////////////////////////////////////////// int chperm(const char *fname, int perm) { #ifdef USING_WIN32 return _chmod(fname,perm); #else #if defined(HAVE_SYS_STAT_H) && defined(HAVE_SYS_TYPES_H) && defined(HAVE_UNISTD_H) return chmod(fname,perm); #endif #endif return 0; } ///////////////////////////////////////////////////////////// #define BLOCKSIZE 4096 // constant experession needed for VC++ 6 int create_empty_file(const STD_string& filename, LONGEST_INT nbytes, fopenMode mode) { Log odinlog("","create_empty_file"); LONGEST_INT nblocks=nbytes/BLOCKSIZE; LONGEST_INT rest=nbytes%BLOCKSIZE; char buff[BLOCKSIZE]; LONGEST_INT i; for(i=0; i odinlog("","offset_pagesize"); result_offset=offset; result_rest=0; #ifdef HAVE_UNISTD_H int psize=getpagesize(); if(psize) { result_offset=(offset/psize)*psize; result_rest=offset%psize; } #endif ODINLOG(odinlog,normalDebug) << "offset/result_offset/result_rest=" << offset << "/" << result_offset << "/" << result_rest << STD_endl; } #endif /////////////////////////////////////////////// void* filemap(const STD_string& filename, LONGEST_INT nbytes, LONGEST_INT offset, bool readonly, int& fd) { Log odinlog("","filemap"); void* result=0; fd=-1; LONGEST_INT fsize=filesize(filename.c_str()); LONGEST_INT total=nbytes+offset; ODINLOG(odinlog,normalDebug) << "nbytes/fsize/total/readonly = " << nbytes << "/" << fsize << "/" << total << "/" << readonly << STD_endl; // check size in readonly mode if(readonly) { if(fsize" << filename << "<" << STD_endl; return result; } } } #ifdef HAVE_SYS_MMAN_H // The Unix (mmap) way of file mapping ODINLOG(odinlog,normalDebug) << "Using mmap" << STD_endl; LONGEST_INT offset_psize; int rest_psize; offset_pagesize(offset, offset_psize, rest_psize); int flags=O_RDWR; if(readonly) flags=O_RDONLY; fd = OPEN( filename.c_str(), flags ); ODINLOG(odinlog,normalDebug) << "fd = " << fd << STD_endl; if (fd < 0) { ODINLOG(odinlog,errorLog) << "unable to open file >" << filename << "< - " << lasterr() << STD_endl; return result; } if(filesize(filename.c_str())" << filename << "< to small for filemap" << STD_endl; close(fd); fd=-1; return result; } int prot=PROT_READ | PROT_WRITE; if(readonly) prot=PROT_READ; char* byte_ptr=(char*)MMAP( 0, nbytes+rest_psize, prot, MAP_SHARED, fd, offset_psize ); if ( byte_ptr==MAP_FAILED ) { ODINLOG(odinlog,errorLog) << "Cannot filemap file >" << filename << "< - " << lasterr() << STD_endl; close(fd); fd=-1; return 0; } result=byte_ptr+rest_psize; #else // Emulate mmap by allocating memory and reading it from file ODINLOG(odinlog,normalDebug) << "Using fread" << STD_endl; const char* modeString=modestring(overwriteMode); if(readonly) modeString=modestring(readMode); fd=(int)FOPEN(filename.c_str(), modeString); if(!fd) { ODINLOG(odinlog,errorLog) << "fopen: " << lasterr() << STD_endl; return result; } if(offset>0) { if(FSEEK((FILE*)fd, offset, SEEK_SET)) { ODINLOG(odinlog,errorLog) << "fseek: " << lasterr() << STD_endl; fclose((FILE*)fd); return result; } } result=(void*)new char[nbytes]; fread( result, nbytes, sizeof(char), (FILE*)fd); if(readonly) { // We close and reset the file pointer here so that fileunmap() knows that the file is readonly fclose((FILE*)fd); fd=0; // Zero indicates readonly mode } #endif return result; } /////////////////////////////////////////////// void fileunmap(int fd, void* start, LONGEST_INT nbytes, LONGEST_INT offset) { Log odinlog("","fileunmap"); ODINLOG(odinlog,normalDebug) << "fd/start/length=" << fd << "/" << start << "/" << nbytes << STD_endl; #ifdef HAVE_SYS_MMAN_H // The Unix (mmap) way of file mapping LONGEST_INT offset_psize; int rest_psize; offset_pagesize(offset, offset_psize, rest_psize); void* mstart=(char*)start-rest_psize; LONGEST_INT mlength=nbytes+rest_psize; if ( msync(mstart, mlength, MS_SYNC) ) ODINLOG(odinlog,errorLog) << "msync: " << lasterr() << STD_endl; if ( munmap(mstart, mlength) ) ODINLOG(odinlog,errorLog) << "munmap: " << lasterr() << STD_endl; close(fd); #else // Emulate munmap by writing memory to file, de-allocating memory and closing the file if(fd>0) { // File is mapped with read/write access if(offset>0) { if(FSEEK((FILE*)fd, offset, SEEK_SET)) { ODINLOG(odinlog,errorLog) << "fseek: " << lasterr() << STD_endl; fclose((FILE*)fd); delete[] (char*)start; return; } } if(!fwrite(start, sizeof(char), nbytes, (FILE*)fd)) { ODINLOG(odinlog,errorLog) << "fwrite: " << lasterr() << STD_endl; } fclose((FILE*)fd); } delete[] (char*)start; #endif } /////////////////////////////////////////////// STD_string tempfile() { STD_string result; const char* ptr=tmpnam(NULL); if(ptr) result=ptr; #ifdef USING_WIN32 result=STD_string(secure_getenv("TEMP"))+SEPARATOR_STR+result; #endif return result; } #endif // #ifndef NO_FILEHANDLING ///////////////////////////////////////////////////////////// const char* lasterr() { #ifdef USING_WIN32 LPVOID msgbuf; FormatMessage( FORMAT_MESSAGE_ALLOCATE_BUFFER | FORMAT_MESSAGE_FROM_SYSTEM, NULL, GetLastError(), MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT), (LPTSTR) &msgbuf, 0, NULL); static STD_string result=(const char *)msgbuf; LocalFree(msgbuf); return result.c_str(); #else #ifdef HAVE_UNISTD_H return strerror(errno); #endif #endif return ""; } ///////////////////////////////////////////////////////////// void sleep_ms(unsigned int ms) { if(!ms) return; #ifdef USING_WIN32 Sleep(ms); #else #if defined(HAVE_TIME_H) && defined(HAVE_NANOSLEEP) timespec ts; ts.tv_sec=ms/1000; ts.tv_nsec=(ms%1000)*1000000; nanosleep(&ts,NULL); #endif #endif } ///////////////////////////////////////////////////////////// double current_time_s() { Log odinlog("","current_time_s"); double result=-1; #ifdef USING_WIN32 FILETIME ft; GetSystemTimeAsFileTime(&ft); SYSTEMTIME currenttime; if(!FileTimeToSystemTime(&ft,¤ttime)) { ODINLOG(odinlog,errorLog) << lasterr() << STD_endl; return result; } result=3600.0*double(currenttime.wHour) + 60.0*double(currenttime.wMinute) + double(currenttime.wSecond) + 1e-3*double(currenttime.wMilliseconds); #else #if defined(HAVE_SYS_TIME_H) && defined(HAVE_TIME_H) && defined(HAVE_GETTIMEOFDAY) timeval currenttime; gettimeofday(¤ttime,0); result=double(currenttime.tv_sec) + 1e-6*double(currenttime.tv_usec); #endif #endif return result; } ////////////////////////////////////////////////////////// #ifndef NO_CMDLINE int getCommandlineOption(int argc, char *argv[], const char *option, char *returnvalue, int maxchar,bool modify) { int i,b=0; for (i=1;i1) { /* if( *argv[argc-2]!='-') { */ strncpy(returnvalue,argv[argc-1],maxchar-1);returnvalue[maxchar-1]='\0'; if(modify) argv[argc-1][0]='\0'; return(1); /* } */ } return(0); } int hasHelpOption(int argc, char *argv[]) { if(isCommandlineOption(argc,argv,"--version")) { STD_cout << VERSION << STD_endl; exit(0); // return immediately for help2man } return isCommandlineOption(argc,argv,"-h")+ isCommandlineOption(argc,argv,"--help")+ isCommandlineOption(argc,argv,"-help"); } const char* helpUsage() { return "-h, --help, -help, --version : Print help text or version information"; } #endif ////////////////////////////////////////////////////////////////////////////////////////////// // From GSL, i.e. from gsl_sf_bessel_j0() double sinc(double x) { if(x==0.0) return 1.0; if(fabs(x) < 0.5) { const double y = x*x; const double c1 = -1.0/6.0; const double c2 = 1.0/120.0; const double c3 = -1.0/5040.0; const double c4 = 1.0/362880.0; const double c5 = -1.0/39916800.0; const double c6 = 1.0/6227020800.0; return 1.0 + y*(c1 + y*(c2 + y*(c3 + y*(c4 + y*(c5 + y*c6))))); } else { return sin(x)/x; } } ////////////////////////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class TjToolsTest : public UnitTest { public: TjToolsTest() : UnitTest(TjTools::get_compName()) {} private: bool check() const { Log odinlog(this,"check"); #ifndef NO_FILEHANDLING STD_string dir(tempfile()); if(createdir(dir.c_str())) { ODINLOG(odinlog,errorLog) << "createdir failed" << STD_endl; return false; } STD_string testcont="content"; STD_string srcfile=dir+SEPARATOR_STR+"src"; if(write(testcont, srcfile)) { ODINLOG(odinlog,errorLog) << "write failed" << STD_endl; return false; } int ntestfiles=5; for(int i=0; i #include /** * @addtogroup tjutils * @{ */ /** * Returns the complex number 'z' as a formatted string */ STD_string ctos(const STD_complex& z); /** * Parses an returns string 's' as complex number */ STD_complex stoc(const STD_string& s); //////////////////////////////////////////////////////////// // functions for using complex numbers with Blitz++, // even if the STD_complex class is not std::complex inline STD_complex float2real(float a) {return STD_complex(a,0.0f);} inline STD_complex float2imag(float b) {return STD_complex(0.0f,b);} inline float creal(STD_complex c) {return c.real();} inline float cimag(STD_complex c) {return c.imag();} inline float cabs(STD_complex c) {return float(sqrt(c.real()*c.real()+c.imag()*c.imag()));} //{return STD_abs(c);} // std::abs produces inf with GCC4 on amd64 inline float phase(STD_complex c) {return STD_arg(c);} inline STD_complex logc(STD_complex c) {return STD_log(c);} inline STD_complex expc(STD_complex c) {return STD_exp(c);} inline STD_complex conjc(STD_complex c) {return STD_conj(c);} /** * Comparison operator for the norm of the complex numbers c1 and c2 */ inline bool operator < (const STD_complex& c1, const STD_complex& c2) {return STD_abs(c1) (const STD_complex& c1, const STD_complex& c2) {return STD_abs(c1)>STD_abs(c2);} /** @} */ #endif odin-1.8.5/tjutils/tjvector.cpp0000644000175000017500000005170311712547771013463 00000000000000#include "tjvector.h" #include "tjtypes.h" #include "tjtest.h" #include "tjlog_code.h" // required for interpolation #ifdef HAVE_LIBGSL #include #include #else #include "replacements/gsl_replacement.cpp" #endif #ifdef HAVE_DIRENT_H #include #endif #ifdef USING_WIN32 #include #endif const char* VectorComp::get_compName() {return "vector";} LOGGROUNDWORK(VectorComp) ///////////////////////////////////////////////////////////////////////////////////////////////////////////// fvector real(const cvector& cv) { unsigned int n=cv.size(); fvector result(n); for (unsigned int i=0; i odinlog("","tokens"); svector result; const int n=tokenstring.length(); STD_string sepstr(" "); if(custom_separator) sepstr[0]=custom_separator; // fill the list with the tokens int beginpos=0; int endpos; STD_string onetoken; int beginquote=0; int endquote=0; while(beginpos>=0 && beginpos =0 && endpos>=0) { STD_string substring(tokenstring.substr(beginpos,endpos-beginpos)); beginquote+=noccur(substring,STD_string(1,escape_begin)); endquote+=noccur(substring,STD_string(1,escape_end)); onetoken+=substring; bool token_complete=true; if( (escape_begin==escape_end) && (beginquote%2) ) token_complete=false; if( (escape_begin!=escape_end) && (beginquote>endquote) ) token_complete=false; if(token_complete) { result.push_back(onetoken); onetoken=""; beginquote=endquote=0; } else { onetoken+=sepstr; } } beginpos=endpos; } return result; } //////////////////////////////////////// STD_string tokenstring(const svector& tokens,unsigned int linewidth) { Log odinlog("","tokenstring"); unsigned int stringsize=0; unsigned int n=tokens.size(); ODINLOG(odinlog,normalDebug) << "creating string from " << n << " tokens" << STD_endl; ODINLOG(odinlog,normalDebug) << "linewidth = " << linewidth << STD_endl; unsigned int i; for(i=0;i result; bool success=true; #ifdef USING_WIN32 // browse directory the Windows way _finddata_t fileinfo; STD_string files_match=dirname+"\\*"; long findhandle=_findfirst(files_match.c_str(), &fileinfo ); if(findhandle==-1) { ODINLOG(odinlog,normalDebug) << "(" << dirname << ") " << lasterr() << STD_endl; success=false; } while(findhandle!=-1) { STD_string curr_file(fileinfo.name); bool store=true; if(only_dirs) { if(fileinfo.attrib!=_A_SUBDIR) store=false; } if(discard_dotfiles) { if(curr_file[(unsigned int)0]=='.') store=false; } if(store) result.push_back(curr_file); if(_findnext(findhandle, &fileinfo )==-1) { _findclose(findhandle); findhandle=-1; } } #else #ifdef HAVE_DIRENT_H // browse directory the UNIX way struct dirent *ep; DIR* dp = opendir(dirname.c_str()); if (dp != NULL) { while ( (ep = readdir (dp)) ) { STD_string curr_file(ep->d_name); bool store=true; if(only_dirs && ep->d_type!=DT_DIR) store=false; if(discard_dotfiles) { if(curr_file[(unsigned int)0]=='.') store=false; } if(store) result.push_back(curr_file); } closedir (dp); } else success=false; #endif #endif if(!success) { ODINLOG(odinlog,errorLog) << "Couldn't open directory >" << dirname << "< - " << lasterr() << STD_endl; } result.sort(); return list2vector(result); } ///////////////////////////////////////////////////////////////////////////////////////////////////////////// STD_string svector::printbody() const { STD_string result; for(unsigned int i=0; i odinlog("tjvector","interpolate1D(complex)"); unsigned int i; STD_complex* newdata=new STD_complex[newsize]; for(i=0; i simple adding blocks unsigned int blocksize=oldsize/newsize; ODINLOG(odinlog,normalDebug) << "blocksize=" << blocksize << STD_endl; for(unsigned int inew=0; inew=3) itype=gsl_interp_cspline; // for few points if(oldsize>=5) itype=gsl_interp_akima; // this seems to be the best algorithm for non-smooth data gsl_spline *spline_re = gsl_spline_alloc (itype, oldsize); gsl_spline *spline_im = gsl_spline_alloc (itype, oldsize); gsl_spline_init (spline_re, x, data_re, oldsize); gsl_spline_init (spline_im, x, data_im, oldsize); for(i=0; imaxold) newx=maxold; float re=gsl_spline_eval (spline_re, newx, acc_re); float im=gsl_spline_eval (spline_im, newx, acc_im); newdata[i]=STD_complex(re,im); } gsl_spline_free (spline_re); gsl_spline_free (spline_im); gsl_interp_accel_free(acc_re); gsl_interp_accel_free(acc_im); delete[] x; delete[] data_re; delete[] data_im; // Deal with edge effects, i.e. coordinates outside the old range at the edges if(subpixel_shift==0.0) { int nedge=int(0.5*secureDivision(newsize,oldsize)+0.5); if(nedge>0 && nedge=0 && isrc=0 && idst=0 && isrc=0 && idst odinlog("tjvector","interpolate1D(float)"); STD_complex* oldcomplexdata=new STD_complex[oldsize]; unsigned int i; for(i=0;i odinlog("tjvector","interpolate1D(double)"); STD_complex* oldcomplexdata=new STD_complex[oldsize]; unsigned int i; for(i=0;i odinlog("tjvector","interpolate1D(int)"); STD_complex* oldcomplexdata=new STD_complex[oldsize]; unsigned int i; for(i=0;i tjvector::tjvector(unsigned int n) : STD_vector(n, T(0)) { Log odinlog("tjvector","tjvector(unsigned int)"); ODINLOG(odinlog,normalDebug) << "n=" << n << STD_endl; c_array_cache=0; } template tjvector::tjvector(const T *array, unsigned int n) : STD_vector() { STD_vector::resize(n); set_c_array((unsigned char*)array,n); c_array_cache=0; } template tjvector::tjvector(const STD_vector& v) : STD_vector(v) { c_array_cache=0; } template tjvector::tjvector(const tjvector& tv) : STD_vector(tv) { c_array_cache=0; } template tjvector::~tjvector() { Log odinlog("tjvector","~tjvector"); if(c_array_cache) { ODINLOG(odinlog,normalDebug) << "deleting c_array_cache=" << (void*)c_array_cache << STD_endl; delete[] c_array_cache; } } template tjvector& tjvector::resize(unsigned int newsize) { Log odinlog("tjvector","resize"); unsigned int oldsize=STD_vector::size(); if(newsize==oldsize) return *this; STD_vector old(*this); STD_vector::resize(newsize); for(unsigned int i=0; i unsigned int tjvector::length () const {return STD_vector::size();} template unsigned int tjvector::fill_linear(const T& min,const T& max) { if ((length()-1)==0) tjvector::operator = (min); else { T incr=(max-min)/(T)(length()-1); for(unsigned int i=0;i T tjvector::sum() const { Log odinlog("","sum"); T result=T(0); ODINLOG(odinlog,normalDebug) << "initial value=" << result << STD_endl; for(unsigned int i=0;i::begin(),STD_vector::end(),value); #endif return *this; } template tjvector& tjvector::operator = (const STD_vector& vec) { STD_vector::operator = (vec); return *this; } template tjvector& tjvector::operator = (const tjvector& tv) { Log odinlog("tjvector","operator = (const tjvector&)"); STD_vector::operator = (tv); return *this; } template STD_string tjvector::printbody() const { unsigned int n=length(); svector tokens; tokens.resize(n); for(unsigned int i=0;i T tjvector::maxvalue() const { if(!length()) return T(0); T result=(*this)[0]; for(unsigned int i=1;iresult) result=(*this)[i]; return result; } template T tjvector::minvalue() const { if(!length()) return T(0); T result=(*this)[0]; for(unsigned int i=1;i const T* tjvector::c_array() const { Log odinlog("tjvector","c_array"); if(c_array_cache) { ODINLOG(odinlog,normalDebug) << "deleting c_array_cache=" << (void*)c_array_cache << STD_endl; delete[] c_array_cache; c_array_cache=0; } c_array_cache=new T[length()]; ODINLOG(odinlog,normalDebug) << "allocated c_array_cache=" << (void*)c_array_cache << STD_endl; for(unsigned int i=0;i tjvector& tjvector::set_c_array(const unsigned char* array, unsigned int n) { Log odinlog("tjvector","set_c_array"); if(length()==n) { for(unsigned int i=0;i T tjvector::maxabs() const{ return T(STD_max(cabs(minvalue()),cabs(maxvalue()))); } template T tjvector::normalize() { Log odinlog("tjvector","normalize"); T maxnorn=maxabs(); ODINLOG(odinlog,normalDebug) << "maxnorn=" << maxnorn << STD_endl; if(!(maxnorn==T(0))) (*this)/=maxnorn; return maxnorn; } template tjvector& tjvector::interpolate(unsigned int newsize, float subpixel_shift) { Log odinlog("tjvector","interpolate"); unsigned int oldsize=length(); ODINLOG(odinlog,normalDebug) << "oldsize/newsize/subpixel_shift=" << oldsize << "/" << newsize << "/" << subpixel_shift << STD_endl; T* olddata=new T[oldsize]; unsigned int i; for(i=0;i int tjvector::load(const STD_string& fname) { Log odinlog("tjvector","load"); #ifndef NO_FILEHANDLING if(fname=="") return 0; LONGEST_INT fsize=filesize(fname.c_str()); LONGEST_INT nelements=fsize/sizeof(T); FILE* file_ptr=FOPEN(fname.c_str(),modestring(readMode)); if(file_ptr==NULL) { ODINLOG(odinlog,errorLog) << "unable to open file >" << fname << "<, " << lasterr() << STD_endl; return(-1); } if((LONGEST_INT)STD_vector::size() != nelements) resize(nelements); T* buff=new T[nelements]; if(fread(buff,sizeof(T),nelements,file_ptr)!=nelements) { ODINLOG(odinlog,errorLog) << "unable to read data from file >" << fname << "<, " << lasterr() << STD_endl; } else { (*this)=tjvector(buff,nelements); } if(file_ptr!=NULL) fclose(file_ptr); delete[] buff; #endif return 0; } template int tjvector::write(const STD_string& fname, fopenMode mode, LONGEST_INT nelements) const { Log odinlog("tjvector","write"); #ifndef NO_FILEHANDLING if(fname=="") return 0; if(nelements>(LONGEST_INT)(length()) || nelements<0) { nelements=length(); } FILE* file_ptr=FOPEN(fname.c_str(),modestring(mode)); if(file_ptr==NULL) { ODINLOG(odinlog,errorLog) << "unable to create/open file >" << fname << "<, " << lasterr() << STD_endl; return(-1); } if(fwrite(c_array(),sizeof(T),nelements,file_ptr)!=nelements) { ODINLOG(odinlog,errorLog) << "unable to write data to file >" << fname << "<, " << lasterr() << STD_endl; } if(file_ptr!=NULL) fclose(file_ptr); #endif return 0; } ///////////////////////////////////////////////////////////////////////////////////////////////////////////// template class tjvector; template class tjvector; template class tjvector; template class STD_vector; template class tjvector; #ifndef NO_UNIT_TEST class VectorTest : public UnitTest { public: VectorTest() : UnitTest(VectorComp::get_compName()) {} private: bool check() const { Log odinlog(this,"check"); // Test sum() ivector iv1(2); iv1[0]=1; iv1[1]=3; ivector iv2(2); iv2[0]=2; iv2[1]=4; int calculated=(iv1+iv2).sum(); int expected=10; if(calculated!=expected) { ODINLOG(odinlog,errorLog) << "sum(): calculated/expected=" << calculated << "/" << expected << STD_endl; return false; } // Test interpolation by converting high-res sine to and from low-res version int srcsize=1000; fvector srcvec(srcsize); for(int i=0; i0.005*srcsize) { // No more than 0.5% on average ODINLOG(odinlog,errorLog) << "interpolate(): absdiff=" << absdiff << STD_endl; return false; } // Test tokenizer svector gottoks=tokens("aa_bbb__eee", '_', '<', '>'); svector exptoks; exptoks.resize(4); exptoks[0]="aa"; exptoks[1]="bbb"; exptoks[2]=""; exptoks[3]="eee"; if(gottoks!=exptoks) { ODINLOG(odinlog,errorLog) << "tokens: got/expected=" << gottoks.printbody() << "/" << exptoks.printbody() << STD_endl; return false; } return true; } }; void alloc_VectorTest() {new VectorTest();} // create test instance #endif odin-1.8.5/tjutils/tjtypes.cpp0000644000175000017500000000146311713467630013317 00000000000000#include "tjtypes.h" unsigned int TypeTraits::typesize(const STD_string& typelabel) { if(typelabel==TypeTraits::type2label((u8bit)0)) return 1; if(typelabel==TypeTraits::type2label((s8bit)0)) return 1; if(typelabel==TypeTraits::type2label((u16bit)0)) return 2; if(typelabel==TypeTraits::type2label((s16bit)0)) return 2; if(typelabel==TypeTraits::type2label((u32bit)0)) return 4; if(typelabel==TypeTraits::type2label((s32bit)0)) return 4; if(typelabel==TypeTraits::type2label((float)0)) return sizeof(float); if(typelabel==TypeTraits::type2label((double)0)) return sizeof(double); if(typelabel==TypeTraits::type2label((STD_complex)0)) return sizeof(STD_complex); // if(typelabel==TypeTraits::type2label(STD_string(""))) return sizeof(STD_string); // string does not have fixed size return 0; } odin-1.8.5/tjutils/tjprofiler.h0000644000175000017500000000513711322062342013427 00000000000000/*************************************************************************** tjprofiler.h - description ------------------- begin : Mon Aug 5 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJPROFILER_H #define TJPROFILER_H #include #include #include #include /** * @addtogroup tjutils * @{ */ /** * A class to profile your program, i.e. to see how much time is spent * in each function. Create a local object of this class in each function * you want to analyze with the functions name as the constructors argument. * The function name serves as a key to measure the execution time in * each function if this function is called successively. * the result of can be obtained by the 'dump_final_result()' function. * In addition, a function is provided to retrieve the current memory usage. */ class Profiler : public StaticHandler { public: Profiler(const STD_string& func_name); ~Profiler(); /** * Resets the time counters. */ static void reset(); /** * Dumps the results to the current log and resets the time counters. */ static void dump_final_result(); /** * Returns the current memory usage as a readable string. */ static STD_string get_memory_usage(); // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); // for debugging List static const char* get_compName(); private: STD_string func_label; double starttime; struct elapsed { elapsed() : time_spent(0.0) {} double time_spent; }; struct FuncMap : public STD_map, public Labeled {}; static SingletonHandler func_map; }; /** @} */ #endif odin-1.8.5/tjutils/tjembed.h0000644000175000017500000000473511322062342012664 00000000000000/*************************************************************************** tjembed.h - description ------------------- begin : Tue Mar 11 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJEMBED_H #define TJEMBED_H #include /** * @addtogroup tjutils * @{ */ template class Embed { public: Embed() {} ~Embed() { clear_instances(); } void clear_instances() { for(typename STD_list::iterator it=instances.begin();it!=instances.end();++it) delete (*it); instances.clear(); } T& set_embed_body (const E& embeddedBody) { T* embedptr=static_cast(this); T* newinst; if(embedptr) newinst=new T(*embedptr); else newinst=new T(); newinst->set_body(embeddedBody); newinst->set_label(STD_string(newinst->get_label())+itos(instances.size())); instances.push_back(newinst); return *newinst; } T& set_embed_body (E& embeddedBody) { T* embedptr=static_cast(this); T* newinst; if(embedptr) newinst=new T(*embedptr); else newinst=new T(); newinst->set_body(embeddedBody); newinst->set_label(STD_string(newinst->get_label())+itos(instances.size())); instances.push_back(newinst); return *newinst; } typedef typename STD_list::iterator institer; institer get_inst_begin() {return instances.begin();} institer get_inst_end() {return instances.end();} typedef typename STD_list::const_iterator constinstiter; constinstiter get_const_inst_begin() const {return instances.begin();} constinstiter get_const_inst_end() const {return instances.end();} private: STD_list instances; }; /** @} */ #endif odin-1.8.5/tjutils/tjlog.cpp0000644000175000017500000001570711322062342012725 00000000000000#include "tjlog.h" #include "tjvector.h" #include "tjhandler_code.h" STD_string LogMessage::str(unsigned int maxwidth, bool include_comp) const { // crop beginning of strings if too long STD_string objCrop; unsigned int len=obj.length(); if(len>MAX_LOG_STRINGSIZE) objCrop=obj.substr(len-MAX_LOG_STRINGSIZE, MAX_LOG_STRINGSIZE); else objCrop=obj; STD_string funcCrop; len=func.length(); if(len>MAX_LOG_STRINGSIZE) funcCrop=func.substr(len-MAX_LOG_STRINGSIZE, MAX_LOG_STRINGSIZE); else funcCrop=func; const char* member_separator=""; if(obj.length()) member_separator="."; STD_string line; if(include_comp) line+=comp+STD_string(MAX_COMPONENT_SIZE-comp.length(),' ')+"|"; if(level==errorLog) line+="ERROR: "; if(level==warningLog) line+="WARNING: "; line+=objCrop; if(obj.length()) line+="."; line+=funcCrop+" : "+txt; if( maxwidth && (line.length()>maxwidth) ) { // zero linewidth indicates infinite length line=line.substr(0,maxwidth); line+=STD_string("..."); } return line; } ////////////////////////////////////////////////////////////////////////////////////////////////// void default_tracefunction(const LogMessage& msg) { fprintf(stderr,msg.str().c_str()); // Use stderr because 'real' cerr is not available with STREAM_REPLACEMENT fflush(stderr); // print immediately } ////////////////////////////////////////////////////////////////////////////////////////////////// struct LogBaseAlloc : public LogBase {}; void LogBase::set_log_level(const char* compname, logPriority level) { LogBaseAlloc alloc; // allocate global // modify level of component already registered STD_map::const_iterator it=global->components.find(compname); if(it!=global->components.end()) { log_component_fptr fp=it->second; fp(level); } // store initialization level global->init_level[compname]=level; // disable uniform initialization level global->uniform_init_level=ignoreArgument; } void LogBase::set_uniform_log_level(logPriority level) { LogBaseAlloc alloc; // allocate global // modify levels of components already registered for(STD_map::const_iterator it=global->components.begin();it!=global->components.end();++it) { log_component_fptr fp=it->second; if(fp) fp(level); } // set all initialization levels to the uniform level for(STD_map::iterator it2=global->init_level.begin();it2!=global->init_level.end();++it2) { it2->second=level; } global->uniform_init_level=level; } #ifndef NO_CMDLINE void LogBase::parse_log_cmdline_options(int argc, char *argv[], const char* opt, logPriority base) { char value[ODIN_MAXCHAR]; // parse cmdline opts while(getCommandlineOption(argc,argv,opt,value,ODIN_MAXCHAR)) { STD_string arg(value); STD_string::size_type pos=arg.find(":"); if(pos==STD_string::npos) { set_uniform_log_level(logPriority(base+atoi(arg.c_str()))); } else { STD_string compname=extract(arg,"",":"); STD_string levelstr=extract(arg,":",""); set_log_level(compname.c_str(),logPriority(base+atoi(levelstr.c_str()))); } } } bool LogBase::set_log_levels(int argc, char *argv[], bool trigger_error) { LogBaseAlloc alloc; // allocate global if(trigger_error && global && global->components.size()) { STD_cerr << "ERROR: LogBase::set_log_levels: global already initialized with the following components:" << STD_endl; // trigger error if static members have already initialized log handlers for(STD_map::iterator it=global->components.begin();it!=global->components.end();++it) { STD_cerr << " " << it->first << STD_endl; } return true; } parse_log_cmdline_options(argc,argv, "-v", noLog); parse_log_cmdline_options(argc,argv, "-d", RELEASE_LOG_LEVEL); // backwards compatability return false; } #endif STD_string LogBase::get_usage() { STD_string result; result+="-v or for debugging/tracing all components or a single component, respectively. "; result+="Possible values for loglevel are: "; int upperLevel=numof_log_priorities; #ifndef ODIN_DEBUG upperLevel=RELEASE_LOG_LEVEL+1; #endif for(int i=0; icomponents)[name]=func; // set initial log level from cache, if available if(global->uniform_init_level!=ignoreArgument) { func(global->uniform_init_level); } else { STD_map::iterator it2=global->init_level.find(name); if(it2!=global->init_level.end()) func(it2->second); } return true; } return false; } void LogBase::unregister_component(const char* name) { // STD_cout << "LogBase::unregister_component: name=" << name << STD_endl; if(global) { STD_map::iterator it=global->components.find(name); if(it!=global->components.end()) global->components.erase(it); } } static STD_string levels_retval; const char* LogBase::get_levels() { if(!global) return ""; levels_retval=""; for(STD_map::iterator it=global->components.begin(); it!=global->components.end(); ++it) { // STD_cout << "LogBase::get_levels: it->first=" << (void*)(it->first) << STD_endl; levels_retval+=STD_string(it->first)+" "; log_component_fptr fp=it->second; if(fp) levels_retval+=itos(fp(ignoreArgument))+"\n"; } return levels_retval.c_str(); } void LogBase::set_levels(const char* str) { svector lines(tokens(str,'\n')); for(unsigned int i=0; i=2) { set_log_level(tokens_per_line[0].c_str(), logPriority(atoi(tokens_per_line[1].c_str()))); } } } void LogBase::flush_oneline(const STD_string& txt, logPriority level) { if(global && global->tracefunc) { // check for global because it might be called after Static::destroy_all LogMessage msg; msg.level=level; msg.comp=compLabel; if(objLabel) msg.obj=objLabel; if(namedObj) msg.obj=namedObj->get_label(); msg.func=funcName; msg.txt=txt; global->tracefunc(msg); } } void LogBase::set_log_output_function(tracefunction func) { LogBaseAlloc alloc; // allocate global global->tracefunc=func; } void LogBase::init_static() { global.init("LogBaseGlobal"); } void LogBase::destroy_static() { global.destroy(); } template class SingletonHandler; SingletonHandler LogBase::global; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/tjutils/tjembed.cpp0000644000175000017500000000002611322062342013204 00000000000000#include "tjembed.h" odin-1.8.5/tjutils/tjthread_code.h0000644000175000017500000000606011712547771014063 00000000000000#include #include template void ThreadedLoop::WorkThread::run() { Log odinlog("WorkThread","run"); while(1) { process.wait(); process.reset(); // Reset for next event ODINLOG(odinlog,normalDebug) << "catched process signal, cont=" << tloop->cont << STD_endl; if(!tloop->cont) break; ODINLOG(odinlog,normalDebug) << "processing thread " << begin << "/" << end << STD_endl; status=tloop->kernel(*tloop->in_cache, *out_cache, local, begin, end); ODINLOG(odinlog,normalDebug) << "signaling finished=" << status << STD_endl; finished.signal(); if(!status) break; } } ////////////////////////////////////////////////////////////////////////// template bool ThreadedLoop::init(unsigned int numof_threads, unsigned int loopsize) { Log odinlog("ThreadedLoop","init"); mainbegin=0; mainend=loopsize; #ifndef NO_THREADS destroy(); // stop old threads ODINLOG(odinlog,normalDebug) << "numof_threads=" << numof_threads << STD_endl; if(numof_threads>1) { threads.resize(numof_threads-1); // the main thread is also used unsigned int onesize=loopsize/numof_threads; unsigned int rest=loopsize%numof_threads; unsigned int count=0; for(unsigned int i=0; i<(numof_threads-1); i++) { threads[i]=new WorkThread(this); threads[i]->begin=count; count+=onesize; if(iend=count; threads[i]->start(); } mainbegin=count; count+=onesize; if((numof_threads-1) void ThreadedLoop::destroy() { Log odinlog("ThreadedLoop","destroy"); #ifndef NO_THREADS cont=false; // Stop threads for(unsigned int i=0; iprocess.signal(); threads[i]->wait(); delete threads[i]; } threads.resize(0); #endif } template bool ThreadedLoop::execute(const In& in, STD_vector& outvec) { Log odinlog("ThreadedLoop","execute"); #ifdef NO_THREADS outvec.resize(1); return kernel(in, outvec[0], mainlocal, mainbegin, mainend); #else unsigned int nthreads=threads.size(); outvec.resize(nthreads+1); if(nthreads) { in_cache=∈ cont=true; for(unsigned int i=0; iout_cache=&(outvec[i]); threads[i]->status=true; threads[i]->process.signal(); } } bool result=kernel(in, outvec[nthreads], mainlocal, mainbegin, mainend); // Use mainthread also for kernel if(nthreads) { for(unsigned int i=0; ifinished.wait(); // Wait for result threads[i]->finished.reset(); if(!threads[i]->status) result=false; } ODINLOG(odinlog,normalDebug) << "finished.wait() done" << STD_endl; } return result; #endif } odin-1.8.5/tjutils/tjcstd.h0000644000175000017500000000377211322062342012545 00000000000000/*************************************************************************** tjcstd.h - description ------------------- begin : Thu Jun 16 2004 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJCSTD_H #define TJCSTD_H #ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif // boilerplate C headers #include #include #include #include #include #include #ifdef HAVE_CTYPE_H #include #endif // missing C functions #ifndef HAVE_CTYPE_H int isdigit (int c); int isspace (int c); int islower (int c); int tolower (int c); int isupper (int c); int toupper (int c); #endif #ifndef HAVE_J1 double j1(double x); #endif #ifndef HAVE_ACOSH double acosh(double x); #endif #ifdef VXWORKS // fix broken exp function #define exp exp4vxworks double exp4vxworks(double x); #endif #ifndef HAVE_DL void *dlopen (const char *filename, int flag); const char *dlerror(void); void *dlsym(void *handle, char *symbol); int dlclose (void *handle); #endif //make VStudio 2005 happy with snprintf #ifdef USING_WIN32 #ifndef HAVE_SNPRINTF #define snprintf _snprintf #endif //HAVE_SNPRINTF #endif //USING_WIN32 #endif odin-1.8.5/tjutils/tjstd.cpp0000644000175000017500000003150411322062342012727 00000000000000#include "tjutils.h" #include "tjcstd.h" #include "tjstream.h" #include "tjtest.h" #include "tjlog.h" //////////////////////////////////////////////////////////////////////////// #ifdef STL_REPLACEMENT STD_ostream & operator << (STD_ostream & s, tjstd_complex c) { char sign[2]; if (c.im>=0.0) { sign[0]='+';sign[1]='\0';} else sign[0]='\0'; return s << c.re << sign << c.im << "i"; } #endif //////////////////////////////////////////////////////////////////////////// #ifdef STRING_REPLACEMENT tjstd_string::tjstd_string () : sdata(0), length_cache(0) {} tjstd_string::tjstd_string (unsigned int n,const char c) : sdata(new char [n+1]), length_cache(n) { for(unsigned int i=0;i=n)) { return nullchar; } else { return sdata[i]; } } const char& tjstd_string::operator [] (unsigned int i) const { unsigned int n=length(); if( i<0 || i>=n) { return nullchar; } else { return sdata[i]; } } tjstd_string operator + (const tjstd_string& s1, const tjstd_string& s2) { tjstd_string result; result.concat2strings(s1,s2); return result; } tjstd_string operator + (const tjstd_string& s1, const char* s2) { tjstd_string result; result.concat2strings(s1,tjstd_string(s2)); return result; } tjstd_string operator + (const char* s1, const tjstd_string& s2) { tjstd_string result; result.concat2strings(tjstd_string(s1),s2); return result; } tjstd_string& tjstd_string::operator += (const tjstd_string& s2) { concat2strings(*this,s2); return *this; } bool operator == (const tjstd_string& s, const tjstd_string& t) {return tjstd_string::compare2strings(s.sdata, t.sdata);} bool operator == (const tjstd_string& s, const char* t) {return tjstd_string::compare2strings(s.sdata, t);} bool operator == (const char* s, const tjstd_string& t) {return tjstd_string::compare2strings(s, t.sdata);} bool operator != (const tjstd_string& s, const tjstd_string& t) {return !tjstd_string::compare2strings(s.sdata, t.sdata);} bool operator != (const tjstd_string& s, const char* t) {return !tjstd_string::compare2strings(s.sdata, t);} bool operator != (const char* s, const tjstd_string& t) {return !tjstd_string::compare2strings(s, t.sdata);} bool operator < (const tjstd_string& s, const tjstd_string& t) { unsigned int p=0; unsigned int q=0; while( (p!=s.length()) && (q!=t.length()) && (toupper(s[p]) == toupper(t[q])) ) { ++p; ++q; } if(p==s.length()) return q!=t.length(); if(q==t.length()) return false; return ( toupper(s[p]) < toupper(t[q]) ); } bool operator > (const tjstd_string& s, const tjstd_string& t) { if(s==t) return false; return !(s> (STD_istream& s, tjstd_string& t) { char c=0; // remove trailing whitespaces while(s.get(c)) { if(!isspace(c)) { s.putback(c); break; } } tjstd_string buffer(STREAM2PARSE_CHUNK_SIZE,'\0'); t=""; int ibuff=0; while(s.get(c) && !isspace(c)) { buffer[(unsigned int)ibuff]=c; ibuff++; if(ibuff==STREAM2PARSE_CHUNK_SIZE) { t+=buffer; buffer=tjstd_string(STREAM2PARSE_CHUNK_SIZE,'\0'); ibuff=0; } } t+=buffer; // remove following whitespaces while(s.get(c)) { if(!isspace(c)) { s.putback(c); break; } } return s; } tjstd_string tjstd_string::substr(unsigned int beginpos,unsigned int sublength) const { unsigned int end=beginpos+sublength; if(beginpos > end) return ""; if(beginpos<0) beginpos=0; if( end <0) end=0; unsigned int len=length(); if(beginpos>=len) beginpos=len; if(end >=len) end=len; unsigned int resultlength=end-beginpos; tjstd_string result(end-beginpos); for(unsigned int i=0; i(thislength-startpos)) return npos; const char* thisstr=(const char*)c_str(); const char* searchstr=(const char*)searchstring.c_str(); unsigned int nshifts=(thislength-startpos)-searchlength+1; for(unsigned int ishift=0; ishift& ilist) const { Log odinlog(this,"listtest_dump_list"); ODINLOG(odinlog,errorLog) << "list=" << STD_endl; for(STD_list::const_iterator it=ilist.begin(); it!=ilist.end(); ++it) { ODINLOG(odinlog,errorLog) << (*it) << STD_endl; } } /////////////////////////////////////////////////////////////////////////// void listtest_init_list(STD_list& ilist) const { int i; ilist.clear(); ///////////// preparing list of random number between 0 and 9 for(i=0; i9) randval=9; if(i%3) ilist.push_back(randval); else ilist.push_front(randval); } } /////////////////////////////////////////////////////////////////////////// void listtest_digit_count(STD_list& ilist, int* digit_count) const { STD_list::const_iterator it; int i; for(i=0; i<10; i++) digit_count[i]=0; for(it=ilist.begin(); it!=ilist.end(); ++it) { digit_count[*it]++; } } /////////////////////////////////////////////////////////////////////////// bool listtest_check_list() const { Log odinlog(this,"listtest_check_list"); STD_list::const_iterator it; int i; STD_list ilist; int digit_count[10]; listtest_init_list(ilist); listtest_digit_count(ilist,digit_count); ///////////// checking sort() ilist.sort(); // checking linear ordering with ++ operator int lastdigit=-1; for(it=ilist.begin(); it!=ilist.end(); ++it) { if(lastdigit>=0) { if(lastdigit>(*it)) { ODINLOG(odinlog,errorLog) << "(sort) with ++: inconsistent ordering" << STD_endl; listtest_dump_list(ilist); return false; } } lastdigit=(*it); } // checking linear ordering with -- operator lastdigit=-1; it=ilist.end(); while(it!=ilist.begin()) { --it; if(lastdigit>=0) { if(lastdigit<(*it)) { ODINLOG(odinlog,errorLog) << "(sort) with --: inconsistent ordering" << STD_endl; listtest_dump_list(ilist); return false; } } lastdigit=(*it); } // checking digit_count int digit_count_test[10]; for(i=0; i<10; i++) digit_count_test[i]=0; for(it=ilist.begin(); it!=ilist.end(); ++it) { digit_count_test[*it]++; } for(i=0; i<10; i++) { if(digit_count_test[i]!=digit_count[i]) { ODINLOG(odinlog,errorLog) << "(sort) inconsistent digit_count" << STD_endl; listtest_dump_list(ilist); return false; } } ///////////// checking unique() ilist.unique(); unsigned int n_different_digits=0; for(i=0; i<10; i++) { if(digit_count[i]) n_different_digits++; } ODINLOG(odinlog,normalDebug) << "n_different_digits=" << n_different_digits << STD_endl; if(ilist.size()!=n_different_digits) { ODINLOG(odinlog,errorLog) << "(unique) inconsistent list after unique" << STD_endl; listtest_dump_list(ilist); return false; } ///////////// checking remove() listtest_init_list(ilist); ilist.remove(3); listtest_digit_count(ilist,digit_count); if(digit_count[3]) { ODINLOG(odinlog,errorLog) << "(remove) elements still there after remove" << STD_endl; listtest_dump_list(ilist); return false; } ///////////// checking clear() ilist.clear(); if(ilist.size()) { ODINLOG(odinlog,errorLog) << "(clear) elements still there after clear" << STD_endl; listtest_dump_list(ilist); return false; } /////////// checking STD_find ilist.clear(); ilist.push_back(1); ilist.push_back(3); ilist.push_back(4); if(STD_find(ilist.begin(), ilist.end(), 3) == ilist.end()) { ODINLOG(odinlog,errorLog) << "STD_find does not find existing element 3" << STD_endl; listtest_dump_list(ilist); return false; } if(STD_find(ilist.begin(), ilist.end(), 2) != ilist.end()) { ODINLOG(odinlog,errorLog) << "STD_find finds non-existing element 2" << STD_endl; listtest_dump_list(ilist); return false; } return true; } /////////////////////////////////////////////////////////////////////////// bool check_map() const { Log odinlog(this,"check_map"); STD_map imap; imap["12"]=12; imap["34"]=34; imap["56"]=56; int expected, returned; expected=34; returned=imap["34"]; if(expected!=returned) { ODINLOG(odinlog,errorLog) << "testing [] operator: expected/returned=" << expected << "/" << returned << STD_endl; return false; } STD_map::iterator it=imap.find("56"); expected=56; returned=it->second; if(expected!=returned) { ODINLOG(odinlog,errorLog) << "testing find: expected/returned=" << expected << "/" << returned << STD_endl; return false; } imap.erase(imap.find("34")); expected=2; returned=imap.size(); if(imap.size()!=2) { ODINLOG(odinlog,errorLog) << "testing erase: expected/returned=" << expected << "/" << returned << STD_endl; return false; } return true; } bool check() const { Log odinlog(this,"check"); for(unsigned int i=0; i #include #include /** * @addtogroup tjutils * @{ */ /////////////////////////////////////////////////////////////// class StateComponent { public: static const char* get_compName(); }; /////////////////////////////////////////////////////////////// template class State : public Labeled { public: typedef bool (T::* transition) (); State(T* statemachine, const char* statelabel, State* prerequired_state, transition tr) : Labeled(statelabel), machine(statemachine), pre_state(prerequired_state), trans(tr) { Log odinlog(this,"State()"); } bool obtain_state() { Log odinlog(this,"obtain_state"); // return if we are already in the desired state if(machine->current_state==this) return true; // try a registered direct transition if(machine->direct_transition(this)) return true; if(pre_state) { // check whether a prerequisite state exists and obtain that state if(!pre_state->obtain_state()) return false; } bool result=(machine->*trans)(); // perform the transition if(result) machine->current_state=this; return result; } private: T* machine; State* pre_state; transition trans; }; /////////////////////////////////////////////////////////////// template struct DirectTransition { DirectTransition(State* init, State* dest, typename State::transition tr) : init_state(init), dest_state(dest), trans(tr) { Log odinlog("DirectTransition","DirectTransition()"); } bool operator == (const DirectTransition& dt) const {return init_state==dt.init_state && dest_state==dt.dest_state && trans==dt.trans;} bool operator != (const DirectTransition& dt) const {return !(*this==dt);} bool operator < (const DirectTransition& dt) const {return init_state* init_state; State* dest_state; typename State::transition trans; }; /////////////////////////////////////////////////////////////// template class StateMachine { protected: StateMachine(State* first_state) : current_state(first_state) { Log odinlog("StateMachine","StateMachine()"); } const STD_string& get_current_state_label() const {return current_state->get_label();} void register_direct_trans(State* init, State* dest, typename State::transition tr) { direct_trans.push_back( DirectTransition(init,dest,tr) ); } bool direct_transition(State* dest) { typename STD_list >::iterator it; for(it=direct_trans.begin(); it!=direct_trans.end(); ++it) { if( (it->init_state==current_state) && (it->dest_state==dest) ) { typename State::transition tt=it->trans; bool result=((T*)(this)->*tt)(); if(result) current_state=dest; return result; } } return false; } private: friend class State; STD_list > direct_trans; State* current_state; }; /** @} */ #endif odin-1.8.5/tjutils/tjheap.h0000644000175000017500000000347611322062342012526 00000000000000/*************************************************************************** tjheap.h - description ------------------- begin : Thu Jul 31 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJHEAP_H #define TJHEAP_H #ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif // pointer for external trace function typedef void (*heaptracefunction)(const char*); class Heap { public: static void malloc_stats(); static void set_trace_function(heaptracefunction func) {tracefunc=func;} static heaptracefunction tracefunc; }; //#ifdef CUSTOM_HEAP //#include //#ifndef STL_REPLACEMENT //#include //#endif // overloading new/delete if a custom heap (block of static memory) is used //#ifndef STL_REPLACEMENT //void* operator new(size_t size) throw (std::bad_alloc); //#else //void* operator new(size_t size); //#endif //void* operator new[](size_t size); //void operator delete(void* mptr); //void operator delete[](void* mptr); //#endif #endif odin-1.8.5/tjutils/tjhandler.cpp0000644000175000017500000000506711322062342013557 00000000000000#include "tjhandler.h" #include "tjlog.h" #include "tjlog_code.h" const char* HandlerComponent::get_compName() {return "Handler";} LOGGROUNDWORK(HandlerComponent) //////////////////////////////////////////////////////////////////////// void SingletonBase::set_singleton_map_external(SingletonMap* extmap) { // Log uses SingletonHandler -> do not use Log in here singleton_map_external=extmap; // in order to cache ptr properly, no singletons should be allocated at this point if(singleton_map && singleton_map->size()) { STD_cerr << "ERROR: SingletonBase::set_singleton_map_external: There are already singletons allocated:" << STD_endl; for(SingletonMap::iterator it=singleton_map->begin(); it!=singleton_map->end(); ++it) { STD_cerr << it->first << "/" << (void*)it->second << STD_endl; } } } SingletonBase::SingletonBase() { if(!singleton_map) singleton_map=new SingletonMap; } SingletonMap* SingletonBase::get_singleton_map() { // NOTE: Debug uses SingletonHandler -> do not use Debug in here if(!singleton_map) singleton_map=new SingletonMap; return singleton_map; } STD_string SingletonBase::get_singleton_label(SingletonBase* sing_ptr) { Log odinlog("SingletonBase","get_singleton_label"); STD_string result; if(!(singleton_map || singleton_map_external)) { ODINLOG(odinlog,normalDebug) << "neither singleton_map nor singleton_map_external available" << STD_endl; return result; } SingletonMap::iterator mapbegin=singleton_map->begin(); SingletonMap::iterator mapend =singleton_map->end(); if(singleton_map_external) { mapbegin=singleton_map_external->begin(); mapend =singleton_map_external->end(); } for(SingletonMap::iterator it=mapbegin; it!=mapend; ++it) { if(it->second==sing_ptr) result=it->first; } ODINLOG(odinlog,normalDebug) << "result(" << (void*)sing_ptr << ")=" << result << STD_endl; return result; } void* SingletonBase::get_external_map_ptr(const STD_string& sing_label) { // NOTE: Log uses SingletonHandler -> do not use Log in here if(singleton_map_external) { if(singleton_map_external->find(sing_label)==singleton_map_external->end()) { STD_cerr << "ERROR: SingletonBase::get_external_map_ptr: singleton >" << sing_label << "< not found in singleton_map_external" << STD_endl; return 0; } return (*singleton_map_external)[sing_label]->get_ptr(); } return 0; } SingletonMap* SingletonBase::singleton_map=0; SingletonMap* SingletonBase::singleton_map_external=0; //////////////////////////////////////////////////////////////////////// odin-1.8.5/tjutils/tjstatic.h0000644000175000017500000000661311322062342013074 00000000000000/*************************************************************************** tjstatic.h - description ------------------- begin : Sun Jul 7 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJSTATIC_H #define TJSTATIC_H #include #include /** * @addtogroup tjutils * @{ */ //////////////////////////////////////////////////////////////////// class Static { public: Static() {} virtual ~Static() {} // destroy all static objects manually static void destroy_all(); static void append_to_destructor_list(Static* sp); protected: static STD_list* destructor_list; }; //////////////////////////////////////////////////////////////////// template struct StaticAlloc : public virtual Static { StaticAlloc() { } ~StaticAlloc() { T::destroy_static(); } }; //////////////////////////////////////////////////////////////////// /** * This template class handles static members of all classes that * must be initialised exactly once. The rationale behind this * is that some of the classes posses static members on which * a certain action has to be performed EXACTLY once BEFORE * anything else happens with that class. The 'StaticHandler' serves as * as a base class for classes that require this feature. * It makes this easier by keeping track of how often the static * members have been initialised so that this is done only once. * The following steps must be performed to make use of the * StaticHandler: * * -# Deriving the class C from the template class StaticHandler * by adding 'public StaticHandler' to the list of base * classes * -# Adding the static member function * 'static void init_static();' * to the public section of the class. This function should * contain the actions that will be performed only once for * the static members. * -# Adding the static member function * 'static void destroy_static();' * to the public section of the class. This function should * contain the actions to deallocate memory allocated by init_static() * -# Adding the line 'bool StaticHandler::staticdone=false;' * to the source code of the class C */ template class StaticHandler { public: StaticHandler() { if(!staticdone) { // fast check staticdone=true; // must be assigned before call to T::init_static() to avoid infinite loops Static* sp=new StaticAlloc; Static::append_to_destructor_list(sp); T::init_static(); } } private: static bool staticdone; }; /** @} */ #endif odin-1.8.5/tjutils/tjarray.cpp0000644000175000017500000004152511322062342013257 00000000000000#include "tjarray.h" #include "tjtypes.h" #include "tjtest.h" ndim::ndim (unsigned long d) : STD_vector(d) { } // ndim nn(3); ndim::ndim (const STD_string& s) : STD_vector() { Log odinlog("ndim","ndim(const STD_string&)"); unsigned long incosistent=0; STD_string tt=shrink(s); ODINLOG(odinlog,normalDebug) << "ndim::ndim (const STD_string& s): after shrinking >" << tt << "<" << STD_endl; if(tt[(unsigned int)0] != '(') incosistent++; if(tt[tt.length()-1] != ')') incosistent++; STD_string innertext=replaceStr(extract(tt,"(",")",true),",",""); // if (typeofcontent(innertext)!=intnumbers) incosistent++; if(!incosistent) { ODINLOG(odinlog,normalDebug) << "ndim::ndim (const STD_string& s): no inconsistences in >" << tt << "<" << STD_endl; tt=replaceStr(tt,"(",","); tt=replaceStr(tt,")",","); ODINLOG(odinlog,normalDebug) << "ndim::ndim (const STD_string& s): string used for dim extraction: >" << tt << "<" << STD_endl; svector extends(tokens(tt,',')); unsigned int n=extends.size(); resize(n); for(unsigned int i=0;i odinlog("ndim","--()"); unsigned long n=size(); if (n <= 0) ODINLOG(odinlog,errorLog) << "reduce to negative dimension ?!" << STD_endl; else { ndim tt(*this); n--; resize(n); for(unsigned long i=0;i odinlog("ndim","--(int)"); unsigned long n=size(); if (n <= 0) ODINLOG(odinlog,errorLog) << "reduce to negative dimension ?!" << STD_endl; else { ndim tt(*this); n--; resize(n); for(unsigned long i=0;i odinlog("ndim","extent2index"); unsigned long totalIndex=0,subsize; if (dim() != mm.dim()) ODINLOG(odinlog,errorLog) <<"dimension mismatch: dim()!=mm.dim()=" << dim() << "!=" << mm.dim() << STD_endl; if(!dim()) return 0; ndim nn(*this); for(unsigned long i=0;i=0;i--){ nn[i]=temp%((*this)[i]); temp=temp/(*this)[i]; } return nn; } bool ndim::operator == (const ndim& nn) const { unsigned long i,flag=0; if (dim()==nn.dim()) { for(i=0;i= n ) return *this; ndim oldndim(*this); resize(newdim); unsigned long extent_factor=1; while(oldndim.dim()>newdim) { extent_factor=oldndim[0]; --oldndim; oldndim[0]*=extent_factor; } for(unsigned int i=0;i indexlist; unsigned long i; for(i=0;i1) indexlist.push_back((*this)[i]); } resize(indexlist.size()); i=0; for(STD_list::iterator it=indexlist.begin(); it!=indexlist.end(); ++it) { (*this)[i]=(*it); i++; } #else STD_vector::iterator new_end; new_end=std::remove(begin(),end(),(unsigned long)(1)); erase(new_end,end()); #endif if((size()==0) && at_least_one_element) { resize(1); (*this)[0]=1; } return *this; } #ifndef NO_UNIT_TEST class NdimTest : public UnitTest { public: NdimTest() : UnitTest("ndim") {} private: bool check() const { Log odinlog(this,"check"); ndim nn_reference(3); nn_reference[0]=4; nn_reference[1]=7; nn_reference[2]=9; nn_reference.add_dim(2,true); nn_reference.add_dim(3,false); ndim nn_parse(" ( 2, 4, 7, 9, 3 )"); if(nn_parse!=nn_reference) { ODINLOG(odinlog,errorLog) << "Mismatch: nn_reference/nn_parse=" << STD_string(nn_reference) << "/" << STD_string(nn_parse) << STD_endl; return false; } return true; } }; void alloc_NdimTest() {new NdimTest();} // create test instance #endif /**************************************************************/ /****************** Template code *******************/ /**************************************************************/ /*------------------------------------------------------*/ template tjarray::tjarray () : V() { extent.resize(1); extent[0] = 0; } template tjarray::tjarray (unsigned long n1) {redim(create_extent(n1));} template tjarray::tjarray (unsigned long n1, unsigned long n2) {redim(create_extent(n1,n2));} template tjarray::tjarray (unsigned long n1, unsigned long n2, unsigned long n3) {redim(create_extent(n1,n2,n3));} template tjarray::tjarray (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4) {redim(create_extent(n1,n2,n3,n4));} template tjarray::tjarray (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5) {redim(create_extent(n1,n2,n3,n4,n5));} template tjarray::tjarray (const tjarray &ta) : V(ta) { extent=ta.extent; } template tjarray::tjarray (const V& sv) : V(sv) { extent.resize(1); extent[0]=sv.size(); } template tjarray::tjarray (const ndim &nn) { V::resize(nn.total()); extent=nn; } template tjarray& tjarray::operator = (const tjarray& ta) { Log odinlog("tjarray","operator = (const tjarray&)"); V::operator = (ta); extent=ta.extent; return *this; } template tjarray& tjarray::operator = (const T& value) { for(unsigned int i=0; i V& tjarray::resize (unsigned int newsize) { Log odinlog("tjarray","resize"); extent.resize (1); extent[0]=newsize; V::resize(extent.total()); return *this; } template tjarray& tjarray::redim (const ndim &nn) { Log odinlog("tjarray","redim"); ODINLOG(odinlog,normalDebug) << "nn=" << STD_string(nn) << STD_endl; unsigned int newtot=nn.total(); if(total()!=newtot) V::resize(newtot); extent=nn; return *this; } template tjarray& tjarray::redim (unsigned long n1) {redim(create_extent(n1)); return *this;} template tjarray& tjarray::redim (unsigned long n1, unsigned long n2) {redim(create_extent(n1,n2)); return *this;} template tjarray& tjarray::redim (unsigned long n1, unsigned long n2, unsigned long n3) {redim(create_extent(n1,n2,n3)); return *this;} template tjarray& tjarray::redim (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4) {redim(create_extent(n1,n2,n3,n4)); return *this;} template tjarray& tjarray::redim (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5) {redim(create_extent(n1,n2,n3,n4,n5)); return *this;} //#endif template const ndim& tjarray::get_extent () const { return extent; } template T& tjarray::operator () (const ndim& ii) { Log odinlog("tjarray","operator ()"); unsigned long totalIndex=extent.extent2index(ii); unsigned long totalExtent=extent.total(); ODINLOG(odinlog,normalDebug) << "totalIndex/totalExtent=" << totalIndex << "/" << totalExtent << STD_endl; if(totalIndex>=totalExtent) return element_dummy; else return (*this)[totalIndex]; } template const T& tjarray::operator () (const ndim& ii) const { Log odinlog("tjarray","operator () const"); unsigned long totalIndex=extent.extent2index(ii); unsigned long totalExtent=extent.total(); ODINLOG(odinlog,normalDebug) << "totalIndex/totalExtent=" << totalIndex << "/" << totalExtent << STD_endl; if(totalIndex>=totalExtent) return element_dummy; else return (*this)[totalIndex]; } template T& tjarray::operator () (unsigned long n1) {return tjarray::operator () (create_extent(n1));} template T& tjarray::operator () (unsigned long n1, unsigned long n2) {return tjarray::operator () (create_extent(n1,n2));} template T& tjarray::operator () (unsigned long n1, unsigned long n2, unsigned long n3) {return tjarray::operator () (create_extent(n1,n2,n3));} template T& tjarray::operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4) {return tjarray::operator () (create_extent(n1,n2,n3,n4));} template T& tjarray::operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5) {return tjarray::operator () (create_extent(n1,n2,n3,n4,n5));} template const T& tjarray::operator () (unsigned long n1) const {return tjarray::operator () (create_extent(n1));} template const T& tjarray::operator () (unsigned long n1, unsigned long n2) const {return tjarray::operator () (create_extent(n1,n2));} template const T& tjarray::operator () (unsigned long n1, unsigned long n2, unsigned long n3) const {return tjarray::operator () (create_extent(n1,n2,n3));} template const T& tjarray::operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4) const {return tjarray::operator () (create_extent(n1,n2,n3,n4));} template const T& tjarray::operator () (unsigned long n1, unsigned long n2, unsigned long n3, unsigned long n4, unsigned long n5) const {return tjarray::operator () (create_extent(n1,n2,n3,n4,n5));} template unsigned long tjarray::dim() const {return extent.dim();} template unsigned long tjarray::size(unsigned long i) const {return extent[i];} template unsigned long tjarray::total() const {return extent.total();} template unsigned long tjarray::length() const {return total();} template unsigned int tjarray::elementsize() const {return sizeof(T);} template tjarray& tjarray::assignValues(const tjarray &ta) { Log odinlog("tjvector","assignValues"); if(ta.length()==length()) { for(unsigned int i=0; i"; tokens[i]=val; } return tokenstring(tokens,_DEFAULT_LINEWIDTH_); } template STD_ostream& tjarray::printbody2stream(STD_ostream& s) const { Log odinlog("tjarray","printbody2stream"); unsigned long n=length(); T typedummy; bool stringarr=(TypeTraits::type2label(typedummy)==STD_string("string")); unsigned int width=0; for(unsigned long i=0; i_DEFAULT_LINEWIDTH_) {s << "\n"; width=0;} if(stringarr) {s << "<"; width++;} STD_string val(TypeTraits::type2string((*this)[i])); s << val; width+=val.length(); if(stringarr) {s << ">"; width++;} if(i!=(n-1)) {s << " "; width++;} } return s; // << "\n"; } template ndim tjarray::create_extent(unsigned long n1) { ndim nn(1); nn[0]=n1; return nn; } template ndim tjarray::create_extent(unsigned long n1,unsigned long n2) { ndim nn(2); nn[0]=n1; nn[1]=n2; return nn; } template ndim tjarray::create_extent(unsigned long n1,unsigned long n2,unsigned long n3) { ndim nn(3); nn[0]=n1; nn[1]=n2; nn[2]=n3; return nn; } template ndim tjarray::create_extent(unsigned long n1,unsigned long n2,unsigned long n3,unsigned long n4) { ndim nn(4); nn[0]=n1; nn[1]=n2; nn[2]=n3; nn[3]=n4; return nn; } template ndim tjarray::create_extent(unsigned long n1,unsigned long n2,unsigned long n3,unsigned long n4,unsigned long n5) { ndim nn(5); nn[0]=n1; nn[1]=n2; nn[2]=n3; nn[3]=n4; nn[4]=n5; return nn; } template ndim tjarray::create_index(unsigned long index) const {return extent.index2extent(index);} ///////////////////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class ArrayTest : public UnitTest { public: ArrayTest() : UnitTest("array") {} private: bool check() const { Log odinlog(this,"check"); farray fa(1,2,3,4,5); STD_string expected="( 1, 2, 3, 4, 5 )"; STD_string printed=fa.get_extent(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "farray(...) failed: got extent >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } fa.redim(3,2,1); expected="( 3, 2, 1 )"; printed=fa.get_extent(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "farray.redim(...) failed: got extent >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } float testval=44.0; fa(2,1,0)=testval; if(fa.sum()!=44.0) { ODINLOG(odinlog,errorLog) << "farray.operator (...) failed: " << fa.sum() << "!=" << testval << STD_endl; return false; } return true; } }; void alloc_ArrayTest() {new ArrayTest();} // create test instance #endif /**************************************************************/ /****************** Template instantiations *********/ /**************************************************************/ template class tjarray; template class tjarray; template class tjarray; template class tjarray; template class tjarray; ///////////////////////////////////////////////////////////////////////////// // Helper functions: STD_string print_table(const sarray& table) { Log odinlog("","print_table"); STD_string result; if(table.dim()!=2) { ODINLOG(odinlog,errorLog) << "Dimension of input array != 2" << STD_endl; return result; } int ncols=table.size(0); int nrows=table.size(1); int icol, irow; // Get max width of each column ivector width(ncols); width=0; for(irow=0; irow #include /** * @addtogroup tjutils * @{ */ /** * This class holds nested lists (tree) of values. * Each node can contain a single value, or a list of other nested lists. * In addition, it contains a repetition counter for this node. * Its main purpose is to retrieve value lists (e.g. frequency lists, delay lists, reco indices) from the sequence tree. */ template class ValList : public virtual Labeled { /** * Actual data with reference counting */ struct ValListData { ValListData() : val(0), times(1), sublists(0), elements_size_cache(0), references(0) {} ValListData(const ValListData& vld) : times(vld.times), elements_size_cache(vld.elements_size_cache), references(0) { if(vld.val) val=new T(*vld.val); else val=0; if(vld.sublists) sublists=new STD_list< ValList >(*vld.sublists); else sublists=0; } ~ValListData() { if(sublists) delete sublists; if(val) delete val; } T* val; // zero pointer indicates 'value not set' unsigned int times; STD_list< ValList >* sublists; // zero pointer indicates 'list not set' unsigned int elements_size_cache; // cache for the number of values of one repetition of this node unsigned short references; // reference counter }; public: /** * Empty node with given label and repetitions */ ValList(const STD_string& object_label="unnamedValList", unsigned int repetitions=1); /** * Node with a single value */ ValList(T value); /** * Copy constructor */ ValList(const ValList& vl); ~ValList(); /** * Assignment operator */ ValList& operator = (const ValList& vl); /** * Make node single value */ ValList& set_value(T value); /** * Append another node to this */ ValList& add_sublist(const ValList& vl); /** * Multiply number of repetitions of this node by 'reptimes' */ ValList& multiply_repetitions(unsigned int reptimes) {copy_on_write(); data->times*=reptimes; return *this;} /** * Returns unrolled values of nested list */ STD_vector get_values_flat() const; /** * Returns unrolled values of nested list for one repetition of this list */ STD_vector get_elements_flat() const; /** * Equal operator */ bool operator == (const ValList& vl) const; /** * Comparison operator */ bool operator < (const ValList& vl) const; /** * Acess i'th value in the nested list */ T operator [] (unsigned int i) const; /** * Returns number of values of one repetition of this node */ // unsigned int elements_size() const; /** * Returns number of values */ unsigned int size() const {return data->times*data->elements_size_cache;} /** * Serializes list to a string */ STD_string printvallist() const; /** * Parses list from string */ bool parsevallist(const STD_string& str); /** * Prints value list to stream */ STD_ostream& print2stream(STD_ostream& os) const; /** * Clears the value list */ void clear(); private: friend class ValListTest; bool equalelements (const ValList& vl) const; ValList& increment_repetitions(unsigned int reptimes) {copy_on_write(); data->times+=reptimes; return *this;} unsigned int get_repetitions() const {return data->times;} void flatten_sublists(); void copy_on_write(); ValListData* data; }; /////////////////////////////////////////////////// /** @} */ #endif odin-1.8.5/tjutils/tjlist.h0000644000175000017500000001111111322062342012545 00000000000000/*************************************************************************** tjlist.h - description ------------------- begin : Mon Aug 5 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJLIST_H #define TJLIST_H #include /** * @addtogroup tjutils * @{ */ // for debugging List class ListComponent { public: static const char* get_compName(); }; ////////////////////////////////////////////////////////////// class ListItemBase {}; class ListBase { public: virtual ~ListBase() {} virtual void objlist_remove(ListItemBase* item) = 0; }; ////////////////////////////////////////////////////////////// template class ListItem : public ListItemBase { public: ListItem() {} ~ListItem(); // empty copy and assignment operator to avoid copying of 'objhandlers' member ListItem(const ListItem&) {} ListItem& operator = (const ListItem&) {return *this;} unsigned int numof_references() const {return objhandlers.size();} const ListItemBase& append_objhandler(ListBase& objhandler) const; const ListItemBase& remove_objhandler(ListBase& objhandler) const; private: mutable STD_list objhandlers; }; ///////////////////////////////////////////// /** * This template class handles a list of references to other objects. * In contrast to the STL list, it stores only pointers to the members * of the list instead of storing copies. That means, if a member of the * list is modified, the property of the whole list changes. This list * is well suited to build blocks of objects that will be modified after * they have been inserted into the list, e.g. a list of parameters. * * If you want to use this list, i.e. create an instantiation for a specific * data type T, you must first decide whether to use const objects, i.e. which * will not changed via the list, or non-const objects that can be modified * via the list. In the former case, create a list by instatiating * * List * * otherwise * * List * * Classes which are to be inserted into the list must be derived * from the base class * * ListItem * * This construct ensures that whenever an item of the list is deleted, * it deregisters itself from the list. */ template class List : public ListBase { public: /** * Constructs an empty List */ List(); /** * Destructor */ ~List(); /** * Assignment operator that will result in a list that holds references to all objects for which * 'l' contains a reference */ List& operator = (const List& l); /** * Removes all items from the list */ List& clear(); /** * Appends a reference to 'item' */ List& append(R item); /** * Removes all references to 'item' */ List& remove(R item); /** * Returns the number of items in the list */ unsigned int size() const {return objlist.size();} /** * Iterator for mutable lists */ typedef typename STD_list

    ::iterator iter; /** * Iterator for const lists */ typedef typename STD_list

    ::const_iterator constiter; /** * returns an iterator that points to the head of the list (for mutable lists) */ iter get_begin() {return objlist.begin();} /** * returns an iterator that points to the end of the list (for mutable lists) */ iter get_end() {return objlist.end();} /** * returns an iterator that points to the head of the list (for const lists) */ constiter get_const_begin() const {return objlist.begin();} /** * returns an iterator that points to the end of the list (for const lists) */ constiter get_const_end() const {return objlist.end();} private: void objlist_remove(ListItemBase* item); void link_item(P ptr); void unlink_item(P ptr); STD_list

    objlist; }; /** @} */ #endif odin-1.8.5/tjutils/tjthread.h0000644000175000017500000001267011712547771013075 00000000000000/*************************************************************************** tjthread.h - description ------------------- begin : Mon Dec 12 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef TJTHREAD_H #define TJTHREAD_H #include /** * @addtogroup tjutils * @{ */ //////////////////////////////////////////////////////////////////// // for debugging class ThreadComponent { public: static const char* get_compName(); }; //////////////////////////////////////////////////////////////////// /** * Lock for mutually exclusive (mutex) access in threads. The mutex is recursive. */ class Mutex { public: /** * Constructs unlocked mutex object. */ Mutex(); ~Mutex(); /** * Locks the mutex. */ void lock(); /** * Unlocks the mutex. */ void unlock(); private: friend class Event; // disable copying Mutex(const Mutex&) {} Mutex& operator = (const Mutex&) {return *this;} void* id; }; //////////////////////////////////////////////////////////////////// /** * Lock object using a mutex. */ class MutexLock { public: /** * Constructs a lock using 'mutex'. The mutex is locked for the lifetime of the object. */ MutexLock(Mutex& mutex) : m(mutex) {m.lock();} ~MutexLock() {m.unlock();} private: // disable copying MutexLock(const MutexLock& ml) : m(ml.m) {} // bogus MutexLock& operator = (const MutexLock&) {return *this;} Mutex& m; }; //////////////////////////////////////////////////////////////////// /** * Manual-reset event to synchronize threads. */ class Event { public: /** * Constructs an event object. */ Event(); ~Event(); /** * Waits until any other thread calls signal(). * Returns immediately if this has already happended. */ void wait(); /** * Signal event to all waiting threads. */ void signal(); /** * Manually reset event. */ void reset(); private: // disable copying Event(const Event&) {} Event& operator = (const Event&) {return *this;} void* id; // Extra stuff for pthread Mutex mutex; bool active; }; //////////////////////////////////////////////////////////////////// class ThreadIndex; // forward declaration /** * Base class for threads. Derive from this and implement * the run() function to use it. */ class Thread { public: /** * Constructs thread object with the given label. */ Thread(); virtual ~Thread(); /** * Starts the thread. * 'stack_size' is used as the threads stack size if not zero (in which case the * systems default stack size is used). * Returns 'true' only on sucess. */ bool start(unsigned int stack_size=0); /** * Waits for the thread to finish. Returns 'true' only on sucess. */ bool wait(); /** * Implement to run threads execution path. */ virtual void run() = 0; /** * Returns thread-unique ID of the current thread. */ static int self(); private: // disable copying Thread(const Thread&) {} Thread& operator = (const Thread&) {return *this;} void clear_id(); void* id; ThreadIndex* index; // give each thread a unique index }; //////////////////////////////////////////////////////////////////// /** * Class to parallelize loops. */ template class ThreadedLoop { public: /** * Default constructor. */ ThreadedLoop() : mainbegin(0), mainend(0) {} virtual ~ThreadedLoop() {destroy();} /** * Initialize to use 'numof_threads' executing 'loopsize' jobs in parallel. * Starts the worker threads. */ bool init(unsigned int numof_threads, unsigned int loopsize); /** * Stops the worker threads. */ void destroy(); /** * Execute loop using input 'in' and storing result from each thread in 'outvec'. */ bool execute(const In& in, STD_vector& outvec); private: /** * Overload this function to do the work of one thread using input 'in', * generating output 'out' with thread-local storage 'local' for the the loop inidices (begin <= i < end). */ virtual bool kernel(const In& in, Out& out, Local& local, unsigned int begin, unsigned int end) = 0; class WorkThread : public Thread { friend class ThreadedLoop; WorkThread(ThreadedLoop* tl) : tloop(tl) {} void run(); ThreadedLoop* tloop; unsigned int begin; unsigned int end; Event process; Event finished; volatile bool status; Out* out_cache; Local local; }; unsigned int mainbegin; unsigned int mainend; Local mainlocal; friend class WorkThread; STD_vector threads; const In* in_cache; volatile bool cont; }; /** @} */ #endif odin-1.8.5/tjutils/tjfeedback.cpp0000644000175000017500000000235611322062342013664 00000000000000#include "tjfeedback.h" #include "tjtools.h" ///////////////////////////////////////////////////////////////////////////// bool ProgressMeter::increase_counter(const char* subj) { MutexLock lock(mutex); display->increase(subj); return display->refresh(); } bool ProgressMeter::refresh_display() { MutexLock lock(mutex); return display->refresh(); } ProgressMeter& ProgressMeter::new_task(unsigned int total_steps, const char* txt) { MutexLock lock(mutex); if(display) display->init(total_steps,txt); return *this; } ///////////////////////////////////////////////////////////////////////////// #ifndef NO_CMDLINE void ProgressDisplayConsole::init(unsigned int nsteps, const char* txt) { counter=0; old_perc=0; nsteps_cache=nsteps; done=false; if(txt) STD_cout << txt << " " << STD_flush; } void ProgressDisplayConsole::increase(const char* subj) { if(done) return; counter++; unsigned int perc=(unsigned int)(100.0*secureDivision(counter,nsteps_cache)); if(perc>old_perc) { if(perc>=100) { STD_cout << "done" << STD_endl; done=true; } else { if(!(perc%10)) STD_cout << perc << "%" << STD_flush; else if(!(perc%2)) STD_cout << "." << STD_flush; } old_perc=perc; } } #endif odin-1.8.5/tjutils/tjtools.h0000644000175000017500000001654211363773555012773 00000000000000/*************************************************************************** tjtools.h - description ------------------- begin : Thu Jul 13 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ // This is a collection of frequently used C-routines #ifndef TJTOOLS_H #define TJTOOLS_H #include /** * @addtogroup tjutils * @{ */ #ifndef PII #define PII 3.14159265358979323846264338327950288 #endif #ifndef ODIN_MAXCHAR #define ODIN_MAXCHAR 4096 #endif #ifdef HAVE_LONG_LONG #define LONGEST_INT long long #else #define LONGEST_INT long #endif // functions of large file extension, define them here so // these macros can re-used in other modules #ifdef HAVE_STAT64 #define STAT stat64 #else #ifdef HAVE_STAT #define STAT stat #endif #endif #ifdef HAVE_OPEN64 #define OPEN open64 #else #define OPEN open #endif #ifdef HAVE_FOPEN64 #define FOPEN fopen64 #else #define FOPEN fopen #endif #ifdef HAVE_FSEEKO64 #define FSEEK fseeko64 #else #ifdef HAVE_FSEEKO #define FSEEK fseeko #else #define FSEEK fseek #endif #endif #ifdef HAVE_FTELLO64 #define FTELL ftello64 #else #ifdef HAVE_FTELLO #define FTELL ftello #else #define FTELL ftell #endif #endif #ifdef HAVE_MMAP64 #define MMAP mmap64 #else #define MMAP mmap #endif /** * * Mode flag when reading/writing raw data to disk: * - readMode: Read-only access * - overwriteMode: If a file with the same name already exists, it is overwritten * - appendMode: If a file with the same name already exists, the data is appended */ enum fopenMode {readMode,overwriteMode,appendMode}; /** * Norm of a double vector */ double norm(double x, double y); /** * Norm of a triple vector */ double norm3(double x,double y,double z); /** * * Maximum value of 3 numbers */ double maxof3(double f1, double f2, double f3); #ifndef NO_FILEHANDLING /** * * Returns mode string suitable for fopen according to 'mode' */ const char* modestring(fopenMode mode); /** * * Returns file size in bytes if file exists, otherwise -1 */ LONGEST_INT filesize(const char *filename); /** * * Returns the current directory of the process */ const char* getpwd(); /** * * Changes the current directory of the process to dirname. On success, zero is returned. On error, -1 is returned. */ int chpwd(const char *dirname); /** * * Creates the given directory. On success, zero is returned. On error, -1 is returned. */ int createdir(const char *dirname); /** * * Returns true if directory 'dirname' exists, otherwise false */ bool checkdir(const char *dirname); /** * * Moves a file 'src' to destination 'dst'. On success, zero is returned. On error, -1 is returned. */ int movefile(const char *src, const char* dst); /** * * Copies a file 'src' to destination 'dst'. On success, zero is returned. On error, -1 is returned. */ int copyfile(const char *src, const char* dst); /** * * Removes the file or directory 'fname'. On success, zero is returned. On error, -1 is returned. */ int rmfile(const char *fname); /** * * Changes permissions of file 'fname' to 'perm'. On success, zero is returned. On error, -1 is returned. */ int chperm(const char *fname, int perm); /** * * Creates a file mapping of file 'filename' with 'nbytes' length starting at 'offset' bytes into the file, * optionally in 'readonly' mode. * The 'fd' will hold the file descriptor (handle) of the mapped file. * Returns a pointer to the mapped memory region. */ void* filemap(const STD_string& filename, LONGEST_INT nbytes, LONGEST_INT offset, bool readonly, int& fd); /** * * Deletes a file mapping of file descriptor 'fd' which maps a region at memory location 'start' of 'nbytes' length * starting at 'offset' bytes into the file. */ void fileunmap(int fd, void* start, LONGEST_INT nbytes, LONGEST_INT offset); /** * * Return a unique name for a temporary file. */ STD_string tempfile(); /** * * Create an empty file, filled with zeroes. Overwrite or append according to 'mode'. * On error, -1 is returned. */ int create_empty_file(const STD_string& filename, LONGEST_INT nbytes, fopenMode mode=overwriteMode); #endif /** * * Returns the last system error as a string */ const char* lasterr(); /** * * Halt process/thread for 'ms' miliseconds. */ void sleep_ms(unsigned int ms); /** * * Returns the current time in s */ double current_time_s(); /** * * If denominator is zero the functions returns 0, otherwise numerator/denominator */ double secureDivision(double numerator, double denominator); /** * * If denominator is zero the functions returns 0, otherwise 1/denominator */ inline double secureInv(double denominator) {return secureDivision(1.0, denominator); } /** * * Same as getenv, but does return "" instead of 0 if variable is not found */ const char* secure_getenv(const char* variable_name); /** * * Returns true if the current platform has little endian byte order, otherwise false */ bool little_endian_byte_order(); /** * * Returns the number of (virtual) CPUs */ unsigned int numof_cores(); /** * * Returns sinc function with accurate results for small x * (in contrast to using sin(x)/x directly) */ double sinc(double x); #ifndef NO_CMDLINE /** * * Copies maximum of 'maxchar' characters from the argv[] which * follows an argv[] that matches 'option' into 'returnvalue'; * returns TRUE if successful; 'maxchar' should NOT be greater * than the number of bytes allocated for 'returnvalue' even if * the number of chars in argv[] is smaller. * If 'modify' is true, remove argument from the list. */ int getCommandlineOption(int argc, char *argv[], const char *option, char *returnvalue, int maxchar,bool modify=true); /** * * Returns TRUE if 'option' is found in argv[] * If 'modify' is true, remove argument from the list. */ int isCommandlineOption(int argc, char *argv[], const char *option,bool modify=true); /** * * Copies maximum of 'maxchar' characters from the last argv[] * that DOESN'T start with '-' into 'returnvalue'; * returns TRUE if successful; 'maxchar' should NOT be greater * than the number of bytes allocated for 'returnvalue' even if * the number of chars in argv[] is smaller */ int getLastArgument(int argc, char *argv[], char *returnvalue, int maxchar,bool modify=true); /** * * Returns whether one of the options '-h, -help, --help or --version' was given */ int hasHelpOption(int argc, char *argv[]); /** * * Returns description of the standard help, version options */ const char* helpUsage(); #endif /** @} */ #endif odin-1.8.5/tjutils/tjindex.cpp0000644000175000017500000001226711322062342013251 00000000000000#include "tjindex.h" #include "tjtest.h" #include "tjlog_code.h" #include "tjhandler_code.h" const char* Index::get_compName() {return "Index";} LOGGROUNDWORK(Index) /////////////////////////////////////////////////////////////////////////////////////////// unsigned int UniqueIndexMap::get_index(STD_list::iterator& index, const STD_string& type, unsigned int max_instances) { Log odinlog(type.c_str(),"get_index"); STD_list& indices=(*this)[type]; if(index==indices.end()) assign_index(index,type); if(max_instances && ((*index)>=max_instances)) { ODINLOG(odinlog,errorLog) << "maximum number of indices exceeded for type " << type << STD_endl; return 0; } ODINLOG(odinlog,normalDebug) << "returning index=" << *index << STD_endl; return (*index); } void UniqueIndexMap::remove_index(const STD_list::iterator& index, const STD_string& type) { Log odinlog(type.c_str(),"remove_index"); STD_list& indices=(*this)[type]; if(index!=indices.end()) { ODINLOG(odinlog,normalDebug) << "Trying to remove index=" << *index << STD_endl; indices.erase(index); contiguous=false; } } unsigned int UniqueIndexMap::assign_index(STD_list::iterator& index, const STD_string& type) { Log odinlog(type.c_str(),"assign_index"); STD_list& indices=(*this)[type]; index=indices.end(); unsigned int i=0; STD_list::iterator iter; if(contiguous){ //if the list is contiguous iter=indices.end(); if(indices.begin()!=indices.end())//use the last member +1 or leave 0 i= *(--indices.end())+1; } else {//if list is not complete find the first "gap" for(iter=indices.begin();iter!=indices.end() && *iter==i;++iter) i++; } index=indices.insert(iter,i);//insert i into the gap (or the end) ODINLOG(odinlog,normalDebug) << "adding index=" << i << STD_endl; for(;iter!=indices.end() && *iter==(i+1);++iter); //check for a gap behind contiguous = (iter==indices.end()); return i; } /////////////////////////////////////////////////////////////////////////////////////////// template class SingletonHandler; SingletonHandler UniqueIndexBase::indices_map; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; /////////////////////////////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST #define INDEX_TESTSIZE 5 class IndexTest : public UnitTest { // Test class class UniqueIndexTest : public UniqueIndex { public: UniqueIndexTest(){}; static const char* get_typename() {return "UniqueIndexTest";} static unsigned int get_max_instances() {return 0;} }; public: IndexTest() : UnitTest("index") {} private: bool compare_and_report(int expected[INDEX_TESTSIZE], UniqueIndexTest* objs[INDEX_TESTSIZE], const char* txt) const { Log odinlog(this,"compare_and_report"); for(unsigned int i=0; i=0) { int returned=objs[i]->get_index(); if(expected[i]!=returned) { ODINLOG(odinlog,errorLog) << txt << "[" << i << "]: expected/returned=" << expected[i] << "/" << returned << STD_endl; return true; } } } return false; } bool check() const { Log odinlog(this,"check"); UniqueIndexTest* objs[INDEX_TESTSIZE]; for(unsigned int i=0; iget_index(); if(endobjindex!=endobjindex_expected) { ODINLOG(odinlog,errorLog) << "endobjindex/_expected=" << endobjindex << "/" << endobjindex_expected << STD_endl; return false; } delete endobj; // Delete in reverse order and check again delete objs[1]; delete objs[3]; objs[1]=new UniqueIndexTest; objs[3]=new UniqueIndexTest; if(compare_and_report(expected, objs, "realloc2")) return false; // Delete begin and end indices delete objs[0]; delete objs[INDEX_TESTSIZE-1]; int expected3[]={-1,1,2,3,-1}; if(compare_and_report(expected3, objs, "begin/end")) return false; // Re-create in reverse order objs[INDEX_TESTSIZE-1]=new UniqueIndexTest; int expected4[]={-1,1,2,3,0}; if(compare_and_report(expected4, objs, "begin/end(realloc1)")) return false; objs[0]=new UniqueIndexTest; int expected5[]={4,1,2,3,0}; if(compare_and_report(expected5, objs, "begin/end(realloc2)")) return false; for(unsigned int i=0; i #include #include "geoeditlabel.h" #define MAGN_FACTOR 2 #define MIN_MATRIX_SIZE 256 class GeoEditView : public QWidget { Q_OBJECT public: GeoEditView(Geometry& geometry, ImageSet& pilot, unsigned int blowup, QWidget *parent); private slots: void geometryChanged(); void emitDone(); void setProjection(bool) {geometryChanged();} void setCrossSection(bool) {geometryChanged();} void sagSet(); void corSet(); void axiSet(); void magnify0(int,int,int) {magnify(0);} void magnify1(int,int,int) {magnify(1);} void magnify2(int,int,int) {magnify(2);} signals: void donePressed(); private: void magnify(int index); unsigned int coarse; Geometry& geometry_cache; ImageSet& pilot_cache; JDXwidget* blockwidget[n_geometry_modes]; GuiGridLayout* grid; STD_list labels; buttonBox* projection; buttonBox* crosssect; geometryMode old_mode; }; #endif odin-1.8.5/geoedit/geoeditlabel.h0000644000175000017500000000522511322062334013610 00000000000000/*************************************************************************** geoeditlabel.h - description ------------------- begin : Tue Apr 16 2002 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef GEOEDITLABEL_H #define GEOEDITLABEL_H #include #include #include #define REL_READVEC_LENGTH 0.2 #define READVEC_ARROW_LENGTH 0.1 #define CROSSSECT_COLOR "Red" #define PROJECTION_COLOR "Green" //////////////////////////////////////// // for debugging geoedit component class GeoEditComp { public: static const char* get_compName(); }; //////////////////////////////////////// class GeoEditLabel : public floatBox3D { Q_OBJECT public: GeoEditLabel(const Image& background, unsigned int coarseFactor, QWidget *parent); void drawImagingArea(const Geometry& ia, bool drawProj, bool drawCross); private: int xcoord2labelxpos(double pos) { return label->xpos2labelxpos(int((double)label->get_nx()*(0.5+secureDivision(pos,backgr.get_geometry().get_FOV(readDirection)))));} int ycoord2labelypos(double pos) { return label->ypos2labelypos(int((double)label->get_ny()*(0.5+secureDivision(pos,backgr.get_geometry().get_FOV(phaseDirection)))));} void drawSliceProjection(const darray& cornersProj, GuiPainter& painter); void drawSliceCrossSection(const darray& connectPoints, double slicethick, GuiPainter& painter, unsigned int slice); void drawVoxelProjection(const darray& cornersProj, GuiPainter& painter); void drawReadVector(const dvector& readvecstart_proj, const dvector& readvec_proj, GuiPainter& painter); // overloading virtual function of floatBox3D void repaint() {if(ia_cache) drawImagingArea(*ia_cache,drawProj_cache,drawCross_cache);} Image backgr; unsigned int coarse; const Geometry* ia_cache; bool drawProj_cache; bool drawCross_cache; }; #endif odin-1.8.5/geoedit/main.cpp0000644000175000017500000000055711322062334012452 00000000000000#include "geoedit.h" int main(int argc, char *argv[]) { // do this here so we do not have to query X server in order to get usage for manual if(hasHelpOption(argc, argv)) {GeoEditApp::usage();exit(0);} GuiApplication a(argc, argv); // debug handler will be initialized here GeoEditApp *geoedit=new GeoEditApp(); return a.start(geoedit->get_widget()); } odin-1.8.5/geoedit/geoedit.cpp0000644000175000017500000000503011322062334013135 00000000000000#include "geoedit.h" #include void GeoEditApp::usage() { STD_cout << "geoedit: Geometry editor of ODIN" << STD_endl; STD_cout << "Usage: geoedit [options] " << STD_endl; STD_cout << "Options:" << STD_endl; STD_cout << "\t -pilot : Load pilot scan as background" << STD_endl; STD_cout << "\t -sample : Load sample as background" << STD_endl; STD_cout << "\t -blowup : Enlarge size of backround by this factor" << STD_endl; STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; } GeoEditApp::GeoEditApp() : geometry("Geometry") { Log odinlog("GeoEditApp","GeoEditApp(...)"); // command line parsing char optval[ODIN_MAXCHAR]; if(hasHelpOption(GuiApplication::argc(),GuiApplication::argv())) {usage();exit(0);} if(GuiApplication::argc()<=1) { filename = get_open_filename("Please select geometryInfo to start with ...", "", "", GuiMainWindow::get_widget()); }else { getLastArgument(GuiApplication::argc(),GuiApplication::argv(),optval,ODIN_MAXCHAR); filename=optval; } if(filename=="") exit(0); if(geometry.load(filename)<=0) { ODINLOG(odinlog,warningLog) << "unable to load " << filename << " as geometry file, will be created" << STD_endl; } ODINLOG(odinlog,normalDebug) << "load done" << STD_endl; if(getCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-pilot",optval,ODIN_MAXCHAR)) { pilot.load(optval); } ODINLOG(odinlog,normalDebug) << "pilot done" << STD_endl; if(getCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-sample",optval,ODIN_MAXCHAR)) { Sample sample("sample",false); if(sample.load(optval)>0) { ODINLOG(odinlog,normalDebug) << "Creating pilot from sample" << STD_endl; pilot=ImageSet(sample); } } ODINLOG(odinlog,normalDebug) << "sample done" << STD_endl; set_caption((STD_string("GeoEdit " VERSION) + " - " + filename).c_str()); unsigned int blowup=1; if(getCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-blowup",optval,ODIN_MAXCHAR)) { blowup=atoi(optval); } view=new GeoEditView(geometry,pilot,blowup,GuiMainWindow::get_widget()); connect(view,SIGNAL(donePressed()),this,SLOT( exitGeoEdit())); ODINLOG(odinlog,normalDebug) << "view done" << STD_endl; GuiMainWindow::show(view); // setCentralWidget(view); } void GeoEditApp::exitGeoEdit() { geometry.write(filename); GuiApplication::quit(); // qApp->quit(); } odin-1.8.5/geoedit/Makefile.am0000644000175000017500000000137411322062334013054 00000000000000 if GUI_ENABLED INCLUDES = $(all_includes) # Auto-generate any needed moc files %_moc.cpp: %.h $(MOC) -o $@ $< bin_PROGRAMS = geoedit geoedit_SOURCES = \ main.cpp \ geoedit.cpp geoedit.h geoedit_moc.cpp \ geoeditlabel.cpp geoeditlabel.h geoeditlabel_moc.cpp \ geoeditview.cpp geoeditview.h geoeditview_moc.cpp geoedit_LDADD = ../odinqt/libodinqt.la ../odindata/libodindata.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la # Auto-generate manual pages, only if not in srcdir %.1: % if test ! -f $(srcdir)/$@ ; 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then $(HELP2MAN) --name="$$(./$< --help | grep $<: | sed s/'$<: '//)" ./$< > $@ ; fi @GUI_ENABLED_TRUE@dist-hook: @GUI_ENABLED_TRUE@ -rm -rf $(distdir)/*_moc.cpp clean-local: -rm -f *_moc.cpp # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/geoedit/geoeditlabel.cpp0000644000175000017500000002013611322062334014141 00000000000000 #include "geoeditlabel.h" #include "geoeditview.h" #include const char* GeoEditComp::get_compName() {return "GeoEdit";} LOGGROUNDWORK(GeoEditComp) //////////////////////////////////////////////////////////////////////////// GeoEditLabel::GeoEditLabel(const Image& background, unsigned int coarseFactor, QWidget *parent ) : floatBox3D(background.get_magnitude().c_array(),0.0,0.0, background.size(xAxis),background.size(yAxis),background.size(zAxis), coarseFactor,parent,background.get_label().c_str()), backgr(background), coarse(coarseFactor), ia_cache(0) { } void GeoEditLabel::drawSliceProjection(const darray& cornersProj, GuiPainter& painter) { painter.setPen(PROJECTION_COLOR,1,true); painter.moveTo(xcoord2labelxpos(cornersProj(0,0)),ycoord2labelypos(cornersProj(0,1))); for(unsigned int icorner=1; icorner<4; icorner++) { painter.lineTo(xcoord2labelxpos(cornersProj(icorner,0)),ycoord2labelypos(cornersProj(icorner,1))); } painter.lineTo(xcoord2labelxpos(cornersProj(0,0)),ycoord2labelypos(cornersProj(0,1))); } void GeoEditLabel::drawSliceCrossSection(const darray& connectPoints, double slicethick, GuiPainter& painter, unsigned int slice) { Log odinlog("GeoEditLabel","drawSliceCrossSection"); int penwidth=(int)(slicethick/backgr.get_geometry().get_FOV(readDirection)*float(backgr.size(xAxis))*float(coarse)); if(penwidth<1) penwidth=1; painter.setPen(CROSSSECT_COLOR,penwidth); int xstart=xcoord2labelxpos(connectPoints(0,0)); int ystart=ycoord2labelypos(connectPoints(0,1)); int xend=xcoord2labelxpos(connectPoints(1,0)); int yend=ycoord2labelypos(connectPoints(1,1)); ODINLOG(odinlog,normalDebug) << "xstart/ystart/xend/yend=" << xstart << "/" << ystart << "/" << xend << "/" << yend << STD_endl; painter.moveTo(xstart,ystart); painter.lineTo(xend,yend); painter.drawText((xend+xstart)/2, (yend+ystart)/2,itos(slice).c_str(),CROSSSECT_COLOR); } void GeoEditLabel::drawVoxelProjection(const darray& cornersProj, GuiPainter& painter) { unsigned int icorner; painter.setPen(PROJECTION_COLOR,1,true); for(unsigned int ilevel=0; ilevel<2; ilevel++) { painter.moveTo(xcoord2labelxpos(cornersProj(ilevel,0,0)),ycoord2labelypos(cornersProj(ilevel,0,1))); for(unsigned int icorner=1; icorner<4; icorner++) { painter.lineTo(xcoord2labelxpos(cornersProj(ilevel,icorner,0)),ycoord2labelypos(cornersProj(ilevel,icorner,1))); } painter.lineTo(xcoord2labelxpos(cornersProj(ilevel,0,0)),ycoord2labelypos(cornersProj(ilevel,0,1))); } for(icorner=0; icorner<4; icorner++) { painter.moveTo(xcoord2labelxpos(cornersProj(0,icorner,0)),ycoord2labelypos(cornersProj(0,icorner,1))); painter.lineTo(xcoord2labelxpos(cornersProj(1,icorner,0)),ycoord2labelypos(cornersProj(1,icorner,1))); } } void GeoEditLabel::drawReadVector(const dvector& readvecstart_proj, const dvector& readvec_proj, GuiPainter& painter) { painter.setPen(PROJECTION_COLOR); dvector readvec_end(2); readvec_end=readvecstart_proj+readvec_proj; dvector readvec_proj_perp(2); readvec_proj_perp[0]=-readvec_proj[1]; readvec_proj_perp[1]= readvec_proj[0]; dvector readvec_arrow_end(2); readvec_arrow_end=readvecstart_proj+(1.0-READVEC_ARROW_LENGTH)*readvec_proj+READVEC_ARROW_LENGTH*readvec_proj_perp; painter.moveTo(xcoord2labelxpos(readvecstart_proj[0]),ycoord2labelypos(readvecstart_proj[1])); painter.lineTo(xcoord2labelxpos(readvec_end[0]),ycoord2labelypos(readvec_end[1])); painter.lineTo(xcoord2labelxpos(readvec_arrow_end[0]),ycoord2labelypos(readvec_arrow_end[1])); } void GeoEditLabel::drawImagingArea(const Geometry& ia, bool drawProj, bool drawCross) { Log odinlog("GeoEditLabel","drawImagingArea"); ia_cache=&ia; drawProj_cache=drawProj; drawCross_cache=drawCross; // init painter label->init_pixmap(); GuiPainter painter(label->pixmap); // first, get corner points in coordinate system of background image ODINLOG(odinlog,normalDebug) << "get_current_z()=" << get_current_z() << STD_endl; darray cornerPoints=ia.get_cornerPoints(backgr.get_geometry(),floatBox3D::get_current_z()); // will be 1 for slicepack mode or 2 for 3D/Voxel mode int n_slice_bounds=cornerPoints.size(3); bool is3d=(n_slice_bounds>1); if(is3d) drawCross=false; darray corners(4,3); darray corners3d(2,4,3); dvector cornervec1(3); dvector cornervec2(3); darray crosspoints(2,2); darray allCornersTemp(4,2); darray allCornersTemp3d(2,4,2); // the coordinate system of the plot axis projAxis1=xAxis; axis projAxis2=yAxis; axis perpax=zAxis; unsigned int n_slices=cornerPoints.size(0); unsigned int midslice=n_slices/2; dvector readvec(3); dvector readvecstart(3); for(unsigned int idir=0;idir<3;idir++) { readvec[idir]=REL_READVEC_LENGTH*(cornerPoints(midslice,upperBound,0,0,idir)-cornerPoints(midslice,lowerBound,0,0,idir)); readvecstart[idir]=cornerPoints(midslice,lowerBound,lowerBound,0,idir); } ODINLOG(odinlog,normalDebug) << "readvec=" << readvec.printbody() << STD_endl; dvector readvec_proj(2); readvec_proj[0]=readvec[projAxis1]; readvec_proj[1]=readvec[projAxis2]; dvector readvecstart_proj(2); readvecstart_proj[0]=readvecstart[projAxis1]; readvecstart_proj[1]=readvecstart[projAxis2]; if(drawProj) drawReadVector(readvecstart_proj,readvec_proj,painter); for(unsigned int j=0;j0.0) && (s<1.0) && (icross<2) ) { crosspoints(icross,0)=cornervec1[projAxis1]+s*(cornervec2[projAxis1]-cornervec1[projAxis1]); crosspoints(icross,1)=cornervec1[projAxis2]+s*(cornervec2[projAxis2]-cornervec1[projAxis2]); icross++; } } } } if(drawProj) { if(is3d) drawVoxelProjection(allCornersTemp3d,painter); else drawSliceProjection(allCornersTemp,painter); } if(drawCross && (icross==2)) { ODINLOG(odinlog,normalDebug) << "crosspoints(" << j << ")=" << crosspoints.printbody() << STD_endl; drawSliceCrossSection(crosspoints,ia.get_sliceThickness(),painter,j); } } painter.end(); label->set_pixmap(); } odin-1.8.5/geoedit/geoedit.10000644000175000017500000000146611734623150012532 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH GEOEDIT "1" "March 2012" "geoedit 1.8.5" "User Commands" .SH NAME geoedit \- Geometry editor of ODIN .SH SYNOPSIS .B geoedit [\fIoptions\fR] \fI\fR .SH DESCRIPTION geoedit: Geometry editor of ODIN .SH OPTIONS .HP \fB\-pilot\fR : Load pilot scan as background .TP \fB\-sample\fR : Load sample as background .HP \fB\-blowup\fR : Enlarge size of backround by this factor .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information odin-1.8.5/geoedit/geoedit.h0000644000175000017500000000260211322062334012604 00000000000000/*************************************************************************** geoedit.h - description ------------------- begin : Mon Apr 15 18:40:55 CEST 2002 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef GEOEDIT_H #define GEOEDIT_H #include "geoeditview.h" //////////////////////////////////////// class GeoEditApp : public QObject, public GuiMainWindow { Q_OBJECT public: GeoEditApp(); static void usage(); private slots: void exitGeoEdit(); private: STD_string filename; ImageSet pilot; Geometry geometry; GeoEditView *view; }; #endif odin-1.8.5/geoedit/geoeditview.cpp0000644000175000017500000001172511322062334014040 00000000000000#include "geoedit.h" #include "geoeditview.h" #include GeoEditView::GeoEditView(Geometry& geometry, ImageSet& pilot, unsigned int blowup, QWidget *parent) : QWidget(parent), geometry_cache(geometry), pilot_cache(pilot) { Log odinlog("GeoEditView","GeoEditView(...)"); old_mode=n_geometry_modes; // invalid value to trigger generation of first widget for(int imode=0; imode0) { coarse=(unsigned int)secureDivision(MIN_MATRIX_SIZE,(nx+ny)/2); if(!coarse) coarse=1; ODINLOG(odinlog,normalDebug) << "coarse[" << i<< "]=" << coarse << STD_endl; img.normalize_magnitude(); GeoEditLabel* imglabel=new GeoEditLabel(img,coarse*blowup,this); if(i==0) connect(imglabel,SIGNAL(clicked(int,int,int)),this,SLOT( magnify0(int,int,int))); if(i==1) connect(imglabel,SIGNAL(clicked(int,int,int)),this,SLOT( magnify1(int,int,int))); if(i==2) connect(imglabel,SIGNAL(clicked(int,int,int)),this,SLOT( magnify2(int,int,int))); grid->add_widget( imglabel, 0, 2*i, GuiGridLayout::Center, 1,2); labels.push_back(imglabel); } } /* ------------ draw projection button -----------------*/ projection=new buttonBox("Hide","Show",true, this, "Projection" ); grid->add_widget( projection, 1,5, GuiGridLayout::Center); connect(projection,SIGNAL(buttonToggled(bool)),this,SLOT( setProjection(bool))); /* ------------ draw cross section button -----------------*/ crosssect=new buttonBox("Hide","Show",true, this, "CrossSection" ); grid->add_widget( crosssect, 2,5, GuiGridLayout::Center); connect(crosssect,SIGNAL(buttonToggled(bool)),this,SLOT( setCrossSection(bool))); /* ------------ set sagittal button -----------------*/ buttonBox *sagbutton=new buttonBox("Set", this, "Sagittal" ); grid->add_widget( sagbutton, 3,5, GuiGridLayout::Center); connect(sagbutton,SIGNAL(buttonClicked()),this,SLOT( sagSet())); /* ------------ set coronal button -----------------*/ buttonBox *corbutton=new buttonBox("Set", this, "Coronal" ); grid->add_widget( corbutton, 4,5, GuiGridLayout::Center); connect(corbutton,SIGNAL(buttonClicked()),this,SLOT( corSet())); /* ------------ set axial button -----------------*/ buttonBox *axibutton=new buttonBox("Set", this, "Axial" ); grid->add_widget( axibutton, 5,5, GuiGridLayout::Center); connect(axibutton,SIGNAL(buttonClicked()),this,SLOT( axiSet())); /* ------------ save & exit button -----------------*/ buttonBox *saveexit=new buttonBox("Done", this, "Save & Exit" ); grid->add_widget( saveexit, 6,5, GuiGridLayout::Center); connect(saveexit,SIGNAL(buttonClicked()),this,SLOT( emitDone())); ODINLOG(odinlog,normalDebug) << "Buttons done" << STD_endl; this->showNormal(); geometryChanged(); } void GeoEditView::geometryChanged() { Log odinlog("GeoEditView","geometryChanged"); geometry_cache.update(); ODINLOG(odinlog,normalDebug) << "update done" << STD_endl; geometryMode mode=geometry_cache.get_Mode(); if(old_mode!=mode) { if(old_mode!=n_geometry_modes) blockwidget[old_mode]->hide(); if(blockwidget[mode]==0) blockwidget[mode]=new JDXwidget(geometry_cache,3,this); blockwidget[mode]->show(); grid->add_widget( blockwidget[mode], 1,0, GuiGridLayout::Center, 6,5); connect(blockwidget[mode],SIGNAL(valueChanged()),this,SLOT(geometryChanged())); } blockwidget[mode]->updateWidget(); old_mode=mode; ODINLOG(odinlog,normalDebug) << "JDXwidget done" << STD_endl; for(STD_list::iterator labelit=labels.begin(); labelit!=labels.end(); ++labelit) { (*labelit)->drawImagingArea(geometry_cache,projection->is_on(),crosssect->is_on()); } ODINLOG(odinlog,normalDebug) << "labels->drawImagingArea done" << STD_endl; } void GeoEditView::emitDone() { emit donePressed(); } void GeoEditView::sagSet() { geometry_cache.set_orientation(sagittal); geometryChanged(); } void GeoEditView::corSet() { geometry_cache.set_orientation(coronal); geometryChanged(); } void GeoEditView::axiSet() { geometry_cache.set_orientation(axial); geometryChanged(); } void GeoEditView::magnify(int index) { Image& img=pilot_cache.get_image(index); STD_string tmpdir=STD_string(secure_getenv("HOME"))+SEPARATOR_STR+".odin"+SEPARATOR_STR+"tmp"+SEPARATOR_STR; createdir(tmpdir.c_str()); STD_string tmpfname=tmpdir+"image4geo.jdx"; img.write(tmpfname); system(("miview -blowup "+itos(coarse)+" "+tmpfname+" &").c_str()); } odin-1.8.5/replacements/0000755000175000017500000000000011735135552012150 500000000000000odin-1.8.5/replacements/Makefile.am0000644000175000017500000000010011322062345014102 00000000000000EXTRA_DIST = cxxwrapper.cpp toolwrapper.cpp gsl_replacement.cpp odin-1.8.5/replacements/Makefile.in0000644000175000017500000002275411734622602014143 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; 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int main(int argc, char* argv[]) { string tool; string toolpath; #include "toolwrapper_config.h" // add path for ppc-compiler binaries string newpath="PATH="+toolpath; const char* oldpath_ptr=getenv("PATH"); if(oldpath_ptr) { string oldpath=oldpath_ptr; // remove blanks which make ccppc fail while(oldpath.find("; ")!=string::npos) oldpath.replace(oldpath.find("; "),2,";"); while(oldpath.find(" ;")!=string::npos) oldpath.replace(oldpath.find(" ;"),2,";"); newpath+=";"+string(oldpath); } _putenv(newpath.c_str()); argv[0]=(char*)tool.c_str(); return _spawnv( _P_WAIT, tool.c_str(), argv ); } odin-1.8.5/replacements/cxxwrapper.cpp0000644000175000017500000000607111322062345014772 00000000000000/** * Since the compiler for MPCU does not create executables directly, * using autoconf is not straighforward. Instead we have to wrap the * compiler for the MPCU into this program to create dummy files * instead of actual executables. */ #include #include #include // Win-style process handling #include #include #include using namespace std; int main(int argc, char* argv[]) { string cxx; string cxxpath; #include "cxxwrapper_config.h" // check if we only compile, i.e. have the -c flag bool only_compile=false; for(int i=1; icache = 0; a->hit_count = 0; a->miss_count = 0; return a; } gsl_interp* gsl_interp_alloc (const gsl_interp_type * T, size_t size) { if (size < T->min_size) { STD_cerr << "gsl_interp_alloc: insufficient number of points for interpolation type" << STD_endl; return 0; } gsl_interp * interp=new gsl_interp; interp->type = T; interp->size = size; if (interp->type->alloc == NULL) { interp->state = NULL; return interp; } interp->state = interp->type->alloc(size); if (interp->state == NULL) { delete interp; STD_cerr << "gsl_interp_alloc: failed to allocate space for interp state" << STD_endl; return 0; } return interp; } gsl_spline* gsl_spline_alloc (const gsl_interp_type * T, size_t size) { gsl_spline * spline = new gsl_spline; spline->interp = gsl_interp_alloc (T, size); if (spline->interp == NULL) { delete spline; STD_cerr << "gsl_interp_alloc: failed to allocate space for interp" << STD_endl; return 0; } spline->x = new double[size]; spline->y = new double[size]; spline->size = size; return spline; } int gsl_interp_init (gsl_interp * interp, const double x_array[], const double y_array[], size_t size) { if (size != interp->size) { STD_cerr << "gsl_interp_init: data must match size of interpolation object" << STD_endl; } interp->xmin = x_array[0]; interp->xmax = x_array[size - 1]; int status = interp->type->init(interp->state, x_array, y_array, size); return status; } int gsl_spline_init (gsl_spline * spline, const double x_array[], const double y_array[], size_t size) { if (size != spline->size) { STD_cerr << "gsl_spline_init: data must match size of spline object" << STD_endl; } memcpy (spline->x, x_array, size * sizeof(double)); memcpy (spline->y, y_array, size * sizeof(double)); int status = gsl_interp_init (spline->interp, x_array, y_array, size); return status; } void gsl_interp_accel_free(gsl_interp_accel * a) {delete a;} void gsl_interp_free (gsl_interp * interp) { if (interp->type->free) interp->type->free (interp->state); delete interp; } void gsl_spline_free (gsl_spline * spline) { gsl_interp_free (spline->interp); delete[] spline->x; delete[] spline->y; delete spline; } /////////////////////////////////////////////////////////////////////// double gsl_interp_eval (const gsl_interp * interp, const double xa[], const double ya[], double x, gsl_interp_accel * a) { double y; int status = interp->type->eval (interp->state, xa, ya, interp->size, x, a, &y); // DISCARD_STATUS(status); return y; } double gsl_spline_eval (const gsl_spline * spline, double x, gsl_interp_accel * a) { return gsl_interp_eval (spline->interp, spline->x, spline->y, x, a); } /////////////////////////////////////////////////////////////////////// size_t gsl_interp_bsearch ( const double x_array[], double x, size_t index_lo, size_t index_hi ) { size_t ilo = index_lo; size_t ihi = index_hi; while (ihi > ilo + 1) { size_t i = (ihi + ilo) / 2; if (x_array[i] > x) ihi = i; else ilo = i; } return ilo; } /////////////////////////////////////////////////////////////////////// size_t gsl_interp_accel_find (gsl_interp_accel * a, const double xa[], size_t len, double x) { size_t x_index = a->cache; if (x < xa[x_index]) { a->miss_count++; a->cache = gsl_interp_bsearch (xa, x, 0, x_index); } else if (x > xa[x_index + 1]) { a->miss_count++; a->cache = gsl_interp_bsearch (xa, x, x_index, len - 1); } else { a->hit_count++; } return a->cache; } /////////////////////////////////////////////////////////////////////// static inline double integ_eval (double ai, double bi, double ci, double di, double xi, double a, double b) { const double t0 = b + a; const double t1 = a * a + a * b + b * b; const double t2 = a * a * a + a * a * b + b * b * a + b * b * b; const double bterm = 0.5 * bi * (t0 - 2.0 * xi); const double cterm = ci / 3.0 * (t1 - 3.0 * xi * (t0 - xi)); const double dterm = di / 4.0 * (t2 - 2.0 * xi * (2.0 * t1 - xi * (3.0 * t0 - 2.0 * xi))); return (b - a) * (ai + bterm + cterm + dterm); } /////////////////////////////////////////////////////////////////////// typedef struct { double * b; double * c; double * d; double * _m; } akima_state_t; /* common creation */ static void * akima_alloc (size_t size) { akima_state_t *state = new akima_state_t; state->b = new double[size]; state->c = new double[size]; state->d = new double[size]; state->_m = new double[size + 4]; return state; } /* common calculation */ static void akima_calc (const double x_array[], double b[], double c[], double d[], size_t size, double m[]) { size_t i; for (i = 0; i < (size - 1); i++) { const double NE = fabs (m[i + 1] - m[i]) + fabs (m[i - 1] - m[i - 2]); if (NE == 0.0) { b[i] = m[i]; c[i] = 0.0; d[i] = 0.0; } else { const double h_i = x_array[i + 1] - x_array[i]; const double NE_next = fabs (m[i + 2] - m[i + 1]) + fabs (m[i] - m[i - 1]); const double alpha_i = fabs (m[i - 1] - m[i - 2]) / NE; double alpha_ip1; double tL_ip1; if (NE_next == 0.0) { tL_ip1 = m[i]; } else { alpha_ip1 = fabs (m[i] - m[i - 1]) / NE_next; tL_ip1 = (1.0 - alpha_ip1) * m[i] + alpha_ip1 * m[i + 1]; } b[i] = (1.0 - alpha_i) * m[i - 1] + alpha_i * m[i]; c[i] = (3.0 * m[i] - 2.0 * b[i] - tL_ip1) / h_i; d[i] = (b[i] + tL_ip1 - 2.0 * m[i]) / (h_i * h_i); } } } static int akima_init (void * vstate, const double x_array[], const double y_array[], size_t size) { akima_state_t *state = (akima_state_t *) vstate; double * m = state->_m + 2; /* offset so we can address the -1,-2 components */ size_t i; for (i = 0; i <= size - 2; i++) { m[i] = (y_array[i + 1] - y_array[i]) / (x_array[i + 1] - x_array[i]); } /* non-periodic boundary conditions */ m[-2] = 3.0 * m[0] - 2.0 * m[1]; m[-1] = 2.0 * m[0] - m[1]; m[size - 1] = 2.0 * m[size - 2] - m[size - 3]; m[size] = 3.0 * m[size - 2] - 2.0 * m[size - 3]; akima_calc (x_array, state->b, state->c, state->d, size, m); return GSL_SUCCESS; } static void akima_free (void * vstate) { akima_state_t *state = (akima_state_t *) vstate; delete[] (state->b); delete[] (state->c); delete[] (state->d); delete[] (state->_m); delete (state); } static int akima_eval (const void * vstate, const double x_array[], const double y_array[], size_t size, double x, gsl_interp_accel * a, double *y) { const akima_state_t *state = (const akima_state_t *) vstate; size_t index; if (a != 0) { index = gsl_interp_accel_find (a, x_array, size, x); } else { index = gsl_interp_bsearch (x_array, x, 0, size - 1); } /* evaluate */ { const double x_lo = x_array[index]; const double delx = x - x_lo; const double b = state->b[index]; const double c = state->c[index]; const double d = state->d[index]; *y = y_array[index] + delx * (b + delx * (c + d * delx)); return GSL_SUCCESS; } } static int akima_eval_deriv (const void * vstate, const double x_array[], const double y_array[], size_t size, double x, gsl_interp_accel * a, double *dydx) { const akima_state_t *state = (const akima_state_t *) vstate; size_t index; // DISCARD_POINTER(y_array); /* prevent warning about unused parameter */ if (a != 0) { index = gsl_interp_accel_find (a, x_array, size, x); } else { index = gsl_interp_bsearch (x_array, x, 0, size - 1); } /* evaluate */ { double x_lo = x_array[index]; double delx = x - x_lo; double b = state->b[index]; double c = state->c[index]; double d = state->d[index]; *dydx = b + delx * (2.0 * c + 3.0 * d * delx); return GSL_SUCCESS; } } static int akima_eval_deriv2 (const void * vstate, const double x_array[], const double y_array[], size_t size, double x, gsl_interp_accel * a, double *y_pp) { const akima_state_t *state = (const akima_state_t *) vstate; size_t index; // DISCARD_POINTER(y_array); /* prevent warning about unused parameter */ if (a != 0) { index = gsl_interp_accel_find (a, x_array, size, x); } else { index = gsl_interp_bsearch (x_array, x, 0, size - 1); } /* evaluate */ { const double x_lo = x_array[index]; const double delx = x - x_lo; const double c = state->c[index]; const double d = state->d[index]; *y_pp = 2.0 * c + 6.0 * d * delx; return GSL_SUCCESS; } } static int akima_eval_integ (const void * vstate, const double x_array[], const double y_array[], size_t size, gsl_interp_accel * acc, double a, double b, double * result) { const akima_state_t *state = (const akima_state_t *) vstate; size_t i, index_a, index_b; if (acc != 0) { index_a = gsl_interp_accel_find (acc, x_array, size, a); index_b = gsl_interp_accel_find (acc, x_array, size, b); } else { index_a = gsl_interp_bsearch (x_array, a, 0, size - 1); index_b = gsl_interp_bsearch (x_array, b, 0, size - 1); } *result = 0.0; /* interior intervals */ for(i=index_a; i<=index_b; i++) { const double x_hi = x_array[i + 1]; const double x_lo = x_array[i]; const double y_lo = y_array[i]; const double dx = x_hi - x_lo; if(dx != 0.0) { if (i == index_a || i == index_b) { double x1 = (i == index_a) ? a : x_lo; double x2 = (i == index_b) ? b : x_hi; *result += integ_eval (y_lo, state->b[i], state->c[i], state->d[i], x_lo, x1, x2); } else { *result += dx * (y_lo + dx*(0.5*state->b[i] + dx*(state->c[i]/3.0 + 0.25*state->d[i]*dx))); } } else { *result = 0.0; return GSL_FAILURE; } } return GSL_SUCCESS; } static const gsl_interp_type akima_type = { "akima", 5, &akima_alloc, &akima_init, &akima_eval, &akima_eval_deriv, &akima_eval_deriv2, &akima_eval_integ, &akima_free }; const gsl_interp_type * gsl_interp_akima = &akima_type; /////////////////////////////////////////////////////////////////// static int linear_init (void * vstate, const double x_array[], const double y_array[], size_t size) { return GSL_SUCCESS; } static int linear_eval (const void * vstate, const double x_array[], const double y_array[], size_t size, double x, gsl_interp_accel * a, double *y) { double x_lo, x_hi; double y_lo, y_hi; double dx; size_t index; if (a != 0) { index = gsl_interp_accel_find (a, x_array, size, x); } else { index = gsl_interp_bsearch (x_array, x, 0, size - 1); } /* evaluate */ x_lo = x_array[index]; x_hi = x_array[index + 1]; y_lo = y_array[index]; y_hi = y_array[index + 1]; dx = x_hi - x_lo; if (dx > 0.0) { *y = y_lo + (x - x_lo) / dx * (y_hi - y_lo); return GSL_SUCCESS; } else { *y = 0.0; return GSL_EINVAL; } } static int linear_eval_deriv (const void * vstate, const double x_array[], const double y_array[], size_t size, double x, gsl_interp_accel * a, double *dydx) { double x_lo, x_hi; double y_lo, y_hi; double dx; double dy; size_t index; if (a != 0) { index = gsl_interp_accel_find (a, x_array, size, x); } else { index = gsl_interp_bsearch (x_array, x, 0, size - 1); } /* evaluate */ x_lo = x_array[index]; x_hi = x_array[index + 1]; y_lo = y_array[index]; y_hi = y_array[index + 1]; dx = x_hi - x_lo; dy = y_hi - y_lo; if (dx > 0.0) { *dydx = dy / dx;; return GSL_SUCCESS; } else { *dydx = 0.0; return GSL_EINVAL; } } static int linear_eval_deriv2 (const void * vstate, const double x_array[], const double y_array[], size_t size, double x, gsl_interp_accel * a, double *y_pp) { *y_pp = 0.0; return GSL_SUCCESS; } static int linear_eval_integ (const void * vstate, const double x_array[], const double y_array[], size_t size, gsl_interp_accel * acc, double a, double b, double * result) { size_t i, index_a, index_b; if (acc != 0) { index_a = gsl_interp_accel_find (acc, x_array, size, a); index_b = gsl_interp_accel_find (acc, x_array, size, b); } else { index_a = gsl_interp_bsearch (x_array, a, 0, size - 1); index_b = gsl_interp_bsearch (x_array, b, 0, size - 1); } /* endpoints span more than one interval */ *result = 0.0; /* interior intervals */ for(i=index_a; i<=index_b; i++) { const double x_hi = x_array[i + 1]; const double x_lo = x_array[i]; const double y_lo = y_array[i]; const double y_hi = y_array[i + 1]; const double dx = x_hi - x_lo; if(dx != 0.0) { if (i == index_a || i == index_b) { double x1 = (i == index_a) ? a : x_lo; double x2 = (i == index_b) ? b : x_hi; const double D = (y_hi-y_lo)/dx; *result += (x2-x1) * (y_lo + 0.5*D*((x2-x_lo)+(x1-x_lo))); } else { *result += 0.5 * dx * (y_lo + y_hi); } } } return GSL_SUCCESS; } static const gsl_interp_type linear_type = { "linear", 2, NULL, /* alloc, not applicable */ &linear_init, &linear_eval, &linear_eval_deriv, &linear_eval_deriv2, &linear_eval_integ, NULL, /* free, not applicable */ }; const gsl_interp_type * gsl_interp_linear = &linear_type; /////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////// odin-1.8.5/Makefile.am0000644000175000017500000000566511455553545011463 00000000000000SUBDIRS = tjutils odinpara odinseq odinqt odindata odin pulsar geoedit miview odinreco cmdline-utils sequences samples coils docs replacements EXTRA_DIST = 00odin.h odin.doxygen odin.nsi install.win install.macos TESTS = cmdline-utils/odintestsuite test: install $(TESTPREFIXCMD) ${prefix}/bin/odintestsuite $(MAKE) -C sequences test $(MAKE) -C odinreco test $(MAKE) -C docs/tutorials test manual: all $(PACKAGE).doxygen $(MAKE) -C cmdline-utils manual $(MAKE) -C miview manual $(MAKE) -C odinreco manual doxygen $(PACKAGE).doxygen release: test ! # Please make sure that you have done the following before continuing test ! # - updated versions in configure.in test ! # - updated ChangeLog test ! # - executed svn copy https://od1n.svn.sourceforge.net/svnroot/od1n/trunk/odin https://od1n.svn.sourceforge.net/svnroot/od1n/tags/release_x_y_z -m "Release message" test ! # Press to continue read DUMMY $(MAKE) dist PLATFORMS=StandAlone test ! ########### Generating source dist ############### rm -f */*.1 rm -rf $(PACKAGE)-homepage mkdir -p $(PACKAGE)-homepage rm -rf $(PACKAGE)-upload mkdir -p $(PACKAGE)-upload cp $(PACKAGE)-$(VERSION).tar.gz $(PACKAGE)-upload test ! ########### Generating manual #################### $(MAKE) manual mv manual $(PACKAGE)-homepage test ! ########### Generating tutorial ################## $(MAKE) -C docs/tutorials main.pdf mv docs/tutorials/main.pdf $(PACKAGE)-homepage/odintut.pdf test ! ########### Generating homepage ################## rm -f docs/homepage/*.html $(MAKE) -C docs/homepage homepage cp docs/homepage/*.html docs/homepage/*.jpg docs/homepage/*.png ChangeLog $(PACKAGE)-homepage convert -resize 16x16 docs/homepage/favicon.png $(PACKAGE)-homepage/favicon.ico admin/sitemap.sh $(PACKAGE)-homepage http://od1n.sourceforge.net test ! ########### Success ! ############################ test ! # test ! # Copy content of directory $(PACKAGE)-homepage to wodan,od1n@web.sourceforge.net:/home/groups/o/od/od1n/htdocs/ (via scp) # test ! # Copy content of directory $(PACKAGE)-upload to wodan@frs.sourceforge.net:uploads (via sftp) test ! # Upload content of directory $(PACKAGE)-upload via webinterface test ! # install-data-local: for platform in $(PLATFORMS) ; 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dist-hook: mkdir -p $(distdir)/platforms for platform in $(PLATFORMS) ; do \ cp -r $(srcdir)/platforms/$$platform $(distdir)/platforms ; \ done rm -rf `find $(distdir)/platforms -name .svn` distclean-local: -rm -rf manual $(PACKAGE)-$(VERSION).tar.gz svnclean: distclean for entry in $$(svn status | grep ^? | grep -v platforms/ | awk '{print $$2}') ; do \ echo "Removing non-SVN file/directory $$entry"; \ rm -rf $$entry; \ done # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/00odin.h0000644000175000017500000007126011734622163010654 00000000000000/** * \page odinseq_doc ODIN sequence modelling framework (odinseq library) * * This page describes the design guidelines of the module \ref odinseq * * \section odinseq_intro Introduction * This is a framework for NMR sequence design. It follows * a hardware independent, object oriented design approach to * reach a high degree of flexibilty and portability while * keeping the amount of source code to a minimum. * * \section motivation Motivation * An NMR sequence typically consists of different components * like pulses, gradient shapes and so on. From the physicists * point of view these objects and their relations can be exclusively * described by physical parameters (pulse duration, gradient stength, * echo time, ...). This description does not depend on the current * hardware the sequence is used on. * Furthermore, at this level of abstraction these objects can * be grouped together in different ways to form a variety of NMR * sequences. * * Unfortunately most programming enviroments of contemporary * spectrometers/scanners do not reflect this modularity. A sequence * written in the native enviroment of the machine often contains * a vast amount of redundant source code repeated in every method * and a difficult low-level interface. * Furthermore each manufacturer follows his own approach to write * unportable sequences, which may be a disadvantage for scientists * working on different spectrometers. * * This is the point where this framework could come into play. * It offers a hardware independent programming interface to a C++ * class library. This library then performs all the low-level * operations that are required for playing out the sequence. * * \section design Design Principles * The class hierachy (\ref odinseq) is designed according to the following guidelines: * * \subsection design_hierachy Class Hierachy * Each type of component in an NMR sequence (RF-pulse, gradient pulse, ...) * is identified with a class in the C++ programming language. * The components are ordered in a 'family tree' where each child * is a specialisation of its parent. For instance a constant * gradient (SeqGradConst) on one of the gradient channels has a parent * (SeqGradChan) that represents arbitrarily shaped gradient waveforms. * This inheritance graph is modelled by the inheritence mechanisms for * classes in C++. This approach minimises the amount of code that perform * certain operations on the objects, e.g. a function for * rotating the SeqGradChan class in the spatial domain (set_gradrotmatrix()) * is automatically available for all derived classes. * * \subsection design_seqobj Sequence Objects * In this manual the term 'sequence objects' refers to all components * of an NMR experiment that control the timing of the sequence. * For example RF-pulses, delays and acquisition windows are all specialised * sequence objects. * An (abstract) base class SeqObjBase exists for all sequence objects. * These objects then have a common * interface, e.g. they know how to write themselve to the pulse/gradient * program. * * \subsection design_seqgradobj Gradient Objects * The term 'gradient objects' refers to all components of an NMR sequence * that control the timecourse of the gradient fields, e.g. constant gradients, * phase encoding gradients, gradient waveforms. * An (abstract) base class SeqGradInterface exists for all gradient objects * in the sequence. These objects * then have a common interface, i.e. they know how to write themselve to the gradient * program or how to be combined among themselves. * * \subsection design_seqgrouping Grouping of Sequence Objects * Sequence objects can be grouped together by ordering them along * the time axis. The result is then a new, more complex sequence object. * In analogy to notations commonly used in scientific papers, this * is done by using the \p + operator. For instance two RF-pulses * represented by two objects called \p alpha and \p beta can build * a new sequence object \verbatim alpha + beta \endverbatim which results in a sequence * object which will play out the first pulse and then the second pulse. * * \subsection design_gradgrouping Grouping of Gradient Objects * Gradient objects can also be serialised by using the \p + operator. Furthermore * the \p / operator tries to build a new object that plays out the two operands * in parallel if the timing is apropriate. For example two gradient pulses * \p gp1 and \p gp2, one for the read and another for the phase channel, can be * played out in parallel by using the combination \verbatim gp1 / gp2 \endverbatim * * \subsection design_seqparallel Combining Sequence and Gradient objects * Sequence and gradient objects can also be serialised by the \p + operator. To * play out a gradient and a sequence object in parallel, the \p / operator can be * used. For example let \p alpha be an excitation pulse and \p constgrad a constant * gradient, then the combination \verbatim alpha / constgrad \endverbatim would * give a slice selective pulse. * * \subsection design_seqcontainer Container for Sequence Objects * The sequence object SeqObjList can be used as a container for other * sequence objects. That is, each SeqObjList can have its own sub-sequence that * consists of other sequence components. * If a certain operation is applied to a SeqObjList object, the operation * will also be applied to all elements of the sub-sequence. For example: * \verbatim SeqPuls alpha; // excitation pulse SeqGradConstPulse constgrad; // constant gradient SeqObjList objlist = alpha + constgrad; // alpha is played out after constgrad \endverbatim * Calling the member function * \verbatim objlist.get_duration() \endverbatim would then return the sum of the durations of \p alpha and \p constgrad. * * \subsection design_seqgradcontainer Container for Gradient Objects * The gradient object SeqGradChanList can be used as a container for other * gradient objects which share the same gradient channel. That is, each SeqGradChanList * can have its own sub-sequence that consists of other gradient components. * These sub-objects are then played out subsequently. * This analogous to the above described sequence container. * * \subsection design_append Appending to Container Objects * New objects can be added to the container class SeqObjList * by using the \p += operator. * * \subsection design_loops Sequence Loops ans Vectors * Loops are special sequence containers. They are used to repeat * a certain part of the sequence. Within ODIN, the class SeqObjLoop * accomplishes this task. Two kind of loops are possible when using * this class: Pure repitition loops and vector loops. Repitition * loops simply repeat the specified part of the sequence without * altering it. Let \p loop be of type SeqObjLoop, then heir syntax is: * \verbatim loop ( kernel ) [ n ]; \endverbatim * This statement will return a sequence object that repeats the sequence * object \p kernel \p n times, where \p n is an integer number. * * Vector loops also repeat a specified part of the sequence. Furthermore * they increment the value of a sequence vector each time it is played out. * Sequence vectors are for example phase encoding gradients or pulses * with a frequency list. All sequence vectors share the same base class * SeqVector. Let \p loop be of type SeqObjLoop, then the syntax for vector loops is: * \verbatim loop ( kernel ) [ vector1 ] [ vector2 ] ...; \endverbatim * This statement will return a sequence object that repeats the sequence * object \p kernel while incrementing the values of the attached sequence * vectors \p vector1, \p vector2, ... * The vectors must contain the same number of values. The loop is then * repeated this number of times. * * \subsection design_vectors Specialialized Sequence Vectors * - Gradient pulses with different gradient strengths for phase encoding or diffusion weighting (SeqGradVectorPulse, SeqGradPhaseEnc). * - Sequence objects that drive the transmitter (RF pulses) or receiver (acquisition windows) * contain two vector objects for frequency and phase switching to be used for multislice * experiments or phase cycling (SeqFreqChan and SeqPhaseListVector). * - Delay objects with a variable duration, which is changed for each iteration (SeqDelayVector). * - A list of user-defined rotation matrices that can be attached to gradient-related objects in order * to alter their direction subsequently (SeqRotMatrixVector). * - A container object that holds a list of other sequence objects which are played out * sequentially for each repetition (SeqObjVector). * * * \section units Physical Units * ODIN is consistent corncerning the physical units. That is, everywhere in the library the * following units and their combinations are used: * - [mT] for magnetic field strength * - [mm] as the spatial unit * - [ms] for durations * * This system has shown to be of practical value for NMR because the numbers are then * in a reasonable range. * For example the gradient strength is then given in mT/mm and the frequency is given in * 1/ms=kHz. * The only exception is the angular unit which is treated internally as rad but can be * specified at the interface functions in degree for phaselists and flipangles. * * * * \section coding Coding Standards * \subsection coding_class Building new classes * If you want to write your own class that can be plugged into the ODIN framework, * please use the following form for your class 'SeqMyClass' that is derived from * 'SeqBaseClass': * \verbatim /////////////// *.h stuff: ////////////////////////////// class SeqMyClass : public SeqBaseClass { public: SeqMyClass(const STD_string& object_label, float parameter1, ... ); SeqMyClass(const STD_string& object_label = "unnamedSeqMyClass" ); SeqMyClass(const SeqMyClass& sct); SeqMyClass& operator = (const SeqMyClass& sct); ~SeqMyClass(); private: float parameter1; }; /////////////// *.cpp stuff: //////////////////////////// SeqMyClass::SeqMyClass(const STD_string& object_label, float parameter1_value, ... ) : SeqBaseClass(object_label) { parameter1=parameter1_value; ... } SeqMyClass::SeqMyClass(const STD_string& object_label ) : SeqBaseClass(object_label) { parameter1=0.0; ... } SeqMyClass::SeqMyClass(const SeqMyClass& sct) { SeqMyClass::operator = (sct); } SeqMyClass& SeqMyClass::operator = (const SeqMyClass& sct) { SeqBaseClass::operator = (sct); parameter1=sct.parameter1; ... return *this; } SeqMyClass::~SeqMyClass() { } \endverbatim * Following this standard prevents the base classes from getting confused by not * correctly initialising or copying them. * * \subsection coding_stl Using the C++ standard library * Unfortunately, on some systems the stanard C++ library seems to be either broken * or absent. For these platforms, ODIN contains its own implementation that is a subset of * the original library. * To use the same source code on different platforms, classes of the standard * library are used together with the prefix STD_, e.g. STD_list * instead of std::list. These macros will be replaced by the appropriate classes on * each platform. * * \subsection coding_debug Debugging/Tracing * To generate debugging and tracing output, please use the Log template class instead * of using streams. * Instances of that class offer a stream to log trace messages via the ODINLOG macro: * \verbatim int MyClass::myfunction() { Log odinlog("MyClass","myfunction"); ODINLOG(odinlog,significantDebug) << "Hello World" << STD_endl; } \endverbatim * Which will result in the following output: * \verbatim Seq | MyClass.myfunction : START Seq | MyClass.myfunction : Hello World Seq | MyClass.myfunction : END \endverbatim * It can generate debugging output at different levels of verbosity * and the output is redirected to the native logging channel (console, log file) of * the current platform. Furthermore, it can be completely removed from the executable * for release compilations in a safe way without changing the source code. */ /** * @defgroup odinseq Classes for sequence design (odinseq library) * * \ref odinseq_doc * */ /** * * @defgroup odinseq_internals Internal Classes for sequence design (odinseq library) * * PLEASE DO NOT USE THESE CLASSES DIRECTLY WHEN WRITING SEQUENCES! */ /////////////////////////////////////////////////////////////////////////////////////// /** * \page tjutils_doc Basic data types, vectors and arrays used by ODIN (tjutils library) * * * \section tjutils_intro Introduction * Well known data types, such as integers, floating point numbers, complex numbers, strings, * vectors (1-dimensional) and arrays (multi-dimensional) are used in ODIN. * For all types discussed in this section, there exists a corresponding JCAMP-DX type (\ref jcampdx). * This JCAMPD-DX type is prefixed by 'JDX' and then the data type, e.g. 'STD_string' has a JCAMP-DX * counterpart 'JDXstring' with the same functionality. * In addition, JCAMP-DX parameters can be assigned a label, grouped together with other JCAMP-DX parameters, etc. * * \section vectors Vectors * Vectors are implemented by the tjvector template class which is * derived from the STL vector class. Its interface is therefore * equivalent to that of the std::vector class. * In addition, some useful functions are added. * Some predefined vector classes are created by using the tjvector * template class: * - fvector: vector of float numbers * - dvector: vector of double precision float numbers * - ivector: vector of int numbers * - svector: vector of strings (STD_string objects) * - cvector: vector of complex numbers (STD_complex objects) * * \section arrays Arrays * Multidimensional arrays are covered by the tjarray template class. * It is derived from the tjvector class to store the data. In addition, * the information about the dimensionality and extent in each dimension * is stored separately in the class by an ndim object. * Some predefined array classes and their corresponding JCAMP-DX type are * created by using the tjarray template class: * - farray / JDXfloatArr: array of float numbers * - darray / JDXdoubleArr: array of double precision float numbers * - iarray / JDXintArr: array of int numbers * - sarray / JDXstringArr: array of strings (STD_string objects) * - carray / JDXcomplexArr: array of complex numbers (STD_complex objects) * * Some examples on how to use these arrays: * \verbatim farray fa1(3,3); // creates a 2-dimensional 3x3 array fa1(0,1)=5.7; // assigns 5.7 to the second element in the firs row farray fa2(3,3); // creates another 2-dimensional 3x3 array fa1+fa2; // returns the element-wise sum of the two arrays fa1.redim(1,2,3); // resizes fa1 to a 3-dimensional 1x2x3 array \endverbatim * Please see the class documention for a complete reference. * */ /** * @defgroup tjutils Classes for basic data types and vectors/arrays (tjutils library) * * \ref tjutils_doc * */ /////////////////////////////////////////////////////////////////////////////////////// /** * @defgroup jcampdx JCAMP-DX implementation (odinpara library) * * This page describes the design guidelines of the module \ref jcampdx * * The following framework can be used to deal with single parameters of different * type (int,float,string,...) and multidimensional arrays that are build from these * base types. It is possible to build blocks of parameter, i.e. parameter lists, * that can be written/loaded to/from disk in an easily editable ASCII format. * The file format is designed roughly according to the JCAMP-DX [1,2] standard, but * its main aim was to be compatible with the PARX[3] file format. * * * A very simple examples on how to use this module: * \verbatim JDXint mynumber(23,"mynumber"); // Create an integer parameter with initial value 23 mynumber+=42; // JDXint can be used just as a native int for arithmetics JcampDxBlock block; // A block (list) of parameters block.append(mynumber); // Append the parameter to the block block.write("block.jdx"); // Write block and its parameters to file 'block.jdx' block.load("block.jdx"); // Load block and its parameters from file 'block.jdx' \endverbatim * Please see the class documention for a complete reference. * * * References: * -# JCAMP-DX: A Standard Form of Exchange of Infrared Spectra in Computer * Readable Form, McDONALD, R.S., WILKS, P.A., Apllied Spectroscopy, * Vol.42, No.1, 1988 * -# JCAMP-DX for NMR, DAVIES, A.N., LAMPEN, P., Apllied Spectroscopy, * Vol.47, No.8, 1993 * -# PARX is a preprocessor/compiler framework to interactively modify parameters * that can also be embedded into C-code. * It is part of the Bruker software 'Paravision' that serves as an user interface * for their medical MR-scanners. * * *@author Thies H. Jochimsen */ /////////////////////////////////////////////////////////////////////////////////////// /** * @defgroup odinpara MR Parameters (odinpara library) * * This page describes the design guidelines of the module \ref odinpara_doc * * *@author Thies H. Jochimsen */ /** * \page odinpara_doc Protcol classes in ODIN (odinpara library) * * This module/library contains a set of classes which describe * different aspects of an MR measurement, i.e. the measurement protocol: * - System: The MR system used * - Geometry: The geometry of the scan * - SeqPars: Common sequence parameters * - Study: Information about the current study (patient data, etc.) * - RecoPars: Parameters for automatic reconstruction * * The class Protocol combines the first four of the above in a single * class for convenient access. * * Within sequence classes, instances of these classes are * accessible via the pointers systemInfo, geometryInfo, * commonPars, studyInfo and recoInfo */ /////////////////////////////////////////////////////////////////////////////////////// /** * \page odindata_doc ODIN data processing framework (odindata library) * * This page describes the design guidelines of the module \ref odindata * * \section blitz4nmr Blitz++ for NMR * The Blitz++ library is great for numerical calculations, but it lacks * some functionality that is crucial when using it together with NMR data: * - Convenient input/output of medical image data * - Numerical routines essential for NMR (FFT, gridding, fitting, ...) * - Associating large data files on disk with arrays in memory * * For this reason, ODIN contains two classes that help dealing with these tasks: * - Data: A template class derived from the Blitz++ Array class that * has the ability to be associated with a raw data file for read and * write access. This is done by using the mmap function so that no extra * memory is allocated on contstruction. Instead, the task of reading/writing * is handled transparently by the operating system. Any changes made * to the array in memory are also visible in the file on disk. With this * mechanism, arrays that are larger than the available RAM can be handled * without extra effort. * In addition, member functions Data::autoread() and Data::autowrite() are available to load/store * the data in different file formats using the FileIO module (\ref fileio_doc ). * * - ComplexData: A template class with a * fixed storage type of complex numbers. It contains useful functions * to deal with NMR data (FFT,...). On construction, it can be * associated with raw data on disk (16bit, 32bit, float) and blocks * of the file can be loaded subsequently into memory for further * processing. * * * \section numerics Common Numerical Operations * * In order to offer a framework for other numerical calculations, * the following functions/classes are available within ODIN: * * \subsection numerics_gridding Gridding * Regridding an array from one Cartesian grid to another can be * done using the Data::congrid() member function. * In addition, the functor Gridding can be used to data from a * non-Cartesian grid to a Cartesian grid. * * \subsection numerics_transform Coordinate Transformation * Transforming an array to a new coordinate system by * rotation, scaling and shifting can be done by using * the CoordTransformation functor. * * \subsection numerics_fft Fourier Transform * FFT of a whole complex data set can be calculated by the ComplexData::fft() member function. * If the FFT has to be applied only for certain dimensions, use ComplexData::partial_fft() * * \subsection numerics_linalg Linear Algebra * The functions solve_linear(), pseudo_inverse() and eigenvalues() will solve a sets of linear equations, * calculate the pseudo inverse and eigenvalues, respectively. * * \subsection numerics_fitting Non-Linear Function Fitting * Fitting of functions is accomplished by the two classes * ModelFunction and FunctionFit. The former is * used as a base class to specify the modelling function * by implementing its virtual functions. * The latter is used to do the actual fitting and to * store temporary data of the fit. * * \subsection numerics_linfit Linear Regression * The class LinearFunction can be used for linear fitting. * * \subsection numerics_polfit Polynomial Fit * The function polyniomial_fit() provides pixel-wise fitting * of polynomials using the values of neighbouring pixels. * * \subsection numerics_integration Integration of Functions * Integration of one-dimensional functions can be achieved * by the two classes Integrand and FunctionIntegral. * The former is used as a base class to specify the function * by implementing a virtual functions. * The latter is used to do the actual integration and to * store temporary data. * * \subsection numerics_statistics Basic Statistics * Simple statistics (mean, standard deviation) can be * calculated by the statistics() function. * * \subsection numerics_correlation Correlation Analysis * Correlation of two vectors can be calculated by * the correlation() function. * * \subsection numerics_fileio Convenient File Input/Output * The functions inside FileIO (\ref fileio_doc ) are a convenient way ro * read/write 4-dim Arrays, a variety of formats common * for medical image are supported. * * * */ /////////////////////////////////////////////////////////////////////////////////////// /** * \page fileio_doc Input/Output of medical image data (odindata library) * * \section fileio A unified approach for handling medical image data * This page describes the functionality of the FileIO module. * * \subsection fileio_intro Introduction * When working with different systems for generating and processing of medical images very quickly one problem arises: These systems use different data formats and the available export features of any toolkit mostly support only a subset of the needed formats. The following report describes an approach to design a unified and extensible interface to medical image data. Implemented in an function library this interface can be used to efficently enable custom-built applications to read and write medical image data. * * \subsection fileio_pdmap The Protocol-Data-Map * Unified access to different data formats implies a common interface for accessing this data. * Thus a data structure, which provides a superset of all features of all data formats which shall be supported. * Every medical image consists of image data of any type and metadata related to this image data. This data pair will be dicussed in the following. * * The metadata * which belong to an image usually describe the technical and administrative characteristics of an image. * They consist of some required information like image dimension and used data type, some common information like the age of the subject or the date the image was taken and some optional information like used field strength for MR data. These parameters are either in a header inside the imagefile or in a separate header file. The required and the common parameter are very usefull to distinguish images. They, and with them the whole metadataset, can be used as a unique key to reference this image. In the following this paremeter set will be called the Protocol. * * Some imagefile formats are only capable of storing at least two-dimensional images. In this case N-dimensional datasets are often stored by using several two-dimensional images. The protocols of these images differ only in the remaining coordinates (which needs to be specified in this case). * The system must recognize this and combine them into one N-dimensional dataset when reading. And the inverse approach appiles to writing N-dimensional data in a fileformat which does not support that many dimensions. * * The pair of protocol and dataset can be used as a universal interface to access image data. * While the protocol offers all information to interpret the data, the dataset serves as a coordinate-based interface to the data for reading and writing. * * Multiple protocol-dataset-pairs can efficiently be stored in a associative container where the protocol is the key which maps to the dataset. This enables the system to handle multiple datasets. A particular dataset can always be referenced by its protocol and a list of the available datasets can be obtained by iterating through this protocol-dataset-map (FileIO::ProtocolDataMap). * Also, when reading multiple low-dimensional image files which are part of an high-dimensional image, they all will have the same protocol and thus will be automaticly sorted into one high-dimensional dataset referenced by this protocol. * * \subsection fileio_formats read and write different file formats * To guarantee the flexibility of the system, the input from and the output to files is done via plugins (classes derived from FileFormat) which use the described protocol-dataset-map as front end. * These plugins are gathered at the initialisation and held in a map with the file suffixes they support as key. If available, they are also referenced by a regular expression to detect the supported format directly from that data. * * The selection of the right plugin is done in two ways. If a fileformat is directly requested, the corresponding plugin is used. If the format is not selected explicitly, the system at first tries to get the suffix of the file requested for read or write and guesses the format. * * Many medical image formats exist in several different dialects or have optional extensions which makes it necessary to fine tune them. Thus every plugin can bring a set of additional parameters which than can be used by the client to modify their behavior. * *@author Enrico Reimer */ /** * @defgroup odindata Classes of the ODIN data processing framework (odindata library) * * \ref odindata_doc * \ref fileio_doc * */ /////////////////////////////////////////////////////////////////////////////////////// /** * @defgroup odinreco The reconstruction framework (odinreco) * * \ref odinreco_doc * */ /////////////////////////////////////////////////////////////////////////////////////// /** * @defgroup odinreco_steps Steps(functors) of the reconstruction framework (odinreco) * * These steps(functors) can be used within the \ref odinreco_doc * */ /////////////////////////////////////////////////////////////////////////////////////// /** * \page cmdline_utils Command-line utilities * * miconv: \ref miconv * * micalc: \ref micalc * * miview: \ref miview * * odinreco: \ref odinreco_usage * * gencoil: \ref gencoil * * genmakefile: \ref genmakefile * * gensample: \ref gensample * * swab: \ref swab */ /////////////////////////////////////////////////////////////////////////////////////// /*! \mainpage ODIN Reference Manual * * * \section quick_start Quick Start * * I want to see documentation about ... * * \ref odin_doc * * \ref cmdline_utils * * \ref odinseq_doc * * \ref odinseq * * \ref odindata_doc * * \ref fileio_doc * * \ref odinreco_doc * * \ref odinreco_steps * * \ref tjutils_doc * * \ref odinpara_doc * * *@author Thies H. Jochimsen */ odin-1.8.5/miview/0000755000175000017500000000000011735135552010766 500000000000000odin-1.8.5/miview/miviewview.cpp0000644000175000017500000004450211734622163013610 00000000000000#include "miviewview.h" #include #include #include #include #include #include #include // for showProtocol #include const char* MiViewComp::get_compName() {return "MiView";} LOGGROUNDWORK(MiViewComp) ///////////////////////////////////////////////////////////////// struct FileData { Data data; Protocol prot; statisticResult stat; }; ///////////////////////////////////////////////////////////////// struct SelectionData { Data roi; // 4D to be suitable for autowrite Data profile; }; ///////////////////////////////////////////////////////////////// MiViewOpts::MiViewOpts() { color=false; color.set_cmdline_option("color").set_description("Use color map to display values"); append_member(color,"color"); contrast=0.0; contrast.set_minmaxval(-100, 100); contrast.set_cmdline_option("contrast").set_description("Relative contrast of display"); append_member(contrast,"Contrast"); brightness=0.0; brightness.set_minmaxval(-100, 100); brightness.set_cmdline_option("bright").set_description("Relative brightness of display"); append_member(brightness,"Brightness"); valfile.set_cmdline_option("val").set_description("Save value of ROI/point selection to this file"); append_member(valfile,"valfile"); recfile.set_cmdline_option("rec").set_description("Record clicked coordinates and values into this file"); append_member(recfile,"recfile"); blowup=1; blowup.set_cmdline_option("blowup").set_description("Enlarge display size by this factor"); append_member(blowup,"blowup"); low.set_cmdline_option("low").set_description("Lower windowing boundary: This value will appear black in display"); append_member(low,"low"); upp.set_cmdline_option("upp").set_description("Upper windowing boundary: This value will appear white in display"); append_member(upp,"upp"); dump.set_cmdline_option("dump").set_description("Dump all images as bitmap(bmp) files and exit, use the given filename prefix"); append_member(dump,"dump"); mapfile.set_cmdline_option("map").set_description("Load overlay map (colored voxels superimposed on image) from this file"); append_member(mapfile,"mapfile"); maplow=0.0; maplow.set_cmdline_option("maplow").set_description("Lower windowing boundary for overlay map"); append_member(maplow,"maplow"); mapupp=0.0; mapupp.set_cmdline_option("mapupp").set_description("Upper windowing boundary for overlay map"); append_member(mapupp,"mapupp"); maprect=0.6; maprect.set_cmdline_option("maprect").set_description("Relative size of rectangles which represent voxels of the overlay map"); append_member(maprect,"maprect"); maplegendexport.set_cmdline_option("maplegend").set_description("Export map legend as bitmap to this file"); append_member(maplegendexport,"maplegendexport"); noscale=false; noscale.set_cmdline_option("noscale").set_description("Disable scale in 2D/3D display"); append_member(noscale,"noscale"); } ///////////////////////////////////////////////////////////////// void show_in_xmgr(const Data& data) { STD_string tmpfile="/tmp/miview"+itos(int(current_time_s()))+".asc"; data.write_asc_file(tmpfile); STD_list execs2try; execs2try.push_back("xmgrace"); execs2try.push_back("xmgr"); for(STD_list::const_iterator it=execs2try.begin(); it!=execs2try.end(); ++it) { if(!system(STD_string((*it)+" "+tmpfile+" && rm "+tmpfile+" &").c_str())) break; } } ///////////////////////////////////////////////////////////////// void MiViewView::usage() { Protocol prot; MiViewOpts mopts; FileReadOpts ropts; FilterFactory filter; MiViewFmri fmri; set_defaults(prot); STD_cout << "miview: Viewer for medical image files" << STD_endl; STD_cout << " File formats are automatically identified by their file extension." << STD_endl; STD_cout << "Usage: miview [ options ] " << STD_endl; STD_cout << "Global options:" << STD_endl; STD_cout << mopts.get_cmdline_usage("\t"); STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "fMRI options (Give at least -design and -fmri to activate):" << STD_endl; STD_cout << fmri.get_cmdline_usage("\t"); STD_cout << "File read options:" << STD_endl; STD_cout << prot.get_cmdline_usage("\t"); STD_cout << ropts.get_cmdline_usage("\t"); STD_cout << "Filters:" << STD_endl; STD_cout << filter.get_cmdline_usage("\t"); STD_cout << "Supported file extensions(formats):" << STD_endl; STD_cout << FileIO::autoformats_str("\t") << STD_endl; } void MiViewView::set_defaults(Protocol& prot) { prot.seqpars.set_MatrixSize(readDirection,1); prot.seqpars.set_MatrixSize(phaseDirection,1); prot.seqpars.set_MatrixSize(sliceDirection,1); prot.set_parmode(noedit); } MiViewView::MiViewView(QWidget *parent) : QWidget(parent) { Log odinlog("MiViewView","MiViewView"); char optval[ODIN_MAXCHAR]; file=new FileData(); set_defaults(file->prot); file->prot.parse_cmdline_options(GuiApplication::argc(),GuiApplication::argv()); FileReadOpts ropts; ropts.parse_cmdline_options(GuiApplication::argc(),GuiApplication::argv()); mopts.parse_cmdline_options(GuiApplication::argc(),GuiApplication::argv()); fmri.parse_cmdline_options(GuiApplication::argc(),GuiApplication::argv()); FilterChain filterchain(GuiApplication::argc(),GuiApplication::argv()); JDXfileName fname; if(getLastArgument(GuiApplication::argc(),GuiApplication::argv(),optval,ODIN_MAXCHAR)) { fname=optval; } else { usage(); exit(0); } if(fname=="") { usage(); exit(0); } ProgressDisplayConsole display; ProgressMeter progmeter(display); if(file->data.autoread(fname,ropts,&(file->prot),&progmeter)<=0) exit(-1); ODINLOG(odinlog,normalDebug) << "mem(read): " << Profiler::get_memory_usage() << STD_endl; if(!filterchain.apply(file->prot, file->data)) exit(-1); file->stat=statistics(file->data); ODINLOG(odinlog,infoLog) << "data = " << file->stat << STD_endl; has_bounds=false; lowbound=file->stat.min; uppbound=file->stat.max; if(mopts.low!="") { lowbound=atof(mopts.low.c_str()); has_bounds=true; } if(mopts.upp!="") { uppbound=atof(mopts.upp.c_str()); has_bounds=true; } if(uppbound<=lowbound) has_bounds=false; // check input ODINLOG(odinlog,normalDebug) << "lowbound/uppbound/has_bounds=" << lowbound << "/" << uppbound << "/" << has_bounds << STD_endl; guiprops_cache.pixmap.minsize=mopts.blowup*256; guiprops_cache.fixedsize=false; guiprops_cache.pixmap.autoscale=false; guiprops_cache.pixmap.color=mopts.color; guiprops_cache.pixmap.overlay_rectsize=mopts.maprect; guiprops_cache.pixmap.overlay_minval=mopts.maplow; guiprops_cache.pixmap.overlay_maxval=mopts.mapupp; has_olm=false; if(mopts.mapfile!="") { Data mapdata; if(mapdata.autoread(mopts.mapfile,ropts)>0) { Protocol protdummy; if(!filterchain.apply(protdummy, mapdata)) exit(-1); guiprops_cache.pixmap.overlay_map=mapdata; has_olm=true; // gp.pixmap.overlay_map.normalize(); } } fmriwidget=0; if(fmri.init(ropts,file->prot,filterchain)) { guiprops_cache.pixmap.overlay_map=fmri.get_overlay_map(); // must be present during construction of displaywidget guiprops_cache.pixmap.overlay_firescale=true; fmri.update(); fmri.set_label("fMRI"); fmriwidget=new JDXwidget(fmri, 1, this); connect(fmriwidget,SIGNAL(valueChanged()),this,SLOT(update())); } displaydata.redim(get_nz(),get_ny(),get_nx()); filedata2displaydata(); // will set gui_props of displaydata displaydata.set_label("Data Plot"); displaywidget=new JDXwidget(displaydata, 1, this); exportLegend(mopts.maplegendexport); // Do this after displaywidget is initialized, bur before dump. String will be checked in exportLegend() if(mopts.dump!="") { ODINLOG(odinlog,infoLog) << "Dumping images with prefix " << mopts.dump << STD_endl; displaywidget->write_pixmap(mopts.dump.c_str(), "bmp", true); exit(0); } connect(displaywidget,SIGNAL(clicked(int,int,int)), this,SLOT(slotClicked(int,int,int))); connect(displaywidget,SIGNAL(newProfile(const float*, int, bool, int)), this, SLOT(slotNewProfile(const float*, int, bool, int))); connect(displaywidget,SIGNAL(newMask(const float*, int)), this, SLOT(slotNewMask(const float*, int))); if(has_timecourse()) { repetition.set_label("Repetition"); repetition.set_minmaxval(0, get_nrep()-1); settings.append(repetition); } if(is_image_display() && !has_bounds) { settings.append(mopts.contrast); settings.append(mopts.brightness); } settingswidget=0; int n_settings=settings.numof_pars(); ODINLOG(odinlog,normalDebug) << "n_settings=" << n_settings << STD_endl; if(n_settings) { settings.set_label("Display Settings"); settingswidget=new JDXwidget(settings, 1, this); connect(settingswidget,SIGNAL(valueChanged()),this,SLOT(update())); } tcoursewidget=0; if(has_timecourse()) { GuiProps tcgp; tcgp.fixedsize=false; timecourse.set_gui_props(tcgp); timecourse.set_label("Timecourse"); timecourse.redim(get_nrep()); tcoursewidget=new JDXwidget(timecourse, 1, this); } int ncols=1; int nrows=2; if(settingswidget) ncols++; if(tcoursewidget) nrows++; grid=new GuiGridLayout( this, nrows, ncols); grid->add_widget(displaywidget, 0, 0, GuiGridLayout::Default, 2, 1); if(settingswidget) grid->add_widget(settingswidget, 0, 1); if(fmriwidget) grid->add_widget(fmriwidget, 1, 1); if(tcoursewidget) grid->add_widget(tcoursewidget, 2, 0, GuiGridLayout::Default, 1, 2); selection=new SelectionData(); selection->roi.resize(1,get_nz(),get_ny(),get_nx()); selection->roi=0.0; if(mopts.recfile!="") rmfile(mopts.recfile.c_str()); } void MiViewView::writeImage() { image_fname_cache=get_save_filename("Image File for Screen Dump", image_fname_cache.c_str(), "", this); if(image_fname_cache=="") return; STD_string format=check_and_get_format(image_fname_cache,get_possible_image_fileformats()); if(format!="") { displaywidget->write_pixmap(image_fname_cache.c_str(), format.c_str()); } } void MiViewView::writeROIs() { Log odinlog("MiViewView","writeROIs"); rois_fname_cache=get_save_filename("Data File for ROIs", rois_fname_cache.c_str(), "", this); if(rois_fname_cache=="") return; STD_string format=check_and_get_format(rois_fname_cache,FileIO::autoformats()); if(format!="") { selection->roi.autowrite(rois_fname_cache); } } void MiViewView::writeFmriClusters() { Log odinlog("MiViewView","writeFmriClusters"); clusters_fname_cache=get_save_filename("Data File for fMRI clusters", clusters_fname_cache.c_str(), "", this); if(clusters_fname_cache=="") return; STD_string format=check_and_get_format(clusters_fname_cache,FileIO::autoformats()); if(format!="") { fmri.write_overlay_map(clusters_fname_cache); /* farray olmap(fmri.get_overlay_map()); Data maskdata(1,olmap.size(0),olmap.size(1),olmap.size(2)); maskdata=0.0; for(unsigned int i=0; i0.0) maskdata(maskdata.create_index(i))=1.0; } maskdata.autowrite(clusters_fname_cache); */ } } void MiViewView::writeProfile() { profile_fname_cache=get_save_filename("ASCII File for Profile", profile_fname_cache.c_str(), "", this); if(profile_fname_cache=="") return; selection->profile.write_asc_file(profile_fname_cache); } void MiViewView::writeTimecourse() { tcourse_fname_cache=get_save_filename("ASCII File for Timecourse", tcourse_fname_cache.c_str(), "", this); if(tcourse_fname_cache=="") return; Data tcourse(timecourse); tcourse.write_asc_file(tcourse_fname_cache); } void MiViewView::exportLegend(const STD_string& filename) { Log odinlog("MiViewView","exportLegend"); if(filename=="") return; STD_string format=check_and_get_format(filename,get_possible_image_fileformats()); if(format!="") { ODINLOG(odinlog,infoLog) << "Writing legend of format " << format << " to file " << filename << STD_endl; displaywidget->write_map_legend(filename.c_str(), format.c_str()); } } void MiViewView::writeLegend() { exportLegend(get_save_filename("File for Legend", "", "", this)); } void MiViewView::selectVoxel() { JcampDxBlock block; for(int idir=(n_directions-1); idir>=0; idir--) { // display reversed in dialog pos_cache[idir].set_label(directionLabel[idir]); pos_cache[idir].set_description("Voxel index in "+STD_string(directionLabel[idir])+" direction").set_unit("pixel"); block.append(pos_cache[idir]); } new JDXwidgetDialog(block,n_directions,this,true); slotClicked(pos_cache[readDirection], pos_cache[phaseDirection], pos_cache[sliceDirection]); displaywidget->updateWidget(); } void MiViewView::showProfile() { show_in_xmgr(selection->profile); } void MiViewView::showTimecourse() { show_in_xmgr(timecourse); } void MiViewView::showProtocol() { file->prot.set_parmode(noedit); new JDXwidgetDialog(file->prot,2,this,false,true); } STD_string MiViewView::check_and_get_format(const STD_string& fname, const svector& possible_formats) { Log odinlog("MiViewView","check_and_get_format"); STD_string result; STD_string format=JDXfileName(fname).get_suffix(); for(unsigned int ifmt=0; ifmt odinlog("MiViewView","update"); filedata2displaydata(); displaywidget->updateWidget(); if(fmriwidget) fmriwidget->updateWidget(); } void MiViewView::slotClicked(int x, int y, int z) { Log odinlog("MiViewView","slotClicked"); ODINLOG(odinlog,normalDebug) << "x/y/z=" << x << "/" << y << "/" << z << STD_endl; ODINLOG(odinlog,normalDebug) << "get_nx/ny/nz()=" << get_nx() << "/" << get_ny() << "/" << get_nz() << STD_endl; if(x<0 || x>=get_nx()) return; if(y<0 || y>=get_ny()) return; if(z<0 || z>=get_nz()) return; timecourse=Data(file->data(Range::all(),z,y,x)); if(tcoursewidget) tcoursewidget->updateWidget(); float val=file->data(int(repetition),z,y,x); STD_string msg="f("; if(get_nz()>1) msg+=itos(z)+","; msg+=itos(y)+","+itos(x)+")="+ftos(val); ODINLOG(odinlog,normalDebug) << "msg=" << msg << STD_endl; setMessage(msg.c_str()); val2file(repetition,z,y,x,val); } void MiViewView::slotNewProfile(const float *data, int npts, bool horizontal, int position) { Log odinlog("MiViewView","slotNewProfile"); if(!data) return; selection->profile.resize(npts); selection->profile=Array((float*)data,npts,neverDeleteData); ODINLOG(odinlog,normalDebug) << "profile=" << selection->profile << STD_endl; STD_string msg; if(horizontal) msg="y="; else msg="x="; msg+=itos(position); setMessage(msg.c_str()); } void MiViewView::slotNewMask(const float *data, int slice) { Log odinlog("MiViewView","slotNewMask"); if(!data) return; Range all=Range::all(); Array oneslicemask((float*)data, TinyVector(get_ny(),get_nx()), neverDeleteData); if(sum(oneslicemask)<=0.0) return; selection->roi(0,slice,all,all)=oneslicemask; if(tcoursewidget) { for(int irep=0; irepdata(irep,slice,all,all),&oneslicemask); timecourse[irep]=repstats.mean; } tcoursewidget->updateWidget(); } statisticResult roistats=statistics(file->data(int(repetition),slice,all,all),&oneslicemask); STD_string msg="f(ROI)="+ftos(roistats.mean)+"+/-"+ftos(roistats.meandev); setMessage(msg.c_str()); val2file(repetition,slice,-1,-1,roistats.mean); } MiViewView::~MiViewView() { if(tcoursewidget) delete tcoursewidget; if(settingswidget) delete settingswidget; if(fmriwidget) delete fmriwidget; delete displaywidget; delete grid; delete file; delete selection; } int MiViewView::get_nx() const {return file->data.extent()(3);} int MiViewView::get_ny() const {return file->data.extent()(2);} int MiViewView::get_nz() const {return file->data.extent()(1);} int MiViewView::get_nrep() const {return file->data.extent()(0);} void MiViewView::filedata2displaydata() { Log odinlog("MiViewView","filedata2displaydata"); Range all=Range::all(); if(is_image_display()) { if(has_bounds) { displaydata=Data( (file->data(repetition,all,all,all)-lowbound)/(uppbound-lowbound) ); } else { float min=file->stat.min; float delta=file->stat.max-file->stat.min; ODINLOG(odinlog,normalDebug) << "min/max/delta=" << file->stat.min << "/" << file->stat.max << "/" << delta << STD_endl; if(delta<=0.0) {displaydata=JDXfloat(min); return;} float brightoffset=mopts.brightness/100.0-0.5; float contrfactor=pow(10.0,mopts.contrast/100.0); displaydata=Data( ((file->data(repetition,all,all,all)-min)/delta+brightoffset)*contrfactor+0.5 ); lowbound=(-1.0/(2.0*contrfactor)-brightoffset)*delta+min; uppbound=(+1.0/(2.0*contrfactor)-brightoffset)*delta+min; } if(fmri.is_valid()) { guiprops_cache.pixmap.overlay_map=fmri.get_overlay_map(); fmri.update(); } } else { displaydata=Data(file->data(repetition,all,all,all)); } ODINLOG(odinlog,normalDebug) << "lowbound/uppbound=" << lowbound << "/" << uppbound << STD_endl; if(mopts.noscale) { // this will disable scale ODINLOG(odinlog,normalDebug) << "Disabling scale" << STD_endl; guiprops_cache.scale[displayScale].minval=0.0; guiprops_cache.scale[displayScale].maxval=0.0; } else { guiprops_cache.scale[displayScale].minval=lowbound; guiprops_cache.scale[displayScale].maxval=uppbound; } displaydata.set_gui_props(guiprops_cache); } void MiViewView::val2file(int rep, int z, int y, int x, float val) const { if(mopts.valfile!="") { ::write(ftos(val),mopts.valfile); } if(mopts.recfile!="") { STD_string linestr=itos(rep)+","+itos(z)+","+itos(y)+","+itos(x)+"\t "+ftos(val)+"\n"; ::write(linestr,mopts.recfile, appendMode); } } odin-1.8.5/miview/miview_fmri.cpp0000644000175000017500000002746111734622163013737 00000000000000#include "miview_fmri.h" #include "miviewview.h" // for Log #include #include float glover_hrf(float t) { if(t<=0.0) return 0.0; const double a1=6; const double a2=12; const double b=0.9; const double c=0.35; const double d1=5.4; const double d2=10.8; return pow(t/d1,a1)*exp(-(t-d1)/b) - c * pow(t/d2,a2)*exp(-(t-d2)/b); } ///////////////////////////////////////////////////////////////// struct FmriData { unsigned int brainvoxels; Data fmri; Data mask; Data pmap; Data zmap; Data smap; Data designdata; bool has_mask; Protocol protcopy; // writable copy }; ///////////////////////////////////////////////////////////////// MiViewFmri::MiViewFmri() { valid=false; data=new FmriData(); designfile.set_parmode(hidden).set_cmdline_option("design").set_description("Load fMRI design from this file (comma or space separated)"); append_member(designfile,"designfile"); fmrifile.set_parmode(hidden).set_cmdline_option("fmri").set_description("Load fMRI data from this file"); append_member(fmrifile,"fmrifile"); maskfile.set_parmode(hidden).set_cmdline_option("fmask").set_description("fMRI mask file"); append_member(maskfile,"maskfile"); bonferr=false; bonferr.set_cmdline_option("bonferr").set_description("Use Bonferroni correction"); append_member(bonferr,"Bonferroni Correction"); designavg=0; designavg.set_parmode(hidden).set_cmdline_option("davg").set_description("Smooth the design function using a moving average filter of width N (TR)"); append_member(designavg,"Moving Average"); hrf=false; hrf.set_parmode(hidden).set_cmdline_option("hrf").set_description("Convolve design function by hemodynamic response function prior to correlation (see Glover NeuroImage 9, 416-429)"); append_member(hrf,"hrf"); corr=0.05; corr.set_cmdline_option("corr").set_description("Error probability threshold for correlation"); append_member(corr,"Error Probability"); zscore=0.0; zscore.set_cmdline_option("zscore").set_description("z-Score threshold for correlation"); append_member(zscore,"z-Score"); neighb=1; neighb.set_cmdline_option("neighb").set_description("Minimum next neighbours with significant activation"); append_member(neighb,"Min Neighbours"); sigchange.set_parmode(noedit).set_description("fMRI signal change, averaged over all significant voxels"); append_member(sigchange,"Signal Change"); zsum.set_parmode(noedit).set_description("Sum of the z-scores of all significant voxels"); append_member(zsum,"z-Sum"); zcount.set_parmode(noedit).set_description("Count of all significant voxels"); append_member(zcount,"z-Count"); zaverage.set_parmode(noedit).set_description("Average z-score of all significant voxels"); append_member(zaverage,"z-Average"); design.set_description("fMRI design vector"); append_member(design,"fMRI Design"); tcourse.set_description("average signal in activated voxels"); append_member(tcourse,"fMRI Timecourse"); GuiProps gp; gp.scale[yPlotScaleLeft]=ArrayScale("Change","%"); sigcourse.set_gui_props(gp); sigcourse.set_description("fMRI signal change time course"); append_member(sigcourse,"Relative fMRI Timecourse"); dumptcourse.set_parmode(hidden).set_cmdline_option("scourse").set_description("Dump relative fMRI signal change time course to this file"); append_member(dumptcourse,"dumptcourse"); dumpzmap.set_parmode(hidden).set_cmdline_option("zmap").set_description("Dump z-score map to this file"); append_member(dumpzmap,"dumpzmap"); dumpsmap.set_parmode(hidden).set_cmdline_option("smap").set_description("Dump map of relative fMRI signal change to this file"); append_member(dumpsmap,"dumpsmap"); } MiViewFmri::~MiViewFmri() { delete data; } bool MiViewFmri::init(const FileReadOpts& ropts, const Protocol& prot, const FilterChain& filterchain) { Log odinlog("MiViewFmri","init"); Range all=Range::all(); if(fmrifile=="") return false; ODINLOG(odinlog,infoLog) << "Loading fMRI data ..." << STD_endl; if(data->fmri.autoread(fmrifile,ropts,&(data->protcopy))<=0) { ODINLOG(odinlog,errorLog) << "Unable to load fmrifile " << fmrifile << STD_endl; return false; } if(!filterchain.apply(data->protcopy, data->fmri)) return false; // read and parse design file if(designfile=="") return false; STD_string designstr; if(::load(designstr,designfile)<0) { ODINLOG(odinlog,errorLog) << "Unable to load designfile " << designfile << STD_endl; return false; } designstr=replaceStr(designstr,","," "); svector designvecstr=tokens(designstr); int nrep=designvecstr.size(); design.resize(nrep); tcourse.resize(nrep); sigcourse.resize(nrep); data->designdata.resize(nrep); for(int i=0; iprotcopy.seqpars.get_RepetitionTime(); ODINLOG(odinlog,infoLog) << "Convolving with HRF and TR=" << tr << STD_endl; fvector designcopy(design); design=JDXfloat(0.0); for(int i=0; i0) { ODINLOG(odinlog,infoLog) << "Smoothing design function with moving average filter of width=" << designavg << "(TR)" << STD_endl; int WidthHalf = designavg / 2; fvector designcopy(design); for(int i=0; i=0) && (jdesigndata=design; Protocol maskprot(data->protcopy); // local copy for mask data->has_mask=false; if(maskfile!="") { ODINLOG(odinlog,infoLog) << "Loading fMRI mask ..." << STD_endl; if(data->mask.autoread(maskfile,ropts,&maskprot)<=0) { ODINLOG(odinlog,errorLog) << "Unable to load maskfile " << maskfile << STD_endl; return false; } if(!filterchain.apply(maskprot, data->mask)) return false; TinyVector fmrishape=data->fmri.shape(); fmrishape(0)=1; TinyVector maskshape=data->mask.shape(); maskshape(0)=1; if(fmrishape!=maskshape) { ODINLOG(odinlog,errorLog) << "Shape mismatch: fmrishape/maskshape" << fmrishape << "/" << maskshape << STD_endl; return false; } data->has_mask=true; } int nrep_data=data->fmri.extent(0); if(nrep_data!=nrep) { ODINLOG(odinlog,errorLog) << "Repetition size mismatch: " << nrep_data << "!=" << nrep << STD_endl; return false; } if(!nrep) { return false; } int nz=data->fmri.extent(1); int ny=data->fmri.extent(2); int nx=data->fmri.extent(3); data->pmap.resize(1,nz,ny,nx); data->zmap.resize(1,nz,ny,nx); data->smap.resize(1,nz,ny,nx); data->brainvoxels=0; overlay_map.redim(nz,ny,nx); toberemoved.redim(nz,ny,nx); Data onepixel(nrep); double sigthreshold=0.5*mean(data->fmri); for(int iz=0; izfmri(all,iz,iy,ix); float p=0.0; float z=0.0; float sigchange=0.0; if(mean(onepixel)>sigthreshold) { correlationResult corr=correlation(data->designdata, onepixel); if(corr.r>0.0) { // take only positivie correlation p=corr.p; z=corr.z; sigchange=fmri_eval(onepixel, data->designdata).rel_diff; } data->brainvoxels++; } data->pmap(0,iz,iy,ix)=p; data->zmap(0,iz,iy,ix)=z; data->smap(0,iz,iy,ix)=sigchange; } } } ODINLOG(odinlog,infoLog) << "Correlation analysis with " << data->brainvoxels << " voxels" << STD_endl; valid=true; return true; } const farray& MiViewFmri::get_overlay_map() const { int nz=data->pmap.extent(1); int ny=data->pmap.extent(2); int nx=data->pmap.extent(3); overlay_map=0.0; // reset // Bonferroni correction float corrthresh=corr; unsigned int total_pixels=data->brainvoxels; if(bonferr && total_pixels>0) { corrthresh=1.0-pow(1.0-corr,1.0/float(total_pixels)); } for(int iz=0; izpmap(0,iz,iy,ix); float z=data->zmap(0,iz,iy,ix); bool include=(pzscore); if(data->has_mask && data->mask(0,iz,iy,ix)<=0.0) include=false; if(include) overlay_map(iz,iy,ix)=data->zmap(0,iz,iy,ix); } } } // next-neighbour analysis if(neighb>0) { for(int iz=0; iz=0 && iyc=0 && ixc0.0) neighbours++; } } } } if(neighbours tmpmap(get_overlay_map()); return (tmpmap.autowrite(dumpzmap,FileWriteOpts(),&(data->protcopy))>=0); } void MiViewFmri::update() { Log odinlog("MiViewFmri","update"); Range all=Range::all(); int nz=data->pmap.extent(1); int ny=data->pmap.extent(2); int nx=data->pmap.extent(3); // update tcourse and z-statistic int nrep=tcourse.length(); Data tcourse_all(nrep); tcourse_all=0.0; int nvoxels=0; zsum = 0; tcourse_all=0.0; for(int iz=0; iz0.0) { tcourse_all(all)+=data->fmri(all,iz,iy,ix); zsum += overlay_map(iz,iy,ix); nvoxels++; } } } } zcount = nvoxels; float zavg = secureDivision(zsum,zcount); // calculate stddev of zaverage float zavgerr = 0.0; for(int iz=0; iz0.0) { zavgerr += pow(overlay_map(iz,iy,ix) - zavg,2); } } } } zavgerr = sqrt(secureDivision(zavgerr,zcount-1)); zaverage = ftos(zavg,2) + " +/- " + ftos(zavgerr,2); if(nvoxels) tcourse_all/=float(nvoxels); for(int i=0; idesigndata(i))); // Encode as amplitude and phase tcourse[i]=tcourse_all(i); } // update sigchange fmriResult fr=fmri_eval(tcourse_all, data->designdata); sigchange=ftos(100.0*fr.rel_diff,2)+" +/- "+ftos(100.0*fr.rel_err,2)+"%"; // update sigcourse if(fr.Sbaseline>0.0) { // Use baseline, if available sigcourse.assignValues(tcourse); sigcourse-=fr.Sbaseline; sigcourse*=(100.0/fr.Sbaseline); } else { if(fr.Srest>0.0) { // fallback sigcourse.assignValues(tcourse); sigcourse-=fr.Srest; sigcourse*=(100.0/fr.Srest); } } if(dumptcourse!="") { STD_ofstream file(dumptcourse.c_str()); for(int i=0; i mask(get_overlay_map()); Data smap_mask(data->smap.shape()); smap_mask=where(Array(mask)>0.0, Array(data->smap), float(0.0)); smap_mask.autowrite(dumpsmap,FileWriteOpts(),&(data->protcopy)); } } odin-1.8.5/miview/main.cpp0000644000175000017500000000340311322062342012322 00000000000000/*************************************************************************** main.cpp - description ------------------- begin : Thu Aug 31 16:27:06 CEST 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #include "miview.h" int main(int argc, char *argv[]) { // do this here so we do not have to query X server in order to get usage for manual if(argc<=1) {MiViewView::usage();exit(0);} if(hasHelpOption(argc, argv)) {MiViewView::usage();exit(0);} char lastarg[ODIN_MAXCHAR]; char parname[ODIN_MAXCHAR]; STD_string parstring; parname[0]='\0'; getLastArgument(argc,argv,lastarg,ODIN_MAXCHAR,false); if(getCommandlineOption(argc,argv,"-jdx",parname,ODIN_MAXCHAR,false)) { parstring=STD_string("::")+parname; } GuiApplication a(argc, argv); // debug handler will be initialized here MiView* miview=new MiView(); miview->set_caption((STD_string("MiView - ") + lastarg + parstring).c_str()); return a.start(miview->get_widget()); } odin-1.8.5/miview/Makefile.am0000644000175000017500000000152611322062342012732 00000000000000 if GUI_ENABLED INCLUDES = $(all_includes) # Auto-generate any needed moc files %_moc.cpp: %.h $(MOC) -o $@ $< bin_PROGRAMS = miview miview_SOURCES = \ miviewview.cpp miviewview.h miviewview_moc.cpp \ miview_fmri.cpp miview_fmri.h \ miview.cpp miview.h miview_moc.cpp \ main.cpp miview_LDADD = ../odindata/libodindata.la ../odinqt/libodinqt.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la # Auto-generate manual pages, only if not in srcdir %.1: % if test ! -f $(srcdir)/$@ ; then $(HELP2MAN) --name="$$(./$< --help | grep $<: | sed s/'$<: '//)" ./$< > $@ ; fi # Manual pages for distribution dist_man_MANS = miview.1 manual: $(bin_PROGRAMS) for prog in $(bin_PROGRAMS); do ./$$prog -h > ./`basename $$prog $(EXEEXT)`.usage ; done endif dist-hook: -rm -rf $(distdir)/*_moc.cpp clean-local: -rm -f *_moc.cpp *.usage odin-1.8.5/miview/Makefile.in0000644000175000017500000005302611734622602012755 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; 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It was generated by help2man 1.38.2. .TH MIVIEW "1" "March 2012" "miview 1.8.5" "User Commands" .SH NAME miview \- Viewer for medical image files .SH SYNOPSIS .B miview [ \fIoptions \fR] \fI\fR .SH DESCRIPTION miview: Viewer for medical image files .IP File formats are automatically identified by their file extension. .SS "Global options:" .HP \fB\-blowup\fR: Enlarge display size by this factor (default=1) .HP \fB\-bright\fR: Relative brightness of display (default=0.0) .HP \fB\-color\fR: Use color map to display values .HP \fB\-contrast\fR: Relative contrast of display (default=0.0) .HP \fB\-dump\fR: Dump all images as bitmap(bmp) files and exit, use the given filename prefix .HP \fB\-low\fR: Lower windowing boundary: This value will appear black in display .HP \fB\-map\fR: Load overlay map (colored voxels superimposed on image) from this file .HP \fB\-maplegend\fR: Export map legend as bitmap to this file .HP \fB\-maplow\fR: Lower windowing boundary for overlay map (default=0.0) .HP \fB\-maprect\fR: Relative size of rectangles which represent voxels of the overlay map (default=0.60) .HP \fB\-mapupp\fR: Upper windowing boundary for overlay map (default=0.0) .HP \fB\-noscale\fR: Disable scale in 2D/3D display .HP \fB\-rec\fR: Record clicked coordinates and values into this file .HP \fB\-upp\fR: Upper windowing boundary: This value will appear white in display .HP \fB\-val\fR: Save value of ROI/point selection to this file .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .SS "fMRI options (Give at least -design and -fmri to activate):" .HP \fB\-bonferr\fR: Use Bonferroni correction .HP \fB\-corr\fR: Error probability threshold for correlation (default=0.050) .HP \fB\-davg\fR: Smooth the design function using a moving average filter of width N (TR) (default=0) .HP \fB\-design\fR: Load fMRI design from this file (comma or space separated) .HP \fB\-fmask\fR: fMRI mask file .HP \fB\-fmri\fR: Load fMRI data from this file .HP \fB\-hrf\fR: Convolve design function by hemodynamic response function prior to correlation (see Glover NeuroImage 9, 416\-429) .HP \fB\-neighb\fR: Minimum next neighbours with significant activation (default=1) .HP \fB\-scourse\fR: Dump relative fMRI signal change time course to this file .HP \fB\-smap\fR: Dump map of relative fMRI signal change to this file .HP \fB\-zmap\fR: Dump z\-score map to this file .HP \fB\-zscore\fR: z\-Score threshold for correlation (default=0.0) .SS "File read options:" .HP \fB\-date\fR: Date of scan [yyyymmdd] (default=20120328yyyymmdd) .HP \fB\-fp\fR: FOV in phase direction [mm] (default=220.0mm) .HP \fB\-fr\fR: FOV in read direction [mm] (default=220.0mm) .HP \fB\-fs\fR: FOV in slice direction [mm] (default=5.0mm) .HP \fB\-nr\fR: Number of consecutive measurements (default=1) .HP \fB\-nx\fR: Number of points in read direction (default=1) .HP \fB\-ny\fR: Number of points in phase direction (default=1) .HP \fB\-nz\fR: Number of points in slice direction (default=1) .HP \fB\-pbirth\fR: Patients date of birth [yyyymmdd] (default=00000000yyyymmdd) .HP \fB\-pid\fR: Unique patient identifier (default=Unknown) .HP \fB\-pname\fR: Full patient name (default=Unknown) .HP \fB\-psex\fR: Patients sex (options=M F O , default=O) .HP \fB\-pweight\fR: Patients weight [kg] (default=50.0kg) .HP \fB\-scient\fR: Scientist Name (default=Unknown) .HP \fB\-sd\fR: Inter\-slice distance (from center to center) [mm] (default=10.0mm) .HP \fB\-serd\fR: Series Description (default=Unknown) .HP \fB\-serno\fR: Series Number (default=1) .HP \fB\-st\fR: Slice thickness [mm] (default=5.0mm) .HP \fB\-stud\fR: Study Description (default=Unknown) .HP \fB\-tcname\fR: Name of transmit coil (default=Unknown) .HP \fB\-te\fR: Time\-to\-echo of the sequence [ms] (default=80.0ms) .HP \fB\-time\fR: Time of scan [hhmmss] (default=165543hhmmss) .HP \fB\-tr\fR: Time between consecutive excitations [ms] (default=1000.0ms) .HP \fB\-cplx\fR: Treat data as complex and extract the given component (options=none abs pha real imag , default=none) .HP \fB\-ds\fR: Dataset index to extract if multiple datasets are read .HP \fB\-filter\fR: Read only those datasets which protocol parameter 'key' contains the string 'value' (given in the format 'key=value') .HP \fB\-fmap\fR: For reduced memory usage, keep filemapping after reading (raw) data, but writing into the array will result in a crash .HP \fB\-jdx\fR: If multiple JDX arrays are present, select this .HP \fB\-rdialect\fR: Read data using given dialect of the format. (default is no dialect) .HP \fB\-rf\fR: Read format, use it to override file extension (options=autodetect 3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk , default=autodetect) .HP \fB\-skip\fR: Skip this amount of bytes before reading the raw data (default=0) .SS "Filters:" .HP \fB\-align\fR : Align data to the geometry (voxel locations) of an external file .HP \fB\-automask\fR : Create mask using automatic histogram\-based threshold .HP \fB\-detrend\fR : Remove slow drift over time .HP \fB\-genmask\fR : Create mask including all voxels with value in given range .HP \fB\-isotrop\fR : make image voxels isotrop through interpolation (image geometry will not change) .HP \fB\-lowpass\fR : Lowpass filtering .HP \fB\-max\fR : Clip all values above maximum value .HP \fB\-maxip\fR : Perform maximum intensity projection over given direction .HP \fB\-merge\fR : Merge datasets into a single dataset by expanding the time dimension .HP \fB\-min\fR : Clip all values below mininum value .HP \fB\-minip\fR : Perform minimum intensity projection over given direction .HP \fB\-noNaN\fR : Replaces every NaN by the given value .HP \fB\-pflip\fR : Flip data in phase direction .HP \fB\-prange\fR : Select range in phase direction .HP \fB\-proj\fR : Perform projection over given direction .HP \fB\-quantilmask\fR : Create mask including all voxels above the given fractional threshold .HP \fB\-resample\fR : Temporal resize of image data .HP \fB\-resize\fR : Spatial resize of image data .HP \fB\-reslice\fR : reslices the image to a given orientation .HP \fB\-rflip\fR : Flip data in read direction .HP \fB\-rot\fR : In\-plane rotation .HP \fB\-rrange\fR : Select range in read direction .HP \fB\-scale\fR : Rescale image values .HP \fB\-sflip\fR : Flip data in slice direction .HP \fB\-shift\fR : Shift data spatially .HP \fB\-splice\fR : splices the image in the given direction .HP \fB\-srange\fR : Select range in slice direction .HP \fB\-swapdim\fR <[rps][\-],[rps][\-],[rps][\-]> : swap/reflect dimensions by specifying a direction triple with optional reflection sign appended .HP \fB\-tile\fR : Combine slices into a square 2D image .HP \fB\-trange\fR : Select range in time direction .HP \fB\-typemax\fR : Clip all values above maximum of a specific datatype .HP \fB\-typemin\fR : Clip all values below mininum of a specific datatype .HP \fB\-usemask\fR : Create 1D dataset including all values within mask from file .SS "Supported file extensions(formats):" .TP 3db (Iris3D binary data) .TP asc (ASCII, dialects: tcourse ) .TP coi (JCAMP\-DX data sets) .TP dat (Matlab ascii 2D data matrix) .TP dcm (DICOM, dialects: siemens ) .TP double (double raw data) .TP float (float raw data) .TP gz (GNU\-Zip container for other formats) .TP hdr (NIFTI/ANALYZE, dialects: fsl ) .TP idx (3D\-indices of non\-zeroes in ASCII) .TP ima (DICOM, dialects: siemens ) .TP jdx (JCAMP\-DX image format) .TP mag (DICOM, dialects: siemens ) .TP mhd (MetaImage) .TP nii (NIFTI/ANALYZE, dialects: fsl ) .TP ph (DICOM, dialects: siemens ) .TP png (Portable Network Graphics) .TP pos (x\-y positions of non\-zeroes in ASCII) .TP pro (ODIN measurement protocols) .TP reg (Ansoft HFSS ASCII) .TP s16bit (signed 16 bit raw data) .TP s32bit (signed 32 bit raw data) .TP s8bit (signed 8 bit raw data) .TP smp (JCAMP\-DX data sets) .TP u16bit (unsigned 16 bit raw data) .TP u32bit (unsigned 32 bit raw data) .TP u8bit (unsigned 8 bit raw data) .TP vtk (Visualization Toolkit) odin-1.8.5/miview/miview.h0000644000175000017500000000421611322062342012346 00000000000000/*************************************************************************** miview.h - description ------------------- begin : Thu Aug 31 16:27:06 CEST 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef MIVIEW_H #define MIVIEW_H #include "miviewview.h" /** * \page miview View medical images * \verbinclude miview/miview.usage * * \section miview_examples Some examples how to use miview: * * Display DICOM file 'image.dcm': * \verbatim miview image.dcm \endverbatim * * * Display magnitude of float-type complex signal data stored in 'data.raw': * \verbatim miview -rf float -abs data.raw \endverbatim * * * Display short (16 bit) raw data file '2dseq' of size 256x256 * \verbatim miview -nx 256 -ny 256 -rf short 2dseq \endverbatim */ #define IDS_MIVIEW_ABOUT "MiView user interface\nVersion " VERSION \ "\n(w) 2000-2005 by Thies Jochimsen\n\n" class MiView : public QObject, public GuiMainWindow { Q_OBJECT public: MiView(); public slots: void slotHelpAbout(); void slotStatusMsg(const char* text) {GuiMainWindow::set_status_message(text);} void quit(); private: MiViewView *view; GuiPopupMenu* fileMenu; GuiPopupMenu* exportMenu; GuiPopupMenu* showMenu; GuiPopupMenu* helpMenu; }; #endif odin-1.8.5/miview/miviewview.h0000644000175000017500000000763211322062342013246 00000000000000/*************************************************************************** miviewview.h - description ------------------- begin : Thu Jun 20 19:02:26 CEST 2002 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef MIVIEWVIEW_H #define MIVIEWVIEW_H #include #include #include #include #include // miview modules #include "miview_fmri.h" class Protocol; // forward declaration struct FileData; // forward declaration struct SelectionData; // forward declaration //////////////////////////////////////// // for debugging MiView component class MiViewComp { public: static const char* get_compName(); }; //////////////////////////////////////// struct MiViewOpts : JcampDxBlock { JDXbool color; JDXfloat contrast; JDXfloat brightness; JDXstring valfile; JDXstring recfile; JDXint blowup; JDXstring low; JDXstring upp; JDXstring dump; JDXstring mapfile; JDXfloat maplow; JDXfloat mapupp; JDXfloat maprect; JDXstring maplegendexport; JDXbool noscale; MiViewOpts(); }; //////////////////////////////////////// class MiViewView : public QWidget { Q_OBJECT public: MiViewView(QWidget *parent); ~MiViewView(); static void set_defaults(Protocol& prot); static void usage(); bool is_image_display() const {return (get_nx()*get_ny())>1;} bool has_timecourse() const {return get_nrep()>1;} bool has_fmri() const {return fmri.is_valid();} bool has_overlay() const {return has_olm;} signals: void setMessage(const char* text); public slots: void writeImage(); void writeROIs(); void writeFmriClusters(); void writeProfile(); void writeTimecourse(); void writeLegend(); void selectVoxel(); void showProfile(); void showTimecourse(); void showProtocol(); private slots: void update(); void slotClicked(int x, int y, int z); void slotNewProfile(const float *data, int npts, bool horizontal, int position); void slotNewMask(const float *data, int slice); private: int get_nx() const; int get_ny() const; int get_nz() const; int get_nrep() const; void filedata2displaydata(); STD_string check_and_get_format(const STD_string& fname, const svector& possible_formats); void exportLegend(const STD_string& filename); void val2file(int rep, int z, int y, int x, float val) const; MiViewOpts mopts; bool has_bounds; // true if set manually float lowbound; float uppbound; FileData* file; // holding the data of the file JDXfloatArr displaydata; GuiProps guiprops_cache; JcampDxBlock settings; JDXint repetition; JDXfloatArr timecourse; bool has_olm; SelectionData* selection; // holding data of user selections GuiGridLayout* grid; JDXwidget* displaywidget; JDXwidget* settingswidget; JDXwidget* tcoursewidget; JDXwidget* fmriwidget; STD_string image_fname_cache; STD_string rois_fname_cache; STD_string clusters_fname_cache; STD_string profile_fname_cache; STD_string tcourse_fname_cache; JDXint pos_cache[n_directions]; // miview modules MiViewFmri fmri; }; #endif odin-1.8.5/miview/miview.cpp0000644000175000017500000000373011322062342012701 00000000000000#include "miview.h" MiView::MiView() { view=new MiViewView(GuiMainWindow::get_widget()); connect(view, SIGNAL(setMessage(const char*)), this, SLOT (slotStatusMsg(const char*))); fileMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); fileMenu->insert_item("&Quit", this, SLOT(quit()), Qt::CTRL+Qt::Key_Q); exportMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); showMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); showMenu->insert_item("Select Voxel", view, SLOT(selectVoxel())); if(view->is_image_display()) { exportMenu->insert_item("Dump current display as image (screenshot)", view, SLOT(writeImage())); exportMenu->insert_item("Export current ROIs", view, SLOT(writeROIs())); exportMenu->insert_item("Export current profile as ASCII", view, SLOT(writeProfile())); if(view->has_timecourse()) exportMenu->insert_item("Export current timecourse as ASCII", view, SLOT(writeTimecourse())); showMenu->insert_item("Show current profile in Xmgr(ace)", view, SLOT(showProfile())); showMenu->insert_item("Show current timecourse in Xmgr(ace)", view, SLOT(showTimecourse())); } if(view->has_fmri()) { exportMenu->insert_item("Export current fMRI clusters", view, SLOT(writeFmriClusters())); } if(view->has_overlay()) { exportMenu->insert_item("Export overlay legend", view, SLOT(writeLegend())); } showMenu->insert_item("Show Protcol", view, SLOT(showProtocol())); helpMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); helpMenu->insert_item("About...", this, SLOT(slotHelpAbout())); GuiMainWindow::insert_menu("&File", fileMenu); GuiMainWindow::insert_menu("Ex&port", exportMenu); GuiMainWindow::insert_menu("S&how", showMenu); GuiMainWindow::insert_menu_separator(); GuiMainWindow::insert_menu("&Help", helpMenu); GuiMainWindow::show(view); } void MiView::slotHelpAbout() { message_question(IDS_MIVIEW_ABOUT, "About...", GuiMainWindow::get_widget()); } void MiView::quit() { GuiApplication::quit(); } odin-1.8.5/miview/miview_fmri.h0000644000175000017500000000425511734622163013400 00000000000000/*************************************************************************** miview_fmri.h - description ------------------- begin : Mon Jan 2 19:02:26 CEST 2006 copyright : (C) 2006 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef MIVIEW_FMRI_H #define MIVIEW_FMRI_H #include #include #include #include // forward declarations class FileReadOpts; class Protocol; class FilterChain; struct FmriData; //////////////////////////////////////////////////////////// class MiViewFmri : public JcampDxBlock { public: MiViewFmri(); ~MiViewFmri(); bool init(const FileReadOpts& ropts, const Protocol& prot, const FilterChain& filterchain); bool is_valid() const {return valid;} const farray& get_overlay_map() const; bool write_overlay_map(const STD_string& filename); void update(); private: JDXstring designfile; JDXstring fmrifile; JDXstring maskfile; JDXbool bonferr; JDXbool hrf; JDXfloat corr; JDXfloat zscore; JDXint designavg; JDXint neighb; JDXstring sigchange; JDXfloat zsum; JDXint zcount; JDXstring zaverage; JDXfloatArr design; JDXfloatArr tcourse; JDXfloatArr sigcourse; JDXstring dumptcourse; JDXstring dumpzmap; JDXstring dumpsmap; FmriData* data; mutable farray overlay_map; mutable farray toberemoved; bool valid; }; #endif odin-1.8.5/odinqt/0000755000175000017500000000000011735135551010763 500000000000000odin-1.8.5/odinqt/intedit.cpp0000644000175000017500000000561311322062347013046 00000000000000#include #include "intedit.h" #include // for itos #include // for strtol intLineEdit::intLineEdit(int minValue, int maxValue, int value, QWidget *parent, const char *name, int width, int height ) { gle = new GuiLineEdit(parent, this, SLOT(emitSignal()), width, height); /* minValue & maxValue unused so far: */ minValue=maxValue=0; set_value(value); } intLineEdit::~intLineEdit() { delete gle; } void intLineEdit::setintLineEditValue( int newValue ) { set_value(newValue); } void intLineEdit::emitSignal() { if(gle->is_modified()) { int value=atoi(gle->get_text()); set_value(value); emit intLineEditValueChanged(value); } } void intLineEdit::set_value(int value) { gle->set_text( itos(value).c_str() ); } ////////////////////////////////////////////////////////////// intLineBox::intLineBox(int value,QWidget *parent, const char *name ) : QGroupBox(name,parent) { grid=new GuiGridLayout( this, 1, 1); le = new intLineEdit( 0, 0, value, this, "LineEdit", TEXTEDIT_WIDTH, TEXTEDIT_HEIGHT ); grid->add_widget( le->get_widget(), 0, 0); connect(le,SIGNAL(intLineEditValueChanged( int )), this,SLOT(emitSignal( int ))); connect(this,SIGNAL(SignalToChild( int )), le, SLOT(setintLineEditValue( int))); } void intLineBox::setintLineBoxValue( int newvalue ) { emit SignalToChild( newvalue ); } void intLineBox::emitSignal( int newvalue ) { emit intLineBoxValueChanged(newvalue); } intLineBox::~intLineBox() { delete le; delete grid; } ////////////////////////////////////////////////////////////// intScientSlider::intScientSlider(int minValue, int maxValue, int Step, int value, QWidget *parent, const char *name ) : QGroupBox(name, parent ) { grid=new GuiGridLayout( this, 1, 4); slider=new GuiSlider(this, minValue, maxValue, Step, value, int(((float)maxValue-(float)minValue)/20.0)); le = new intLineEdit( minValue, maxValue, value, this, "LineEdit" , SLIDER_CELL_WIDTH, SLIDER_CELL_HEIGHT ); grid->add_widget(slider->get_widget(), 0, 0, GuiGridLayout::Default, 1, 3 ); grid->add_widget(le->get_widget(), 0, 3); // cross-wise connection of slider and line edit connect(slider->get_widget(), SIGNAL(valueChanged(int)), le, SLOT(setintLineEditValue(int))); connect(le, SIGNAL(intLineEditValueChanged(int)), slider->get_widget(), SLOT(setValue(int))); // emit signal whenever of one of both has been changed connect(slider->get_widget(),SIGNAL(valueChanged(int)), this,SLOT(emitSignal( int ))); connect(le,SIGNAL(intLineEditValueChanged( int )), this,SLOT(emitSignal( int ))); } void intScientSlider::setintScientSliderValue( int newvalue ) { slider->set_value(newvalue); le->setintLineEditValue(newvalue); } void intScientSlider::emitSignal( int newvalue ) { emit intScientSliderValueChanged(newvalue); } intScientSlider::~intScientSlider(){ delete le; delete slider; delete grid; } odin-1.8.5/odinqt/boolbutton.cpp0000644000175000017500000000216411322062347013573 00000000000000#include "boolbutton.h" buttonBox::buttonBox(const char *text, QWidget *parent, const char *buttonlabel) : QGroupBox(buttonlabel,parent) { grid=new GuiGridLayout( this, 1, 1); gb=new GuiButton(this, this, SLOT(reportclicked()), text); grid->add_widget( gb->get_widget(), 0, 0, GuiGridLayout::VCenter); // connect( gb->get_widget(), SIGNAL(clicked()), SLOT(reportclicked()) ); } buttonBox::buttonBox(const char *ontext,const char *offtext, bool initstate, QWidget *parent, const char *buttonlabel) : QGroupBox(buttonlabel,parent) { grid=new GuiGridLayout( this, 1, 1); gb=new GuiButton(this, this, SLOT(setButtonState()), ontext, offtext, initstate); grid->add_widget( gb->get_widget(), 0, 0, GuiGridLayout::VCenter); // connect( gb->get_widget(), SIGNAL(toggled(bool)), SLOT(setButtonState(bool)) ); } void buttonBox::reportclicked() { emit buttonClicked(); } void buttonBox::setToggleState(bool state) { gb->set_toggled(state); } void buttonBox::setButtonState() { bool state=gb->is_on(); gb->set_text(state); emit buttonToggled(state); } buttonBox::~buttonBox(){ delete gb; delete grid; } odin-1.8.5/odinqt/jdxblockwidget.h0000644000175000017500000001034411363773557014075 00000000000000/*************************************************************************** jdxblockwidget.h - description ------------------- begin : Mon Aug 5 2005 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXBLOCKWIDGET_H #define JDXBLOCKWIDGET_H #include #include "odinqt.h" #include class JDXwidgetDialog; // forward declaration //////////////////////////////////////////////////////////// class JcampDxBlockGrid : public QWidget { Q_OBJECT public: JcampDxBlockGrid(JcampDxBlock& block,unsigned int columns=1,QWidget *parent=0,const char* omittext=""); signals: // public: void valueChanged(); // private: void updateSubWidget(); void deleteSubDialogs(); public slots: void updateWidget(); void deleteDialogs(); void swapSliderTracking() {} void emitValueChanged() {emit valueChanged();} private: friend class JcampDxBlockScrollView; void createDialog(); GuiGridLayout* grid; JcampDxBlock& val; STD_list subdialogs; }; //////////////////////////////////////////////////////////// class JcampDxBlockScrollView : public QObject { Q_OBJECT public: JcampDxBlockScrollView(JcampDxBlock& block, unsigned int columns=1, QWidget *parent=0, const char* omittext=""); ~JcampDxBlockScrollView(); // QSize gridsize() const {return jdxgrid->frameSize();} QWidget* get_widget() {return scroll->get_widget();} signals: void valueChanged(); public slots: void updateWidget() {jdxgrid->updateWidget();} void deleteDialogs() {jdxgrid->deleteDialogs();} void swapSliderTracking() {jdxgrid->swapSliderTracking();} void emitValueChanged() {emit valueChanged();} private: friend class JcampDxBlockWidget; void createDialog() {jdxgrid->createDialog();} GuiScroll* scroll; JcampDxBlockGrid* jdxgrid; }; //////////////////////////////////////////////////////////// class JcampDxBlockWidget : public QGroupBox { Q_OBJECT public: JcampDxBlockWidget(JcampDxBlock& jdxblock,unsigned int columns=1,QWidget *parent=0,bool doneButton=false,bool is_dialog=false,const char* omittext="", bool storeLoadButtons=false, bool readonly=false); ~JcampDxBlockWidget(); // QSize gridsize() const {if(jdxscroll) return jdxscroll->gridsize(); else return QSize();} signals: void valueChanged(); void doneButtonPressed(); public slots: void updateWidget() {if(jdxscroll) jdxscroll->updateWidget();} void deleteDialogs() {if(jdxscroll) jdxscroll->deleteDialogs();} void swapSliderTracking() {if(jdxscroll) jdxscroll->swapSliderTracking();} void createDialog(); void emitValueChanged() {emit valueChanged();} private slots: void emitDone(); void storeBlock(); void loadBlock(); private: GuiGridLayout *grid; GuiButton *pb_done; GuiButton *pb_edit; GuiButton *pb_store; GuiButton *pb_load; JcampDxBlock& parblock; JcampDxBlockScrollView* jdxscroll; GuiListView* noeditlist; STD_vector noedititems; }; //////////////////////////////////////////////////////////// class JDXwidgetDialog : public QObject, public GuiDialog { Q_OBJECT public: JDXwidgetDialog(JcampDxBlock& ldr,unsigned int columns=1,QWidget *parent=0, bool modal=false, bool readonly=false); ~JDXwidgetDialog(); public slots: void updateWidget(); void emitChanged(); private: GuiGridLayout *grid; JcampDxBlockWidget *jdx; private slots: void callDone(); signals: void finished(); void valueChanged(); }; #endif odin-1.8.5/odinqt/jdxwidget.h0000644000175000017500000001473711322062347013053 00000000000000/*************************************************************************** jdxwidget.h - description ------------------- begin : Mon Apr 15 2002 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXWIDGET_H #define JDXWIDGET_H #include #include "odinqt.h" #include #include /////////////////////////////////////////////////////////////// #define _MAX_SLIDER_STEPS_ 100 #define _MAX_LABEL_LENGTH_ 15 #define _FLOAT_DIGITS_ 3 #define _INFOBOX_LINEWIDTH_ 50 #define _MAX_SUBWIDGETS_FOR_ALIGNCENT_ 5 /////////////////////////////////////////////////////////////// // forward declarations to decouple headers as far as possible class JcampDxClass; class intScientSlider; class intLineBox; class floatScientSlider; class floatLineBox; class enumBox; class buttonBox; class floatBox1D; class floatBox3D; class complexfloatBox1D; class stringBox; class floatLineBox3D; class JDXwidgetDialog; class JcampDxBlockWidget; class JDXeditCaller; /////////////////////////////////////////////////////////////// /** * * This class produces a widget according to a given JCAMP-DX parameter or a block * of them so that the parameter(s) can be edited interactively */ class JDXwidget : public QWidget { Q_OBJECT public: /** * *Constructs a widget for the parameter(s) 'ldr' with the following additional options: * - columns: If creating a widget for a block of parameters they will be grouped in the given number of columns * - parent: The parent widget * - doneButton: If creating a widget for a block of parameters a 'Done' push button will be added if this option is set to 'true' * The push button will then emit the doneButtonPressed() signal if clicked * - omittext: Text to blind out in the label of each parameter * - storeLoadButtons: Add buttons to store/load the parameters to/from file * */ JDXwidget(JcampDxClass& ldr,unsigned int columns=1, QWidget *parent=0, bool doneButton=false, const char* omittext="", bool storeLoadButtons=false); ~JDXwidget(); // members for 2D/3D plot void write_pixmap(const char* fname, const char* format, bool dump_all=false) const; void write_map_legend(const char* fname, const char* format) const; signals: /** * This signal will be emitted whenever one of the parameters is changed */ void valueChanged(); /** * This signal will be emitted whenever the 'Done' button is clicked */ void doneButtonPressed(); // signals for 2D/3D plot void clicked(int x, int y, int z); void newProfile(const float *data, int npts, bool horizontal, int position); void newMask(const float* data, int slice); // private: void updateSubWidget(); void deleteSubDialogs(); void newintval(int); void newfloatval(float); void newenumval(int); void newboolval(bool); void newfloatArr1( const float*, int, float, float); // void newdoubleArr1( const double*, int, float, float); void newfloatArr2( const float*, float, float); void newfloatArrMap(const float*, float, float, float); void newcomplexArr( const float*, const float*, int, float, float); void newfuncval(int); void newstringval(const char*); void newfilenameval(const char*); void newformulaval(const char*); void newtripleval(float,float,float); public slots: /** * Tell the widget that the parameter(s) were changed outside and that it has to update its view */ void updateWidget(); /** * Delete all dialogs that may have popped up during editing the parameters */ void deleteDialogs(); private slots: void emitValueChanged(); void emitDone(); void emitClicked(int x, int y, int z) {emit clicked(x,y,z);} void emitNewProfile(const float *data, int npts, bool horizontal, int position) {emit newProfile(data, npts, horizontal, position);} void emitNewMask(const float *data, int slice) {emit newMask(data,slice);} void changeJDXint( int ); void changeJDXfloat( float ); void changeJDXenum( int ); void changeJDXbool ( bool ); void changeJDXaction(); void changeJDXfunction( int ); void changeJDXstring(const char*); void changeJDXfileName(const char*); void browseJDXfileName(); void changeJDXformula(const char*); void changeJDXtriple(float,float,float); void infoJDXformula(); void editJDXfunction(); void infoJDXfunction(); public: STD_string get_label() const; unsigned int get_rows() const {return rows;} unsigned int get_cols() const {return cols;} private: void set_widget(QWidget *widget, GuiGridLayout::Alignment alignment = GuiGridLayout::Default, bool override_enabled=false); unsigned int get_sizedfarray_size_and_factor(unsigned int& nx, unsigned int& ny, unsigned int& nz) const; void create_or_update_floatArrwidget(const farray& arr, bool initial); GuiGridLayout* grid; QWidget* widget_cache; JcampDxBlockWidget* blockwidget; intScientSlider* intslider; intLineBox* intedit; floatScientSlider* floatslider; floatLineBox* floatedit; enumBox* enumwidget; buttonBox* boolwidget; buttonBox* actionwidget; QLabel* floatArrempty; floatBox1D* floatArrwidget1; floatLineBox* floatArredit; floatBox3D* floatArrwidget2; complexfloatBox1D* complexArrwidget; stringBox* stringwidget; stringBox* filenamewidget; enumBox* funcwidget; stringBox* formulawidget; floatLineBox3D* triplewidget; // float 2D/3D stuff farray sizedfarray; farray mapfarray; ndim oldfarraysize; farray overlay_map; QWidget* vport; JcampDxClass& val; STD_string ldrlabel; STD_string ldrlabel_uncut; bool label_cut; STD_list subdialogs; unsigned int rows,cols; }; #endif odin-1.8.5/odinqt/float1d.h0000644000175000017500000000360611322062347012405 00000000000000/*************************************************************************** float1d.h - description ------------------- begin : Sun Aug 27 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FLOAT1D_H #define FLOAT1D_H #include "complex1d.h" /** * This class displays a float array in a nice box with title */ class floatBox1D : public complexfloatBox1D { Q_OBJECT public: floatBox1D(const float *data,int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel=0, const char *yAxisLabel=0, float min_x=0.0, float max_x=0.0, bool detachable=false); floatBox1D(const double *data,int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel=0, const char *yAxisLabel=0, float min_x=0.0, float max_x=0.0, bool detachable=false); public slots: void refresh(const float* data,int n, float min_x, float max_x); void refresh(const float* data,int n) {refresh (data,n,0.0,0.0);} void refresh(const double* data,int n, float min_x, float max_x); void refresh(const double* data,int n) {refresh (data,n,0.0,0.0);} }; #endif odin-1.8.5/odinqt/float2d.h0000644000175000017500000000735111322062347012407 00000000000000/*************************************************************************** float2d.h - description ------------------- begin : Sun Aug 27 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FLOAT2D_H #define FLOAT2D_H #include #include "odinqt.h" #include "plot.h" class QPixmap; // forward declaration /** * QLabel containing a QPixmap to draw 2D float array */ class floatLabel2D : public QLabel { Q_OBJECT public: floatLabel2D(const float *data, float lowbound, float uppbound, unsigned int nx, unsigned int ny, unsigned int coarseFactor, QWidget *parent, const char *name, const float *overlay_map, float lowbound_map, float uppbound_map, unsigned int nx_map, unsigned int ny_map, bool map_firescale, float map_rectsize, bool colormap); ~floatLabel2D(); int xpos2labelxpos(int pos); int ypos2labelypos(int pos); int labelxpos2xpos(int pos); int labelypos2ypos(int pos); int xypos2index(int xpos,int ypos); unsigned int get_nx() const {return nx_cache;} unsigned int get_ny() const {return ny_cache;} void init_pixmap(bool clear=true); void set_pixmap(); void write_pixmap(const char* fname, const char* format) const; QLabel* get_map_legend(QWidget *parent) const; void write_map_legend(const char* fname, const char* format) const; QPixmap *pixmap; protected: void mousePressEvent (QMouseEvent *); void mouseReleaseEvent (QMouseEvent *); void mouseMoveEvent ( QMouseEvent * ); public slots: void refresh(const float *data, float lowbound, float uppbound); void refreshMap(const float *map, float map_lowbound, float map_uppbound, float rectsize); private slots: void drawprofil(int position,int direction); void drawcross(int xposition,int yposition); void drawroi(); signals: void clicked(int xposition,int yposition); void newProfile(const float *data, int npts, bool horizontal, int position); void newMask(const float *data); private: static int scale_width(float lowbound, float uppbound); void draw_text(GuiPainter& gp, int xpos, int ypos, const char* txt) const; void draw_scale_text(GuiPainter& gp, int ypos, float val) const; static int check_range(int val, int min, int max); int get_map_hue(float relval) const; int get_map_value(float relval) const; int get_map_saturation(float relval) const; int scalespace_cache; GuiPainter* roi_painter; mutable QPixmap* legend_pixmap; unsigned char* imagebuff; unsigned int len; const float* data_cache; unsigned int nx_cache; unsigned int ny_cache; float lowbound_cache; float uppbound_cache; unsigned int nx_map_cache; unsigned int ny_map_cache; float lowbound_map_cache; float uppbound_map_cache; bool fire_map_cache; float *profile_x; float *profile_y; unsigned int coarseFactor_cache; bool colormap_cache; long unsigned int i; STD_list roi_polygon; float* roi_mask; bool mouse_moved; }; #endif odin-1.8.5/odinqt/float3d.h0000644000175000017500000000655411322062347012414 00000000000000/*************************************************************************** float3d.h - description ------------------- begin : Thu Nov 10 2005 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FLOAT3D_H #define FLOAT3D_H #include #include "float2d.h" /** * QGroupBox that contains a floatLabel2D and a slider to display 3D float arrays */ class floatBox3D : public QGroupBox { Q_OBJECT public: floatBox3D(const float *data, float lowbound, float uppbound, long int nx, long int ny, long int nz, int coarseFactor, QWidget *parent, const char *name, const float *overlay_map=0, float lowbound_map=0.0, float uppbound_map=0.0, unsigned int nx_map=0, unsigned int ny_map=0, unsigned int nz_map=0, bool map_firescale=false, float map_rectsize=0.8, bool colormap=false); ~floatBox3D(); void write_pixmap(const char* fname, const char* format, bool dump_all=false) const; QLabel* get_map_legend(QWidget* parent) const {return label->get_map_legend(parent);} void write_map_legend(const char* fname, const char* format) const {label->write_map_legend(fname, format);} public slots: void refresh(const float* data, float lowbound, float uppbound); void refreshMap(const float* map, float lowbound_map, float uppbound_map, float rectsize) {map_cache=map; label->refreshMap(map_cache+onemapsize*get_current_z(),lowbound_map,uppbound_map,rectsize);} private slots: void emitClicked(int xposition, int yposition) {emit clicked(xposition,yposition,get_current_z());} void emitNewProfile(const float *data, int npts, bool horizontal, int position) {emit newProfile(data, npts, horizontal, position);} void emitNewMask(const float *data) {emit newMask(data,get_current_z());} protected slots: void changez(int iz); signals: void clicked(int x, int y, int z); void newProfile(const float *data, int npts, bool horizontal, int position); void newMask(const float* data, int slice); protected: floatLabel2D* label; // GeoEditLabel needs access to it int get_current_z() const; private: virtual void repaint() {} // overload this function to draw additional stuff after changez void repaint_slice(int iz) const; GuiSlider* zslider; QLabel* zval; GuiGridLayout *grid; QLabel* maplegend; const float* data_cache; unsigned int oneimagesize; unsigned int nz_cache; float lowbound_cache; float uppbound_cache; const float* map_cache; float lowbound_map_cache; float uppbound_map_cache; float rectsize_map_cache; unsigned int onemapsize; float* mask3d; }; #endif odin-1.8.5/odinqt/enumbox.cpp0000644000175000017500000000271111322062347013057 00000000000000#include // for connecting signals #include "enumbox.h" enumBox::enumBox(const svector& items,QWidget *parent,const char *name,bool editButton,bool infoButton ) : QGroupBox(name, parent ) { pb_edit=0; pb_info=0; unsigned int row=1; if(editButton) row++; if(infoButton) row++; grid=new GuiGridLayout( this, 1, row); row=0; cb = new GuiComboBox( this, items ); grid->add_widget( cb->get_widget(), 0, row ); connect( cb->get_widget(), SIGNAL(activated(int)),this, SLOT(emitNewVal(int)) ); row++; if(editButton) { pb_edit = new GuiButton( this, this, SLOT(reportEditClicked()), "Edit" ); grid->add_widget( pb_edit->get_widget(), 0, row, GuiGridLayout::VCenter ); row++; // connect( pb_edit->get_widget(), SIGNAL(clicked()), SLOT(reportEditClicked()) ); } if(infoButton) { pb_info = new GuiButton( this, this, SLOT(reportInfoClicked()), "Info" ); grid->add_widget( pb_info->get_widget(), 0, row, GuiGridLayout::VCenter ); row++; // connect( pb_info->get_widget(), SIGNAL(clicked()), SLOT(reportInfoClicked()) ); } } void enumBox::emitNewVal( int selected ) { old_val=selected; emit newVal(old_val); } void enumBox::reportEditClicked() {emit edit();} void enumBox::reportInfoClicked() {emit info();} void enumBox::setValue( int val ) { old_val=val; cb->set_current_item(val); } enumBox::~enumBox(){ delete cb; if(pb_edit) delete pb_edit; if(pb_info) delete pb_info; delete grid; } odin-1.8.5/odinqt/floatedit.h0000644000175000017500000001120611322062347013021 00000000000000/*************************************************************************** floatedit.h - description ------------------- begin : Sun Aug 27 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FLOATEDIT_H #define FLOATEDIT_H #include #include "odinqt.h" /** * This class implements a line edit with float values only; A number * of digits to display must be specified. */ class floatLineEdit : public QObject { Q_OBJECT public: floatLineEdit(float minValue, float maxValue, float value, int digits, QWidget *parent, const char *name, int width, int height ); ~floatLineEdit(); QWidget* get_widget() {return gle->get_widget();} // required public for range slider void set_value(float value); float get_value() const {return value_cache;} public slots: void setfloatLineEditValue( float value); private slots: void emitSignal(); signals: void floatLineEditValueChanged(float value); private: int digits_cache; float value_cache; GuiLineEdit* gle; }; //////////////////////////////////////////////////////////////// /** * This class implements a slider with float values (of course it's still * discrete !), so you can use rational numbers as its values */ class floatSlider : public QObject { Q_OBJECT public: floatSlider(float minValue, float maxValue, float step, float value, QWidget *parent, const char *name ); ~floatSlider(); QWidget* get_widget(); public slots: void setfloatSliderValue( float value); private slots: void emitSignal( int discrete_value); signals: void floatSliderValueChanged( float newvalue); private: GuiSlider* gs; float minValue_cache; float step_cache; int oldPosition; }; //////////////////////////////////////////////////////////////// /** * This class contains a floatlineedit to display a float value * in a nice box with a label. */ class floatLineBox : public QGroupBox { Q_OBJECT public: floatLineBox(float value, int digits, QWidget *parent, const char *name); ~floatLineBox(); public slots: void setfloatLineBoxValue( float value ); private slots: void emitSignal( float value ); signals: void floatLineBoxValueChanged( float value ); private: GuiGridLayout* grid; floatLineEdit *le; }; //////////////////////////////////////////////////////////////// /** * This class implements a slider useful for scientific applications * by composing a floatSlider and a floatLineEdit into one widget. */ class floatScientSlider : public QGroupBox { Q_OBJECT public: floatScientSlider(float minValue, float maxValue, float Step, float value, int digits, QWidget *parent, const char *name); ~floatScientSlider(); public slots: void setfloatScientSliderValue( float value ); private slots: void emitSignal( float value ); signals: void floatScientSliderValueChanged( float value ); private: float value; floatSlider* slider; GuiGridLayout* grid; floatLineEdit *le; }; /////////////////////////////////////////////////////////////////////// /** * This class contains 3 floatlineedit to display 3 values * in a nice box with a label. */ class floatLineBox3D : public QGroupBox { Q_OBJECT public: floatLineBox3D(float xval, float yval, float zval, int digits, QWidget *parent, const char *name); ~floatLineBox3D(); public slots: void setfloatLineBox3DValue( float xval, float yval, float zval ); private slots: void emitSignal_x( float newval ); void emitSignal_y( float newval ); void emitSignal_z( float newval ); signals: void floatLineBox3DValueChanged( float xval, float yval, float zval ); void SignalToChild_x( float ); void SignalToChild_y( float ); void SignalToChild_z( float ); private: GuiGridLayout* grid; floatLineEdit *lex; floatLineEdit *ley; floatLineEdit *lez; float xcache; float ycache; float zcache; }; #endif odin-1.8.5/odinqt/jdxblockwidget.cpp0000644000175000017500000002317111363773557014432 00000000000000#include "jdxwidget.h" #include "jdxblockwidget.h" ///////////////////////////////////////////////////////////////////////////// JcampDxBlockGrid::JcampDxBlockGrid(JcampDxBlock& block,unsigned int columns,QWidget *parent,const char* omittext) : QWidget(parent), val(block) { Log odinlog(&block,"JcampDxBlockGrid(...)"); grid=0; STD_list subwidgets; STD_list::iterator it; unsigned int numof_pars=block.numof_pars(); JcampDxClass* ldrptr; // fill list with subwidgets for(unsigned int i=0;iisUserDefParameter() && (ldrptr->get_parmode()!=hidden)) { JDXwidget* ldrwidget=0; JcampDxBlock* blockdummy=ldrptr->cast(blockdummy); if(blockdummy) { unsigned int cols4block=1; if(blockdummy->numof_pars()>5) cols4block=2; ldrwidget=new JDXwidget(*ldrptr,cols4block,this,false,omittext); } else ldrwidget=new JDXwidget(*ldrptr,1,this,false,omittext); subwidgets.push_back(ldrwidget); } } unsigned int n_widget_rows=0; unsigned int rowheight=0; unsigned int colstart=0; // calculate n_widget_rows layout for(it=subwidgets.begin(); it!=subwidgets.end(); ++it) { unsigned int colwidth=(*it)->get_cols(); if( (colstart+colwidth) > 2 ) { // goto new row n_widget_rows+=rowheight; colstart=0; rowheight=0; } ODINLOG(odinlog,normalDebug) << "rows(" << (*it)->get_label() << ")=" << (*it)->get_rows() << STD_endl; if ( (*it)->get_rows() > rowheight ) rowheight=(*it)->get_rows(); colstart+=colwidth; } n_widget_rows+=rowheight; ODINLOG(odinlog,normalDebug) << "n_widget_rows/columns" << n_widget_rows << "/" << columns << STD_endl; unsigned int rows=(n_widget_rows/columns); // if(n_widget_rows%columns) rows++; rows++; unsigned int irow=0; unsigned int icolumn=0; rowheight=0; colstart=0; grid = new GuiGridLayout( this, rows , columns*2); ODINLOG(odinlog,normalDebug) << "creating " << rows << "x" << columns*2 << " grid" << STD_endl; for(it=subwidgets.begin(); it!=subwidgets.end(); ++it) { unsigned int colwidth=(*it)->get_cols(); if( (colstart+colwidth) > 2 ) { // goto new row irow+=rowheight; colstart=0; rowheight=0; } // rowheight=(*it)->get_rows(); if ( (*it)->get_rows() > rowheight ) rowheight=(*it)->get_rows(); if( (irow+rowheight) > rows ) { icolumn++; irow=0; } unsigned int coloffset=2*icolumn+colstart; unsigned int rowoffset=irow; colstart+=colwidth; int rowstart=rowoffset; // int rowend=rowoffset+rowheight-1; // int colstart=coloffset; // int colend=coloffset+colwidth-1; ODINLOG(odinlog,normalDebug) << (*it)->get_label() << " at " << "(" << rowstart << "-" << coloffset << "," << rowheight << "-" << colwidth << ")" << STD_endl; grid->add_widget( (*it), rowoffset, coloffset, GuiGridLayout::Center, rowheight, colwidth ); connect((*it),SIGNAL(valueChanged()),this,SLOT(emitValueChanged())); connect(this,SIGNAL(updateSubWidget()),(*it),SLOT(updateWidget())); connect(this,SIGNAL(deleteSubDialogs()),(*it),SLOT(deleteDialogs())); } } void JcampDxBlockGrid::updateWidget() { for(STD_list::iterator it=subdialogs.begin(); it!=subdialogs.end(); ++it) { (*it)->updateWidget(); } emit updateSubWidget(); } void JcampDxBlockGrid::deleteDialogs() { emit deleteSubDialogs(); } void JcampDxBlockGrid::createDialog() { Log odinlog(&val,"createDialog"); JDXwidgetDialog* dlg=new JDXwidgetDialog(val,1,this); subdialogs.push_back(dlg); connect(dlg,SIGNAL(valueChanged()), this,SLOT(emitValueChanged())); emit valueChanged(); } ///////////////////////////////////////////////////////////////////////////// JcampDxBlockScrollView::JcampDxBlockScrollView(JcampDxBlock& block,unsigned int columns,QWidget *parent,const char* omittext) { Log odinlog(&block,"JcampDxBlockScrollView(...)"); jdxgrid=new JcampDxBlockGrid(block,columns,parent,omittext); connect(jdxgrid,SIGNAL(valueChanged()),this,SLOT(emitValueChanged())); scroll=new GuiScroll(jdxgrid,parent); } JcampDxBlockScrollView::~JcampDxBlockScrollView() { delete scroll; } ///////////////////////////////////////////////////////////////////////////// JcampDxBlockWidget::JcampDxBlockWidget(JcampDxBlock& jdxblock,unsigned int columns,QWidget *parent,bool doneButton,bool is_dialog,const char* omittext, bool storeLoadButtons, bool readonly) : QGroupBox(jdxblock.get_label().c_str(), parent ), parblock(jdxblock) { Log odinlog(&jdxblock,"JcampDxBlockWidget(...)"); pb_done=0; pb_edit=0; pb_store=0; pb_load=0; grid=0; jdxscroll=0; noeditlist=0; if(jdxblock.is_embedded() || is_dialog) { int height=1; if(doneButton || storeLoadButtons) height=2; grid=new GuiGridLayout(this, height, 3); // if(jdxblock.get_parmode()==noedit) { if(readonly) { ODINLOG(odinlog,normalDebug) << "noedit mode" << STD_endl; svector columns; columns.resize(4); columns[0]="Name"; columns[1]="Value"; columns[2]="Unit"; columns[3]="Description"; noeditlist=new GuiListView(this, columns); grid->add_widget( noeditlist->get_widget(), 0, 0, GuiGridLayout::Default, 1, 3); unsigned int n=jdxblock.numof_pars(); noedititems.resize(n); for(unsigned int i=0; iset_default(true); pb_dummy->get_widget()->hide(); } if(doneButton) { pb_done = new GuiButton( this, this, SLOT(emitDone()), "Done" ); pb_done->set_default(false); grid->add_widget( pb_done->get_widget(), 1, 2, GuiGridLayout::Center ); // connect( pb_done->get_widget(), SIGNAL(clicked()), this,SLOT(emitDone()) ); } if(storeLoadButtons) { pb_store = new GuiButton( this, this, SLOT(storeBlock()), "Store ..." ); pb_load = new GuiButton( this, this, SLOT(loadBlock()), "Load ..." ); pb_store->set_default(false); pb_load->set_default(false); grid->add_widget( pb_store->get_widget(), 1, 0, GuiGridLayout::Center ); grid->add_widget( pb_load->get_widget(), 1, 1, GuiGridLayout::Center ); // connect( pb_store->get_widget(), SIGNAL(clicked()), this,SLOT(storeBlock()) ); // connect( pb_load->get_widget(), SIGNAL(clicked()), this,SLOT(loadBlock()) ); } } else { // if(block.is_embedded()) jdxscroll=new JcampDxBlockScrollView(jdxblock,columns,0,omittext); connect(jdxscroll,SIGNAL(valueChanged()),this,SLOT(emitValueChanged())); grid=new GuiGridLayout( this, 1 , 1); pb_edit = new GuiButton( this, this, SLOT(createDialog()), "Edit" ); grid->add_widget( pb_edit->get_widget(), 0, 0, GuiGridLayout::Center ); // connect( pb_edit->get_widget(), SIGNAL(clicked()), this,SLOT(createDialog()) ); } } void JcampDxBlockWidget::createDialog() { Log odinlog("JcampDxBlockWidget","createDialog"); ODINLOG(odinlog,normalDebug) << "jdxscroll=" << jdxscroll << STD_endl; if(jdxscroll) jdxscroll->createDialog(); } JcampDxBlockWidget::~JcampDxBlockWidget() { if(pb_done) delete pb_done; if(pb_store) delete pb_store; if(pb_load) delete pb_load; if(grid) delete grid; if(jdxscroll) delete jdxscroll; if(noeditlist) delete noeditlist; for(int i=0; i odinlog(&ldr,"JDXwidgetDialog(...)"); grid=new GuiGridLayout(GuiDialog::get_widget(), 2, 1); jdx=new JcampDxBlockWidget(ldr,columns,GuiDialog::get_widget(),true,true, "", false, readonly); grid->add_widget( jdx, 0, 0 ); connect(jdx,SIGNAL(valueChanged()),this,SLOT(emitChanged())); connect(jdx,SIGNAL(doneButtonPressed()), this,SLOT(callDone()) ); GuiDialog::show(); #if QT_VERSION > 299 if(modal) GuiDialog::exec(); #endif } JDXwidgetDialog::~JDXwidgetDialog() { delete jdx; delete grid; } void JDXwidgetDialog::updateWidget() { jdx->updateWidget(); } void JDXwidgetDialog::callDone() { emit finished(); GuiDialog::done(); } void JDXwidgetDialog::emitChanged() { emit valueChanged(); } odin-1.8.5/odinqt/complex1d.cpp0000644000175000017500000002056211322062347013302 00000000000000#include // for mouse events #include "complex1d.h" #include "plot.h" complexfloatBox1D::complexfloatBox1D(const float *data1,const float *data2,int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel, const char *yAxisLabelLeft, const char *yAxisLabelRight, float min_x, float max_x, bool detachable) : QGroupBox(name, parent ) { Log odinlog("complexfloatBox1D","complexfloatBox1D(const float* ...)"); common_init(name,fixed_size,data1,data2,xAxisLabel,yAxisLabelLeft,yAxisLabelRight,detachable); refresh(data1,data2,n,min_x,max_x); } complexfloatBox1D::complexfloatBox1D(const double *data1,const double *data2,int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel, const char *yAxisLabelLeft, const char *yAxisLabelRight, float min_x, float max_x, bool detachable) : QGroupBox(name, parent ) { Log odinlog("complexfloatBox1D","complexfloatBox1D(const double* ...)"); common_init(name,fixed_size,data1,data2,xAxisLabel,yAxisLabelLeft,yAxisLabelRight,detachable); refresh(data1,data2,n,min_x,max_x); } void complexfloatBox1D::common_init(const char *name, bool fixed_size, bool data1, bool data2, const char *xAxisLabel, const char *yAxisLabelLeft, const char *yAxisLabelRight, bool detachable) { Log odinlog("complexfloatBox1D","common_init()"); detached=0; data1_ptr=0; data2_ptr=0; if(name) name_cache=name; if(xAxisLabel) xAxisLabel_cache=xAxisLabel; if(yAxisLabelLeft) yAxisLabelLeft_cache=yAxisLabelLeft; if(yAxisLabelRight) yAxisLabelRight_cache=yAxisLabelRight; detachable_cache=detachable; if(fixed_size) setFixedSize(_ARRAY_WIDGET_WIDTH_,_ARRAY_WIDGET_HEIGHT_); else setMinimumSize(_ARRAY_WIDGET_WIDTH_,_ARRAY_WIDGET_HEIGHT_); grid=new GuiGridLayout( this, 1, 1); plotter = new GuiPlot(this,fixed_size); ODINLOG(odinlog,normalDebug) << "xAxisLabel/yAxisLabelLeft/yAxisLabelRight=" << xAxisLabel << "/" << yAxisLabelLeft << "/" << yAxisLabelRight << STD_endl; plotter->set_x_axis_label(xAxisLabel); const char* data1_label=0; if(data1) data1_label=yAxisLabelLeft; const char* data2_label=0; if(data2) data1_label=yAxisLabelRight; plotter->set_y_axis_label(data1_label,data2_label); curveid1=0; curveid2=0; if(data1) curveid1 = plotter->insert_curve(false); if(data2) curveid2 = plotter->insert_curve(true); connect( plotter, SIGNAL(plotMousePressed(const QMouseEvent&)), SLOT(mousePressedInPlot(const QMouseEvent&)) ); connect( plotter, SIGNAL(plotMouseReleased(const QMouseEvent&)), SLOT(mouseReleasedInPlot(const QMouseEvent&)) ); grid->add_widget( plotter->get_widget(), 0, 0 ); } void complexfloatBox1D::create_x_cache(float min_x, float max_x, int n) { min_x_cache=min_x; max_x_cache=max_x; n_cache=n; int i; x_cache.resize(n); if(min_x odinlog("complexfloatBox1D","refresh(const float* ...)"); int i; ODINLOG(odinlog,normalDebug) << "data1/data2/n/min_x/max_x=" << data1 << "/" << data2 << "/" << n << "/" << min_x << "/" << max_x << STD_endl; create_x_cache(min_x, max_x, n); const double* x_arr=x_cache.c_array(); // call c_array only once data1_ptr=data2_ptr=0; if(data1) { data1_cache.resize(n); for(i=0; iset_curve_data(curveid1, x_arr, data1_ptr, n, nset_curve_data(curveid1, x_arr, data1_ptr, n, nset_curve_data(curveid2, x_arr, data2_ptr, n, nreplot(); if(detached) detached->refresh(data1_ptr,data2_ptr,n,min_x,max_x); } void complexfloatBox1D::mousePressedInPlot(const QMouseEvent& qme) { Log odinlog("complexfloatBox1D","mouseReleasedInPlot"); if(left_button(&qme,false)) { x_pressed=qme.x(); y_pressed=qme.y(); ODINLOG(odinlog,normalDebug) << "x_pressed/y_pressed=" << x_pressed << "/" << y_pressed << STD_endl; } if(right_button(&qme,false)) { GuiPopupMenu pm(this); pm.insert_item("Autoscale", this, SLOT(autoscale()), Qt::Key_F1); if(detachable_cache) pm.insert_item("Detach", this, SLOT(detach()), Qt::Key_F2); pm.popup(plotter->get_widget()->mapToGlobal(qme.pos())); } } void complexfloatBox1D::autoscale() { plotter->autoscale(); } void complexfloatBox1D::detach() { if(!detached) delete detached; detached=new DetachedComplexfloatBox1D(data1_ptr,data2_ptr,n_cache,this, name_cache.c_str(), false, xAxisLabel_cache.c_str(), yAxisLabelLeft_cache.c_str(), yAxisLabelRight_cache.c_str(), min_x_cache, max_x_cache); } void complexfloatBox1D::mouseReleasedInPlot(const QMouseEvent& qme) { Log odinlog("complexfloatBox1D","mouseReleasedInPlot"); // plotter->enable_outline(false); if(left_button(&qme,false)) { int x_released=qme.x(); int y_released=qme.y(); ODINLOG(odinlog,normalDebug) << "x_released/y_released=" << x_released << "/" << y_released << STD_endl; int low_x=x_pressed; if(x_releasedupp_x) upp_x=x_released; int upp_y=y_pressed; if(y_released>upp_y) upp_y=y_released; double x_axis_low=plotter->get_x(low_x); double x_axis_upp=plotter->get_x(upp_x); if(x_axis_lowset_x_axis_scale(x_axis_low,x_axis_upp); double y1_axis_low=plotter->get_y(upp_y); // reverse y-direction double y1_axis_upp=plotter->get_y(low_y); if(y1_axis_lowset_y_axis_scale(y1_axis_low,y1_axis_upp); ODINLOG(odinlog,normalDebug) << "y1_axis_low/y1_axis_upp=" << y1_axis_low << "/" << y1_axis_upp << STD_endl; double y2_axis_low=plotter->get_y(upp_y,true); // reverse y-direction double y2_axis_upp=plotter->get_y(low_y,true); if(y2_axis_lowset_y_axis_scale(y2_axis_low,y2_axis_upp,true); plotter->replot(); } } complexfloatBox1D::~complexfloatBox1D(){ delete plotter; delete grid; if(detached) delete detached; } ////////////////////////////////////////////////////////////////////////////////// void DetachedComplexfloatBox1D::create_grid() { grid = new GuiGridLayout( GuiDialog::get_widget(), 1, 1 ); grid->add_widget( cfb, 0, 0, GuiGridLayout::Center ); GuiDialog::show(); } DetachedComplexfloatBox1D::DetachedComplexfloatBox1D(const double *data1, const double *data2, int n,complexfloatBox1D *parent, const char *name, bool fixed_size, const char *xAxisLabel, const char *yAxisLabelLeft, const char *yAxisLabelRight, float min_x, float max_x) : GuiDialog(parent,name,false) { Log odinlog("DetachedComplexfloatBox1D","DetachedComplexfloatBox1D"); ODINLOG(odinlog,normalDebug) << "yAxisLabelLeft/xAxisLabel=" << yAxisLabelLeft << "/" << xAxisLabel << STD_endl; cfb=new complexfloatBox1D(data1, data2, n, GuiDialog::get_widget(), name, fixed_size, xAxisLabel, yAxisLabelLeft, yAxisLabelRight, min_x, max_x); create_grid(); } void DetachedComplexfloatBox1D::refresh(const double *data1,const double *data2,int n, float min_x, float max_x) { cfb->refresh(data1,data2,n,min_x,max_x); } DetachedComplexfloatBox1D::~DetachedComplexfloatBox1D() { delete grid; delete cfb; } odin-1.8.5/odinqt/odinqt.cpp0000644000175000017500000010642311363773557012726 00000000000000#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #if QT_VERSION > 0x03FFFF #define QT_VERSION_4 #else #define QT_VERSION_3 #endif #ifdef QT_VERSION_4 #include #include #include #include #include #include #include #include #else #include #include #include #include #endif #include "odinqt.h" #include "odinqt_callback.h" #include const char* OdinQt::get_compName() {return "OdinQt";} LOGGROUNDWORK(OdinQt) /////////////////////////////////////////////////// const char* c_str(const QString& qs) { if(qs.isEmpty()) return ""; #ifdef QT_VERSION_4 return qs.toAscii().constData(); #else return qs; #endif } int layout_border_size() { #ifdef QT_VERSION_4 return 0; #else return (3*QFontInfo(QFont(_FONT_TYPE_, _FONT_SIZE_)).pixelSize()/2); #endif } void init_label(QLabel* ql) { ql->setFrameStyle( QFrame::Box | QFrame::Sunken ); ql->setIndent( 0 ); #ifdef QT_VERSION_4 ql->setCursor(Qt::CrossCursor); #else ql->setCursor(Qt::crossCursor); #endif } bool left_button(const QMouseEvent* qme, bool return_current_state) { #ifdef QT_VERSION_4 if(return_current_state) return (qme->buttons() & Qt::LeftButton); else return (qme->button() & Qt::LeftButton); #else if(return_current_state) return (qme->state() & Qt::LeftButton); else return (qme->button() & Qt::LeftButton); #endif } bool right_button(const QMouseEvent* qme, bool return_current_state) { #ifdef QT_VERSION_4 if(return_current_state) return (qme->buttons() & Qt::RightButton); else return (qme->button() & Qt::RightButton); #else if(return_current_state) return (qme->state() & Qt::RightButton); else return (qme->button() & Qt::RightButton); #endif } bool middle_button(const QMouseEvent* qme, bool return_current_state) { #ifdef QT_VERSION_4 if(return_current_state) return (qme->buttons() & Qt::MidButton); else return (qme->button() & Qt::MidButton); #else if(return_current_state) return (qme->state() & Qt::MidButton); else return (qme->button() & Qt::MidButton); #endif } void add_tooltip(QWidget* w, const char* txt) { #ifdef QT_VERSION_4 w->setToolTip(txt); #else QToolTip::add(w,txt); #endif } void set_platform_defaults(QWidget* w, bool enable) { #ifdef Q_WS_MAC #ifdef QT_VERSION_4 w->setAttribute(Qt::WA_MacMetalStyle,enable); #endif #endif } STD_string get_save_filename(const char* caption, const char* startwith, const char* filter, QWidget* parent) { #ifdef QT_VERSION_4 QFileDialog::Options opts=0; #ifdef Q_WS_MAC opts=QFileDialog::DontUseNativeDialog; // native dialog does not work well, e.g. with symlinks #endif QString fname=QFileDialog::getSaveFileName(parent, caption, startwith, filter, 0, opts); #else QString fname=QFileDialog::getSaveFileName(startwith, filter, parent, "", caption); #endif return c_str(fname); } STD_string get_open_filename(const char* caption, const char* startwith, const char* filter, QWidget* parent) { #ifdef QT_VERSION_4 QFileDialog::Options opts=0; #ifdef Q_WS_MAC opts=QFileDialog::DontUseNativeDialog; // native dialog does not work well, e.g. with symlinks #endif QString fname=QFileDialog::getOpenFileName(parent, caption, startwith, filter, 0, opts); #else QString fname=QFileDialog::getOpenFileName(startwith, filter, parent, "", caption); #endif return c_str(fname); } STD_string get_directory(const char* caption, const char* startwith, QWidget* parent) { #ifdef QT_VERSION_4 QFileDialog::Options opts=QFileDialog::ShowDirsOnly; #ifdef Q_WS_MAC opts|=QFileDialog::DontUseNativeDialog; // native dialog does not work well, e.g. with symlinks #endif QString dname=QFileDialog::getExistingDirectory (parent, caption, startwith,opts); #else QString dname=QFileDialog::getExistingDirectory(startwith, parent, "", caption, true); #endif return c_str(dname); } bool message_question(const char* text, const char* caption, QWidget* parent, bool ask, bool error) { int result=0; if(ask) { // using QMessageBox::Ok and QMessageBox::Cancel does not work on Suse 9,10, // i.e. the order of buttons is mixed up due a patch to Qt, so we do it manually: QString okstr("Ok"); QString cancelstr("Cancel"); #if QT_VERSION > 0x030FFF result=QMessageBox::question(parent, caption, text, okstr, cancelstr); #else result=QMessageBox::information(parent, caption, text, okstr, cancelstr); #endif } else { if(error) result=QMessageBox::critical(parent, caption, text); else result=QMessageBox::information(parent, caption, text); } return (result==0); // return true if default button, which is 'Ok' , is clicked } /////////////////////////////////////////////////// int paintdevice_height(const QPaintDevice* qpd) { #ifdef QT_VERSION_4 return qpd->height(); #else QPaintDeviceMetrics metrics(qpd); return metrics.height(); #endif } int paintdevice_width(const QPaintDevice* qpd) { #ifdef QT_VERSION_4 return qpd->width(); #else QPaintDeviceMetrics metrics(qpd); return metrics.width(); #endif } /////////////////////////////////////////////////// svector get_possible_image_fileformats() { #ifdef QT_VERSION_4 QList fmtlist=QImageReader::supportedImageFormats(); int nfmts=fmtlist.size(); #else QStrList fmtlist=QImageIO::outputFormats(); int nfmts=fmtlist.count(); #endif svector result; result.resize(nfmts); for(int ifmt=0; ifmtsetMargin(layout_border_size()); } GuiGridLayout::~GuiGridLayout() { delete qgl; } void GuiGridLayout::add_widget(QWidget *w, int row, int column, Alignment alignment, int rowSpan, int columnSpan ) { #ifdef QT_VERSION_4 Qt::Alignment align=0; if(alignment==VCenter) align=Qt::AlignVCenter; if(alignment==VCenter) align=Qt::AlignVCenter; qgl->addWidget(w, row, column, rowSpan, columnSpan, align ); #else int align=0; if(alignment==VCenter) align=Qt::AlignVCenter; if(alignment==Center) align=Qt::AlignCenter; if(rowSpan==1 && columnSpan==1) qgl->addWidget( w, row, column, align ); else qgl->addMultiCellWidget( w, row, row+rowSpan-1, column, column+columnSpan-1, align ); #endif } void GuiGridLayout::set_col_stretch(int col, int factor) { #ifdef QT_VERSION_4 qgl->setColumnStretch(col,factor); #else qgl->setColStretch(col,factor); #endif } void GuiGridLayout::set_row_stretch(int row, int factor) { qgl->setRowStretch(row,factor); } void GuiGridLayout::set_col_minsize(int col, int minsize) { #ifdef QT_VERSION_4 qgl->setColumnMinimumWidth(col, minsize); #else qgl->addColSpacing(col, minsize); #endif } void GuiGridLayout::set_row_minsize(int row, int minsize) { #ifdef QT_VERSION_4 qgl->setRowMinimumHeight(row, minsize); #else qgl->addRowSpacing(row, minsize); #endif } /////////////////////////////////////////////////// GuiButton::GuiButton(QWidget *parent, QObject* receiver, const char* member, const char *onlabel,const char *offlabel, bool initstate) { ontext=onlabel; offtext=offlabel; qpb = new QPushButton(parent); if(onlabel && offlabel) { #ifdef QT_VERSION_4 qpb->setCheckable(true); #else qpb->setToggleButton(true); #endif set_toggled(initstate); // set initial text } else { if(ontext) qpb->setText(ontext); } qpb->setAutoDefault(false); // connect( qpb, SIGNAL(toggled(bool)), SLOT(setToggled(bool)) ); qpb->setFixedHeight( qpb->sizeHint().height() ); qpb->setFixedWidth( qpb->sizeHint().width() ); sd=new SlotDispatcher(this,receiver,member); } void GuiButton::set_text(bool state) { if(state) qpb->setText( ontext ); else qpb->setText( offtext ); } void GuiButton::set_toggled(bool state) { if(!(ontext && offtext)) return; set_text(state); #ifdef QT_VERSION_4 qpb->setChecked (state); #else qpb->setOn (state); #endif } void GuiButton::set_default(bool state) { qpb->setDefault (state); } QWidget* GuiButton::get_widget() { return qpb; } bool GuiButton::is_on() const { #ifdef QT_VERSION_4 return qpb->isChecked(); #else return qpb->isOn(); #endif } GuiButton::~GuiButton() { delete sd; delete qpb; } ///////////////////////////////////////////////// GuiLineEdit::GuiLineEdit(QWidget *parent, QObject* receiver, const char* member, int width, int height) { qle=new QLineEdit(parent); if(width>0 && height>0) qle->setFixedSize(width,height); sd=new SlotDispatcher(this,receiver,member); } GuiLineEdit::~GuiLineEdit() { delete sd; delete qle; } void GuiLineEdit::set_text(const char* txt) {qle->setText(txt);} const char* GuiLineEdit::get_text() const {return c_str(qle->text());} bool GuiLineEdit::is_modified() { #ifdef QT_VERSION_4 bool result=qle->isModified(); qle->setModified(false); #else bool result=qle->edited(); qle->setEdited(false); #endif return result; } QWidget* GuiLineEdit::get_widget() {return qle;} /////////////////////////////////////////////////// GuiPopupMenu::GuiPopupMenu(QWidget *parent) : id(0) { #ifdef QT_VERSION_4 qm=new QMenu(parent); #else qpm=new QPopupMenu(parent); #endif } GuiPopupMenu::~GuiPopupMenu() { /* // never deleted #ifdef QT_VERSION_4 delete qm; #else delete qpm; #endif */ } void GuiPopupMenu::insert_item(const char* text, const QObject* receiver, const char* member, int accel) { #ifdef QT_VERSION_4 qm->addAction(text, receiver, member, accel); #else id++; qpm->insertItem(text, receiver, member, accel, id); #endif } void GuiPopupMenu::insert_separator() { #ifdef QT_VERSION_4 qm->addSeparator(); #else qpm->insertSeparator(); #endif } void GuiPopupMenu::popup(const QPoint& p) { #ifdef QT_VERSION_4 qm->exec(p); // synchronous popup #else qpm->exec(p); // synchronous popup #endif } /////////////////////////////////////////////////// GuiSlider::GuiSlider(QWidget *parent, int minValue, int maxValue, int pageStep, int value, int tickInterval) : modified(false) { #ifdef QT_VERSION_4 qs=new QSlider(Qt::Horizontal, parent); qs->setRange(minValue, maxValue); qs->setPageStep(pageStep); qs->setValue(value); qs->setTickPosition(QSlider::TicksBelow); qs->setFocusPolicy( Qt::TabFocus ); #else qs=new QSlider(minValue, maxValue, pageStep, value, QSlider::Horizontal, parent, "QSlider" ); qs->setFocusPolicy( QWidget::TabFocus ); qs->setTickmarks( QSlider::Below ); #endif qs->setMinimumSize(2*SLIDER_CELL_WIDTH,SLIDER_CELL_HEIGHT); qs->setTickInterval(tickInterval ); } int GuiSlider::get_value() const {return qs->value();} void GuiSlider::set_value(int val) {modified=true; qs->setValue(val);} GuiSlider::~GuiSlider() { delete qs; } /////////////////////////////////////////////////// void GuiComboBox::set_names(const svector& names) { #ifdef QT_VERSION_4 for (unsigned int i=0; iinsertItem(i, names[i].c_str()); #else for (unsigned int i=0; iinsertItem( names[i].c_str() ); #endif set_current_item(0); } void GuiComboBox::common_init(QWidget* parent, const svector& names) { #ifdef QT_VERSION_4 qcb = new QComboBox(parent); qcb->setEditable(false); qcb->setSizeAdjustPolicy(QComboBox::AdjustToContents); // Width to fit all entries #else qcb = new QComboBox( FALSE, parent, "comboBox" ); qcb->setFixedWidth(qcb->sizeHint().width()); #endif qcb->setFixedHeight(qcb->sizeHint().height()); set_names(names); } GuiComboBox::GuiComboBox(QWidget* parent, const svector& names) { common_init(parent,names); } GuiComboBox::GuiComboBox(GuiToolBar* parent, const svector& names) { common_init(parent->get_widget(),names); #ifdef QT_VERSION_4 parent->qtb->addWidget(qcb); #endif } void GuiComboBox::set_current_item(int index) { #ifdef QT_VERSION_4 qcb->setCurrentIndex(index); #else qcb->setCurrentItem(index); #endif } int GuiComboBox::get_current_item() const { #ifdef QT_VERSION_4 return qcb->currentIndex(); #else return qcb->currentItem(); #endif } GuiComboBox::~GuiComboBox() { delete qcb; } /////////////////////////////////////////////////// GuiPainter::GuiPainter(QPixmap* qpm) { qpm_cache=qpm; qp=new QPainter(qpm); qp->setPen(_ARRAY_SELECTION_COLOR_); #ifndef QT_VERSION_4 qp->setFont(QFont(_FONT_TYPE_,_FONT_SIZE_)); #endif } GuiPainter::~GuiPainter() { delete qp; } void GuiPainter::moveTo(int x, int y) { #ifdef QT_VERSION_4 x_cache=x; y_cache=y; #else qp->moveTo(x,y); #endif } void GuiPainter::lineTo(int x, int y) { #ifdef QT_VERSION_4 qp->drawLine(x_cache,y_cache,x,y); x_cache=x; y_cache=y; #else qp->lineTo(x,y); #endif } void GuiPainter::repaint(QLabel* dst) { #ifdef QT_VERSION_4 // qp->drawPixmap(0,0,*qpm_cache); bool active=qp->isActive(); if(active) qp->end(); dst->setPixmap(*qpm_cache); if(active) { qp->begin(qpm_cache); qp->setPen(_ARRAY_SELECTION_COLOR_); } #else bitBlt( dst, 2, 2, qpm_cache ); #endif } bool GuiPainter::begin(QPixmap* qpm) { return qp->begin(qpm); } bool GuiPainter::end() { return qp->end(); } void GuiPainter::setPen(const char* pencolor, int linewidth, bool dotted, float lightdark) { Qt::PenStyle ps=Qt::SolidLine; if(dotted) ps=Qt::DotLine; QColor color(pencolor); int lightfactor=100+int(lightdark*90+0.5); QPen pen(color.light(lightfactor)); pen.setWidth(linewidth); pen.setStyle(ps); qp->setPen(pen); } void GuiPainter::fillRect( int x, int y, int w, int h, const QColor& col) { // Transparent: // QBrush qb(col); // qb.setStyle(Qt::Dense4Pattern); // qp->fillRect(QRect(x,y,w,h),qb); qp->fillRect(x,y,w,h,col); } void GuiPainter::drawRect(int x, int y, int w, int h) { qp->drawRect(x,y,w,h); } void GuiPainter::drawText( int x, int y, const QString& txt, const QColor& col) { qp->setPen( col); qp->drawText( x, y, txt); } QRegion* GuiPainter::draw_region(const STD_list& plist) { QRegion* rgn=0; if(plist.size()<3) return rgn; #ifdef QT_VERSION_4 QPolygon qpg(plist.size()); unsigned int index=0; for(STD_list::const_iterator it=plist.begin(); it!=plist.end(); ++it) { qpg.setPoint(index, it->x(), it->y()); index++; } rgn=new QRegion(qpg,Qt::WindingFill); #else QPointArray qpa(plist.size()); unsigned int index=0; for(STD_list::const_iterator it=plist.begin(); it!=plist.end(); ++it) { qpa.setPoint(index, it->x(), it->y()); index++; } rgn=new QRegion(qpa,TRUE); #endif qp->setClipRegion(*rgn); qp->fillRect (0,0,qpm_cache->width(),qpm_cache->height(),QBrush(QColor(_ARRAY_SELECTION_COLOR_),Qt::DiagCrossPattern)); return rgn; } /////////////////////////////////////////////////// GuiApplication::GuiApplication(int argc, char *argv[]) { // Create pristine copy of cmdline args for Qt before anything else argc4qt=argc; argv4qt=new char*[argc]; for(int iarg=0; iarg odinlog("GuiApplication","GuiApplication"); ODINLOG(odinlog,normalDebug) << "argc/argv=" << argc << "/" << argv << STD_endl; argc_cache=argc; argv_cache=argv; qa=new QApplication(argc4qt,argv4qt); #ifndef QT_VERSION_4 qa->setFont(QFont(_FONT_TYPE_, _FONT_SIZE_)); #endif // setting text color back to normal, even if noedit QPalette pal=qa->palette(); #ifdef QT_VERSION_4 pal.setColor(QPalette::Disabled, QPalette::Foreground, pal.color ( QPalette::Active, QPalette::Foreground ) ); pal.setColor(QPalette::Disabled, QPalette::Text, pal.color ( QPalette::Active, QPalette::Text ) ); qa->setPalette(pal); #else pal.setColor(QColorGroup::Foreground, pal.color ( QPalette::Normal, QColorGroup::Foreground ) ); pal.setColor(QColorGroup::Text, pal.color ( QPalette::Normal, QColorGroup::Text ) ); qa->setPalette(pal,true); #endif ODINLOG(odinlog,normalDebug) << "GuiApplication::argc/argv()=" << GuiApplication::argc() << "/" << GuiApplication::argv() << STD_endl; } int GuiApplication::start(QWidget* mainwidget) { #ifndef QT_VERSION_4 qa->setMainWidget(mainwidget); #endif // mainwidget->show(); return qa->exec(); } QObject* GuiApplication::get_object() {return qa;} void GuiApplication::quit() {qApp->quit();} int GuiApplication::argc() {return argc_cache;} char** GuiApplication::argv() {return argv_cache;} void GuiApplication::process_events() {qApp->processEvents();} GuiApplication::~GuiApplication() { qa->quit(); delete qa; // We must delete it to avoid error message when starting as edit widget in Paravision } int GuiApplication::argc4qt; char** GuiApplication::argv4qt; int GuiApplication::argc_cache; char** GuiApplication::argv_cache; /////////////////////////////////////////////////// GuiMainWindow::GuiMainWindow(QWidget* parent) { statusIcon=0; statusText=0; qmw=new QMainWindow(parent); // set_platform_defaults(qmw); // does not work because it alters attributes of all widgets } GuiMainWindow::~GuiMainWindow() { delete qmw; if(statusIcon) delete statusIcon; if(statusText) delete statusText; } void GuiMainWindow::show(QWidget* central_widget, bool show_toolbutton_text) { set_status_message("Ready ...", 2000); // necessary to show status bar in the first place #ifdef QT_VERSION_4 if(show_toolbutton_text) qmw->setToolButtonStyle(Qt::ToolButtonTextBesideIcon); #else qmw->setUsesTextLabel(show_toolbutton_text); #endif central_widget->setFocus(); qmw->setCentralWidget(central_widget); qmw->show(); } void GuiMainWindow::set_caption(const char* text) { STD_string captext(text); #ifdef QT_VERSION_4 qmw->setWindowTitle(captext.c_str()); #else qmw->setCaption(captext.c_str()); #endif } void GuiMainWindow::set_status_message(const char* text, int timeout_ms) { if(statusText) statusText->setText(text); else { #ifdef QT_VERSION_4 qmw->statusBar()->showMessage(text,timeout_ms); #else if(timeout_ms) qmw->statusBar()->message(text); else qmw->statusBar()->message(text,timeout_ms); #endif } } void GuiMainWindow::set_status_xpm(const char** xpm) { QPixmap qp(xpm); if(!statusIcon) { statusIcon=new QLabel(qmw->statusBar()); statusText=new QLabel(qmw->statusBar()); statusText->setMinimumWidth(qmw->width()-qp.width()); #ifdef QT_VERSION_4 qmw->statusBar()->addPermanentWidget(statusIcon); qmw->statusBar()->addPermanentWidget(statusText); #else qmw->statusBar()->addWidget(statusIcon,1,true); qmw->statusBar()->addWidget(statusText,1,true); #endif } statusIcon->setPixmap(qp); } QWidget* GuiMainWindow::get_widget() {return qmw;} void GuiMainWindow::insert_menu( const char* text, GuiPopupMenu* gpm) { #ifdef QT_VERSION_4 gpm->qm->setTitle(text); qmw->menuBar()->addMenu(gpm->qm); #else qmw->menuBar()->insertItem(text, gpm->qpm); #endif } void GuiMainWindow::insert_menu_separator() { #ifdef QT_VERSION_4 qmw->menuBar()->addSeparator(); #else qmw->menuBar()->insertSeparator(); #endif } void GuiMainWindow::close() { qmw->close(); } /////////////////////////////////////////////////// GuiScroll::GuiScroll(QWidget* child, QWidget* parent) { #ifdef QT_VERSION_4 qsa=new QScrollArea(parent); qsa->setWidget(child); qsa->setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOff); qsa->setMinimumWidth(child->width()); #else qsv=new QScrollView(parent); qsv->addChild(child); qsv->setHScrollBarMode(QScrollView::AlwaysOff); qsv->setMinimumWidth(child->width()); #endif } QWidget* GuiScroll::get_widget() { #ifdef QT_VERSION_4 return qsa; #else return qsv; #endif } GuiScroll::~GuiScroll() { #ifdef QT_VERSION_4 delete qsa; #else delete qsv; #endif } /////////////////////////////////////////////////// class QDialogDerived : public QDialog { public: QDialogDerived(GuiDialog* user, QWidget *parent, const char* caption, bool modal) : #ifdef QT_VERSION_4 QDialog(parent) { QDialog::setModal(modal); QDialog::setWindowTitle(caption); #else QDialog(parent,"",modal) { QDialog::setCaption(caption); #endif user_cache=user; } void call_done(int r) { QDialog::done(r); } protected: void paintEvent(QPaintEvent* event) { // overloaded from QWidget QDialog::paintEvent(event); user_cache->repaint(); } void closeEvent(QCloseEvent* event) { // overloaded from QWidget QDialog::closeEvent(event); user_cache->close(); } private: GuiDialog* user_cache; }; GuiDialog::GuiDialog(QWidget *parent, const char* caption, bool modal) { qd=new QDialogDerived(this, parent, caption, modal); } void GuiDialog::show() { qd->show(); } void GuiDialog::cancel() { qd->call_done(0); } void GuiDialog::done() { qd->call_done(1); // GuiDialog::hide(); // deleting causes segfault. why? I dunno ... } void GuiDialog::hide() {qd->hide();} int GuiDialog::exec() {return qd->exec();} QWidget* GuiDialog::get_widget() {return qd;} GuiDialog::~GuiDialog() { delete qd; } ///////////////////////////////////////////////// GuiProgressDialog::GuiProgressDialog(QWidget *parent, bool modal, int total_steps) { #ifdef QT_VERSION_4 qpd=new QProgressDialog("", "Cancel", 0, total_steps, parent); qpd->setModal(modal); #else qpd=new QProgressDialog("", "Cancel", total_steps, parent, "progress", modal); #endif if(total_steps) qpd->setMinimumDuration(1000); else qpd->setMinimumDuration(100); // zero value produces event-timing problems in Qt set_progress(0); } void GuiProgressDialog::set_progress(int progr) { #ifdef QT_VERSION_4 qpd->setValue(progr); #else qpd->setProgress(progr); #endif } int GuiProgressDialog::get_progress() const { #ifdef QT_VERSION_4 return qpd->value(); #else return qpd->progress(); #endif } void GuiProgressDialog::set_total_steps(int steps) { #ifdef QT_VERSION_4 qpd->setMaximum(steps); #else qpd->setTotalSteps(steps); #endif } bool GuiProgressDialog::was_cancelled() const { #ifdef QT_VERSION_4 return qpd->wasCanceled(); #else return qpd->wasCancelled(); #endif } void GuiProgressDialog::reset() { qpd->reset(); set_progress(0); } void GuiProgressDialog::set_text(const char* txt) { qpd->setLabelText(txt); } void GuiProgressDialog::show() { qpd->show(); } void GuiProgressDialog::hide() { qpd->hide(); } GuiProgressDialog::~GuiProgressDialog() { delete qpd; } ///////////////////////////////////////////////// GuiImage::GuiImage(unsigned char* data, int width, int height, bool colormap) { Log odinlog("GuiImage","GuiImage"); ODINLOG(odinlog,normalDebug) << "width/height/colormap=" << width << "/" << height << "/" << colormap << STD_endl; #ifdef QT_VERSION_4 qi=new QImage( data, width, height, QImage::Format_Indexed8); qi->setNumColors (256); #else qi=new QImage( data, width, height, 8, 0, 256, QImage::IgnoreEndian); #endif QColor qc; for(int i=0; i<256; i++) { if(colormap) { int hue=int(240.0*(1.0-float(i)/255.0)); qc.setHsv(hue,255,255); qi->setColor(i, qc.rgb() ); if(i==0) qi->setColor(0, qRgb(0,0,0) ); // lowest value black } else qi->setColor(i, qRgb(i,i,i) ); // simple gray scale } } QPixmap* GuiImage::create_pixmap() const { #ifdef QT_VERSION_4 return new QPixmap(QPixmap::fromImage(*qi)); #else QPixmap* qpm=new QPixmap(); qpm->convertFromImage(*qi); return qpm; #endif } GuiImage::~GuiImage() { delete qi; } ///////////////////////////////////////////////// GuiListView::GuiListView(QWidget *parent, const svector& column_labels, int first_column_width, int min_height, GuiListViewCallback* callback, bool tree) { #ifdef QT_VERSION_4 QStringList qsl; for(unsigned int i=0; i1) width_factor=2; if(tree) { qtrw=new QTreeWidget(parent); qtrw->setColumnCount(column_labels.size()); qtrw->setHeaderLabels(qsl); qtrw->setSortingEnabled(false); if(min_height>0) qtrw->setMinimumHeight(min_height); if(first_column_width>0) qtrw->setMinimumWidth(width_factor*first_column_width); qtrw->header()->resizeSection(0, first_column_width); } else { qtw=new QTableWidget(parent); qtw->setColumnCount(column_labels.size()); qtw->setHorizontalHeaderLabels(qsl); if(min_height>0) qtw->setMinimumHeight(min_height); if(first_column_width>0) { qtw->setMinimumWidth(width_factor*first_column_width); qtw->horizontalHeader()->resizeSection(0, first_column_width); } } #else qlv=new QListView(parent); for(unsigned int i=0; iaddColumn (column_labels[i].c_str()); } if(first_column_width>0) { qlv->setColumnWidthMode(0,QListView::Manual); qlv->setColumnWidth(0,first_column_width); } if(min_height>0) { qlv->setMinimumHeight(min_height); } qlv->setSorting(-1); #endif sd=0; if(callback) sd=new SlotDispatcher(this, callback); } QWidget* GuiListView::get_widget() { #ifdef QT_VERSION_4 if(qtrw) return qtrw; if(qtw) return qtw; return 0; #else return qlv; #endif } GuiListView::~GuiListView() { delete sd; #ifdef QT_VERSION_4 if(qtrw) delete qtrw; if(qtw) delete qtw; #else delete qlv; #endif } ///////////////////////////////////////////////// #ifndef QT_VERSION_4 void create_qstring_list(STD_vector& label, const svector& column_entries) { int ncols=column_entries.size(); if(ncols>8) ncols=8; label.resize(8); for(int i=0; i odinlog("GuiListItem","GuiListItem"); common_init(); #ifdef QT_VERSION_4 int ncols=column_entries.size(); if(!ncols) return; if(parent->qtrw) { // tree view qtrwi=new QTreeWidgetItem(parent->qtrw); for(int icol=0; icolsetText(icol, column_entries[icol].c_str()); } parent_qtrw=parent->qtrw; parent->qtrw->expandItem(qtrwi); //#warning GuiListItem: Implement me: setOpen(true), setSelected(false) } else { qtwi=new QTableWidgetItem[ncols]; int row=parent->qtw->rowCount(); parent->qtw->setRowCount(row+1); for(int icol=0; icolqtw->setItem(row, icol, &(qtwi[icol])); } if(checkable) { qtwi[0].setFlags(qtwi[0].flags() | Qt::ItemIsUserCheckable); Qt::CheckState state=Qt::Unchecked; if(initstate) state=Qt::Checked; qtwi[0].setCheckState(state); } (*tablemap)[&(qtwi[0])]=this; } #else QListViewItem* last=parent->qlv->lastItem(); if(checkable) { qcli=new QCheckListItem (parent->qlv, column_entries[0].c_str(), QCheckListItem::CheckBox); qcli->setOn(initstate); } else { STD_vector label; create_qstring_list(label,column_entries); ODINLOG(odinlog,normalDebug) << "parent->qlv=" << parent->qlv << STD_endl; qlvi=new QListViewItem(parent->qlv, label[0], label[1], label[2], label[3], label[4], label[5], label[6], label[7]); ODINLOG(odinlog,normalDebug) << "qlvi=" << qlvi << STD_endl; if(last) qlvi->moveItem(last); // append at end qlvi->setSelected(false); qlvi->setOpen(true); (*listmap)[qlvi]=this; } #endif } GuiListItem::GuiListItem(GuiListItem* parent, GuiListItem* after, const svector& column_entries) { Log odinlog("GuiListItem","GuiListItem"); common_init(); #ifdef QT_VERSION_4 QTreeWidgetItem* parent_qtrwi=0; if(parent) parent_qtrwi=parent->qtrwi; QTreeWidgetItem* after_qtrwi=0; if(after) after_qtrwi=after->qtrwi; qtrwi=new QTreeWidgetItem(parent_qtrwi, after_qtrwi); for(int icol=0; icolsetText(icol, column_entries[icol].c_str()); } parent_qtrw=parent->parent_qtrw; if(parent_qtrw) parent_qtrw->expandItem(qtrwi); //#warning GuiListItem: Implement me: setOpen(true) #else STD_vector label; create_qstring_list(label,column_entries); QListViewItem* parent_qlvi=0; if(parent) parent_qlvi=parent->qlvi; ODINLOG(odinlog,normalDebug) << "parent/parent_qlvi=" << parent << "/" << parent_qlvi << STD_endl; if(after && after->qlvi) { ODINLOG(odinlog,normalDebug) << "after->qlvi=" << after->qlvi << STD_endl; qlvi=new QListViewItem(parent_qlvi, after->qlvi, label[0], label[1], label[2], label[3], label[4], label[5], label[6], label[7]); } else { ODINLOG(odinlog,normalDebug) << "after=0" << STD_endl; qlvi=new QListViewItem(parent_qlvi, label[0], label[1], label[2], label[3], label[4], label[5], label[6], label[7]); } qlvi->setOpen(true); #endif } bool GuiListItem::is_checked() const { #ifdef QT_VERSION_4 if(qtwi) return ((qtwi[0].checkState())==Qt::Checked); #else if(qcli) return qcli->isOn(); #endif return false; } const char* GuiListItem::get_text() const { #ifdef QT_VERSION_4 if(qtwi) return c_str(qtwi[0].text()); #else if(qcli) return c_str(qcli->text()); #endif return ""; } GuiListItem::~GuiListItem() { #ifdef QT_VERSION_4 if(qtwi) delete[] qtwi; if(qtrwi) delete qtrwi; #else if(qlvi) delete qlvi; if(qcli) delete qcli; #endif } void GuiListItem::init_static() { #ifdef QT_VERSION_4 tablemap=new STD_map; #else listmap=new STD_map; #endif } void GuiListItem::destroy_static() { #ifdef QT_VERSION_4 delete tablemap; #else delete listmap; #endif } STD_map* GuiListItem::listmap; STD_map* GuiListItem::tablemap; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; /////////////////////////////////////////////////////////// GuiProgressBar::GuiProgressBar(QWidget *parent, int total_steps) { #ifdef QT_VERSION_4 qpb=new QProgressBar(parent); qpb->setMinimum(0); qpb->setMaximum(total_steps); #else qpb=new QProgressBar (total_steps, parent); #endif } GuiProgressBar::~GuiProgressBar() { delete qpb; } void GuiProgressBar::set_progress(int progr) { #ifdef QT_VERSION_4 qpb->setValue(progr); #else qpb->setProgress(progr); #endif } void GuiProgressBar::set_min_width(int w) { qpb->setMinimumWidth(w); } QWidget* GuiProgressBar::get_widget() { return qpb; } ////////////////////////////////////////////////////////////////////// GuiScrollBar::GuiScrollBar(QWidget* parent) { qsb=new QScrollBar(Qt::Horizontal, parent); } GuiScrollBar::~GuiScrollBar() { delete qsb; } void GuiScrollBar::set_values(int min, int max, int linestep, int pagestep, int value) { #ifdef QT_VERSION_4 qsb->setMinimum(min); qsb->setMaximum(max); qsb->setSingleStep(linestep); #else qsb->setMinValue(min); qsb->setMaxValue(max); qsb->setLineStep(linestep); #endif qsb->setPageStep(pagestep); qsb->setValue(value); } QScrollBar* GuiScrollBar::get_widget() { return qsb; } ///////////////////////////////////////////////// GuiToolBar::GuiToolBar(GuiMainWindow* parent, const char* label) { qtb=new QToolBar(label, parent->qmw); #ifdef QT_VERSION_4 parent->qmw->addToolBar(qtb); #endif } GuiToolBar::~GuiToolBar() { delete qtb; } QWidget* GuiToolBar::get_widget() { return qtb; } void GuiToolBar::add_separator() { qtb->addSeparator(); } ///////////////////////////////////////////////// GuiToolButton::GuiToolButton(GuiToolBar* parent, const char** xpm, const char* label, QObject* receiver, const char* member, bool checkable, bool initstate ) { #ifdef QT_VERSION_4 qtb=new QToolButton(parent->qtb); if(xpm) qtb->setIcon(QPixmap(xpm)); qtb->setCheckable(checkable); parent->qtb->addWidget(qtb); #else qtb=new QToolButton(parent->qtb); if(xpm) qtb->setIconSet(QPixmap(xpm)); qtb->setToggleButton(checkable); #endif set_on(initstate); if(xpm) set_tooltip(label); else set_label(label); sd=new SlotDispatcher(this,receiver,member); } GuiToolButton::~GuiToolButton() { Log odinlog("GuiToolButton","~GuiToolButton"); ODINLOG(odinlog,normalDebug) << "Deleting sd" << STD_endl; delete sd; #ifndef QT_VERSION_4 ODINLOG(odinlog,normalDebug) << "Deleting qtb" << STD_endl; delete qtb; // will be done by the parent toolbar on Qt4 #endif } bool GuiToolButton::is_on() const { #ifdef QT_VERSION_4 return qtb->isChecked(); #else return qtb->isOn(); #endif } void GuiToolButton::set_on(bool flag) { #ifdef QT_VERSION_4 qtb->setChecked(flag); #else qtb->setOn(flag); #endif } void GuiToolButton::set_enabled(bool flag) { qtb->setEnabled(flag); } void GuiToolButton::set_label(const char* text) { #ifdef QT_VERSION_4 qtb->setText(text); #else qtb->setTextLabel(text); #endif } void GuiToolButton::set_tooltip(const char* text) { add_tooltip(qtb,text); } ///////////////////////////////////////////////// GuiPrinter::GuiPrinter() { qp=new QPrinter(QPrinter::HighResolution); qp->setOrientation(QPrinter::Landscape); } bool GuiPrinter::setup(QWidget* parent) { #ifdef QT_VERSION_4 QPrintDialog* qpd=new QPrintDialog(qp,parent); return bool(qpd->exec()); #else return qp->setup(parent); #endif } QPaintDevice* GuiPrinter::get_device() { return qp; } GuiPrinter::~GuiPrinter() { delete qp; } ///////////////////////////////////////////////// #define TEXTVIEW_MAXLINES 1000 GuiTextView::GuiTextView(QWidget* parent, int minwidth, int minheight) { qte=new QTextEdit(parent); qte->setReadOnly(true); qte->setMinimumSize(minwidth, minheight); #ifdef QT_VERSION_4 qte->document()->setMaximumBlockCount(TEXTVIEW_MAXLINES); // only available for Qt 4.2 or later versions qte->setLineWrapMode(QTextEdit::NoWrap); #else qte->setTextFormat(Qt::LogText); #if QT_VERSION > 0x0301FF qte->setMaxLogLines(TEXTVIEW_MAXLINES); #endif #endif } GuiTextView::~GuiTextView() { delete qte; } void GuiTextView::set_text(const char* txt) { #ifdef QT_VERSION_4 qte->setPlainText(txt); #else qte->setText(txt); #endif scroll_end(); } void GuiTextView::append_text(const char* txt) { qte->append(txt); scroll_end(); } void GuiTextView::scroll_end() { #ifdef QT_VERSION_4 QTextCursor qtc(qte->textCursor()); qtc.movePosition(QTextCursor::End); qtc.movePosition(QTextCursor::StartOfLine); qte->setTextCursor(qtc); qte->ensureCursorVisible(); #else qte->setContentsPos(0,qte->contentsHeight()+TEXTVIEW_MAXLINES); #endif } QWidget* GuiTextView::get_widget() { return qte; } odin-1.8.5/odinqt/jdxwidget.cpp0000644000175000017500000007550211363773557013424 00000000000000 // Include Qt stuff first to avoid ambiguities with 'debug' symbol #include "intedit.h" #include "floatedit.h" #include "float1d.h" #include "complex1d.h" #include "float3d.h" #include "boolbutton.h" #include "enumbox.h" #include "stringbox.h" #include "jdxwidget.h" #include "jdxblockwidget.h" #include #include #include #include #include /** * * Helper class to analayze the value range of a (scalar) JDX parameter */ class RangeHelper { public: double minval; double maxval; RangeHelper(const JcampDxClass& ldr) { minval=ldr.get_minval(); maxval=ldr.get_maxval(); } bool has_range() { if(maxval>minval) return true; else return false; } double get_stepsize(unsigned int maxsteps) { Log odinlog("RangeHelper","get_stepsize"); double result=fabs(maxval-minval)/double(maxsteps); double mantisse=log10(result); mantisse=int(mantisse-1.0); result=double(int(result*pow(10.0,-mantisse)))*pow(10.0,mantisse); ODINLOG(odinlog,normalDebug) << "minval=" << minval << STD_endl; ODINLOG(odinlog,normalDebug) << "maxval=" << maxval << STD_endl; ODINLOG(odinlog,normalDebug) << "mantisse=" << mantisse << STD_endl; ODINLOG(odinlog,normalDebug) << "stepsize=" << result << STD_endl; return result; } }; ///////////////////////////////////////////////////////////////////////// JDXwidget::JDXwidget(JcampDxClass& ldr,unsigned int columns, QWidget *parent, bool doneButton, const char* omittext, bool storeLoadButtons ) : QWidget(parent), val(ldr) { Log odinlog(&val,"JDXwidget(...)"); vport=this; widget_cache=0; blockwidget=0; intslider=0; intedit=0; floatslider=0; floatedit=0; enumwidget=0; boolwidget=0; floatArrempty=0; floatArrwidget1=0; floatArredit=0; // doubleArrwidget1=0; floatArrwidget2=0; complexArrwidget=0; stringwidget=0; filenamewidget=0; funcwidget=0; formulawidget=0; triplewidget=0; grid=0; rows=1; cols=1; if(columns<1) columns=1; bool cast_success=true; ldrlabel_uncut=replaceStr(ldr.get_label(),omittext,"",allOccurences); ldrlabel=ldrlabel_uncut; label_cut=false; if(ldrlabel.length()>_MAX_LABEL_LENGTH_) { label_cut=true; ldrlabel=ldrlabel_uncut.substr(0,_MAX_LABEL_LENGTH_)+"..."; } STD_string unit(ldr.get_unit()); if(unit!="") ldrlabel+=" ["+unit+"]"; ODINLOG(odinlog,normalDebug) << "ldrlabel/omittext=" << ldrlabel << "/" << omittext << STD_endl; grid=new GuiGridLayout( vport, 1, 1, false); ODINLOG(odinlog,normalDebug) << "grid & layout done" << STD_endl; /*---------------- JDX types BEGIN ------------------------*/ /*---------------- JcampDxBlock ------------------------*/ JcampDxBlock* dumblock=ldr.cast(dumblock); if(dumblock) { label_cut=false; if(dumblock->is_embedded()) cols=2; blockwidget=new JcampDxBlockWidget(*dumblock,columns,vport,doneButton,false,omittext,storeLoadButtons); ODINLOG(odinlog,normalDebug) << "JcampDxBlock: JcampDxBlockWidget done" << STD_endl; GuiGridLayout::Alignment alignment = GuiGridLayout::Default; if(dumblock->numof_pars()<_MAX_SUBWIDGETS_FOR_ALIGNCENT_) alignment=GuiGridLayout::VCenter; set_widget(blockwidget ,alignment, true); ODINLOG(odinlog,normalDebug) << "JcampDxBlock: set_widget done" << STD_endl; connect(blockwidget,SIGNAL(valueChanged()),this,SLOT(emitValueChanged())); connect(blockwidget,SIGNAL(doneButtonPressed()),this,SLOT(emitDone())); ODINLOG(odinlog,normalDebug) << "JcampDxBlock: connect done" << STD_endl; } ODINLOG(odinlog,normalDebug) << "JcampDxBlock done" << STD_endl; /*---------------- JDXint ------------------------*/ int* dumint=ldr.cast(dumint); if(dumint) { RangeHelper intrange(ldr); if(intrange.has_range() && ldr.get_parmode()==edit) { cols=2; long step=int(intrange.get_stepsize(_MAX_SLIDER_STEPS_)); if(step<1) step=1; ODINLOG(odinlog,normalDebug) << "processing >" << ldrlabel << "<" << STD_endl; intslider=new intScientSlider(int(intrange.minval),int(intrange.maxval),step,*dumint,vport,ldrlabel.c_str()); set_widget(intslider); connect(intslider,SIGNAL(intScientSliderValueChanged( int )),this,SLOT(changeJDXint( int ))); connect(this,SIGNAL(newintval( int )),intslider,SLOT(setintScientSliderValue( int ))); } else { intedit=new intLineBox(*dumint,vport,ldrlabel.c_str()); set_widget(intedit); connect(intedit,SIGNAL(intLineBoxValueChanged( int )),this,SLOT(changeJDXint( int ))); connect(this,SIGNAL(newintval( int )),intedit,SLOT(setintLineBoxValue( int ))); } } ODINLOG(odinlog,normalDebug) << "JDXint done" << STD_endl; /*---------------- JDXfloat & JDXdouble ------------------------*/ float* dumfloat=ldr.cast(dumfloat); double* dumdouble=ldr.cast(dumdouble); if(dumfloat || dumdouble ) { float val=0.0; if(dumfloat) val=(*dumfloat); if(dumdouble) val=(*dumdouble); RangeHelper floatrange(ldr); if(floatrange.has_range() && ldr.get_parmode()==edit) { cols=2; floatslider=new floatScientSlider(floatrange.minval,floatrange.maxval,floatrange.get_stepsize(_MAX_SLIDER_STEPS_),val,_FLOAT_DIGITS_,vport,ldrlabel.c_str()); set_widget(floatslider); connect(floatslider,SIGNAL(floatScientSliderValueChanged( float )),this,SLOT(changeJDXfloat( float ))); connect(this,SIGNAL(newfloatval( float )),floatslider,SLOT(setfloatScientSliderValue( float ))); } else { floatedit=new floatLineBox(val,_FLOAT_DIGITS_,vport,ldrlabel.c_str()); set_widget(floatedit); connect(floatedit,SIGNAL(floatLineBoxValueChanged( float )),this,SLOT(changeJDXfloat( float ))); connect(this,SIGNAL(newfloatval( float )),floatedit,SLOT(setfloatLineBoxValue( float ))); } } ODINLOG(odinlog,normalDebug) << "JDXfloat & JDXdouble done" << STD_endl; /*---------------- JDXenum ------------------------*/ JDXenum* dumenum=ldr.cast(dumenum); if(dumenum) { enumwidget=new enumBox(dumenum->get_alternatives(),vport,ldrlabel.c_str()); enumwidget->setValue(dumenum->get_item_index()); set_widget(enumwidget); ODINLOG(odinlog,normalDebug) << "widget done" << STD_endl; connect(enumwidget,SIGNAL(newVal( int )), this,SLOT(changeJDXenum( int ))); connect(this,SIGNAL(newenumval( int )),enumwidget,SLOT(setValue( int ))); ODINLOG(odinlog,normalDebug) << "connect done" << STD_endl; } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXenum done" << STD_endl; /*---------------- JDXbool ------------------------*/ bool* dumbool=ldr.cast(dumbool); if(dumbool) { boolwidget=new buttonBox("Yes","No",*dumbool, vport, ldrlabel.c_str()); set_widget(boolwidget); connect(boolwidget,SIGNAL(buttonToggled(bool)), this,SLOT(changeJDXbool( bool ))); connect(this,SIGNAL(newboolval( bool )),boolwidget,SLOT(setToggleState( bool ))); } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXbool done" << STD_endl; /*---------------- JDXaction ------------------------*/ JDXaction* dumaction=ldr.cast(dumaction); if(dumaction && (dumaction->get_parmode()==edit) ) { actionwidget=new buttonBox("Now",vport,ldrlabel.c_str()); set_widget(actionwidget); connect(actionwidget,SIGNAL(buttonClicked()), this,SLOT(changeJDXaction())); } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXaction done" << STD_endl; /*---------------- JDXfloatArr ------------------------*/ farray* dumfarray=ldr.cast(dumfarray); if(dumfarray) { create_or_update_floatArrwidget(*dumfarray,true); } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXfloatArr done" << STD_endl; /*---------------- JDXdoubleArr ------------------------*/ darray* dumdarray=ldr.cast(dumdarray); if(dumdarray) { ODINLOG(odinlog,normalDebug) << "dumdarray=" << (void*)dumdarray << "/" << STD_string(dumdarray->get_extent()) << STD_endl; farray farr(dumdarray->get_extent()); for(unsigned int i=0; idim()=" << dumcarray->dim() << STD_endl; if(dumcarray->dim()==1) { fvector ampvec=amplitude(*dumcarray); fvector phavec=phase(*dumcarray); rows=3; cols=2; ODINLOG(odinlog,normalDebug) << "rows/cols=" << rows << "/" << cols << STD_endl; ArrayScale x_axprops=val.get_gui_props().scale[xPlotScale]; ArrayScale y1_axprops=val.get_gui_props().scale[yPlotScaleLeft]; ArrayScale y2_axprops=val.get_gui_props().scale[yPlotScaleRight]; bool fixedsize=val.get_gui_props().fixedsize; complexArrwidget=new complexfloatBox1D(ampvec.c_array(),phavec.c_array(),dumcarray->length(),vport,ldrlabel.c_str(),fixedsize, x_axprops.get_label_with_unit().c_str(), y1_axprops.get_label_with_unit().c_str(), y2_axprops.get_label_with_unit().c_str(), x_axprops.minval,x_axprops.maxval,val.get_gui_props().fixedsize); set_widget(complexArrwidget, GuiGridLayout::Default, true); connect(this,SIGNAL(newcomplexArr( const float*, const float*, int, float, float)), complexArrwidget,SLOT(refresh( const float*, const float*, int, float, float))); } } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXcomplexArr done" << STD_endl; /*---------------- JDXfunction ------------------------*/ JDXfilter("dummy"); // created dummy to force initialization of registered_functions (in USING_WIN32/DLL) ODINLOG(odinlog,normalDebug) << "Testing for function" << STD_endl; JDXfunction* dumfunc=ldr.cast(dumfunc); if(dumfunc) { ODINLOG(odinlog,normalDebug) << "LDR is function" << STD_endl; cols=2; funcwidget=new enumBox(dumfunc->get_alternatives(),vport,ldrlabel.c_str(),true,true); ODINLOG(odinlog,normalDebug) << "funcwidget done" << STD_endl; funcwidget->setValue(dumfunc->get_function_index()); ODINLOG(odinlog,normalDebug) << "setValue done" << STD_endl; set_widget(funcwidget); ODINLOG(odinlog,normalDebug) << "set_widget done" << STD_endl; connect(funcwidget,SIGNAL(newVal( int )), this,SLOT(changeJDXfunction( int ))); connect(funcwidget,SIGNAL(edit()), this,SLOT(editJDXfunction())); connect(funcwidget,SIGNAL(info()), this,SLOT(infoJDXfunction())); connect(this,SIGNAL(newfuncval( int )),funcwidget,SLOT(setValue( int ))); ODINLOG(odinlog,normalDebug) << "connect done" << STD_endl; } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXfunction done" << STD_endl; /*---------------- JDXstring ------------------------*/ STD_string* dumstring=ldr.cast(dumstring); if(dumstring) { cols=2; stringwidget=new stringBox(dumstring->c_str(),vport,ldrlabel.c_str()); set_widget(stringwidget); connect(stringwidget,SIGNAL(stringBoxTextEntered( const char* )), this,SLOT(changeJDXstring( const char* ))); connect(this,SIGNAL(newstringval( const char* )),stringwidget,SLOT(setstringBoxText( const char* ))); } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXstring done" << STD_endl; /*---------------- JDXfileName ------------------------*/ JDXfileName* dumfileName=ldr.cast(dumfileName); if(dumfileName) { cols=2; filenamewidget=new stringBox(dumfileName->c_str(),vport,ldrlabel.c_str(),"Browse"); set_widget(filenamewidget); connect(filenamewidget,SIGNAL(stringBoxTextEntered( const char* )), this,SLOT(changeJDXfileName( const char* ))); connect(filenamewidget,SIGNAL(stringBoxButtonPressed()), this,SLOT(browseJDXfileName())); connect(this,SIGNAL(newfilenameval( const char* )),filenamewidget,SLOT(setstringBoxText( const char* ))); } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXfileName done" << STD_endl; /*---------------- JDXformula ------------------------*/ JDXformula* dumformula=ldr.cast(dumformula); if(dumformula) { cols=2; formulawidget=new stringBox(dumformula->c_str(),vport,ldrlabel.c_str(),"Syntax"); set_widget(formulawidget); connect(formulawidget,SIGNAL(stringBoxTextEntered( const char* )), this,SLOT(changeJDXformula( const char* ))); connect(formulawidget,SIGNAL(stringBoxButtonPressed()), this,SLOT(infoJDXformula())); connect(this,SIGNAL(newformulaval( const char* )),formulawidget,SLOT(setstringBoxText( const char* ))); } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXformula done" << STD_endl; /*---------------- JDXtriple ------------------------*/ JDXtriple* dumtriple=ldr.cast(dumtriple); if(dumtriple) { cols=2; triplewidget=new floatLineBox3D((*dumtriple)[0],(*dumtriple)[1],(*dumtriple)[2],_FLOAT_DIGITS_,vport,ldrlabel.c_str()); set_widget(triplewidget); connect(triplewidget,SIGNAL(floatLineBox3DValueChanged(float,float,float)), this,SLOT(changeJDXtriple(float,float,float))); connect(this,SIGNAL(newtripleval(float,float,float)),triplewidget,SLOT(setfloatLineBox3DValue(float,float,float))); } else cast_success=false; ODINLOG(odinlog,normalDebug) << "JDXtriple done" << STD_endl; /*---------------- JDX types swith END ------------------------*/ if(!cast_success) ODINLOG(odinlog,normalDebug) << "Unable to proces parameter >" << ldrlabel << "<" << STD_endl; return; } void JDXwidget::write_pixmap(const char* fname, const char* format, bool dump_all) const { if(floatArrwidget2) floatArrwidget2->write_pixmap(fname, format, dump_all); } void JDXwidget::write_map_legend(const char* fname, const char* format) const { if(floatArrwidget2) floatArrwidget2->write_map_legend(fname, format); } JDXwidget::~JDXwidget(){ // do not acces 'val' here because it might be deleted already if(blockwidget) delete blockwidget; if(intslider) delete intslider; if(intedit) delete intedit; if(floatslider) delete floatslider; if(floatedit) delete floatedit; if(enumwidget) delete enumwidget; if(boolwidget) delete boolwidget; if(floatArrempty) delete floatArrempty; if(floatArrwidget1) delete floatArrwidget1; if(floatArredit) delete floatArredit; if(floatArrwidget2) delete floatArrwidget2; // if(doubleArrwidget1) delete doubleArrwidget1; if(complexArrwidget) delete complexArrwidget; if(funcwidget) delete funcwidget; if(stringwidget) delete stringwidget; if(filenamewidget) delete filenamewidget; if(formulawidget) delete formulawidget; if(triplewidget) delete triplewidget; if(grid) delete grid; } STD_string JDXwidget::get_label() const {return val.get_label();} void JDXwidget::set_widget(QWidget *widget, GuiGridLayout::Alignment alignment, bool override_enabled) { Log odinlog(&val,"set_widget"); widget_cache=widget; parameterMode parmode=val.get_parmode(); ODINLOG(odinlog,normalDebug) << "parmode(" << ldrlabel << ")=" << parmode << STD_endl; if(parmode==hidden) return; bool enabled=true; if(parmode>=noedit) enabled=false; if(override_enabled) enabled=true; ODINLOG(odinlog,normalDebug) << "enabled=" << enabled << STD_endl; widget_cache->setEnabled(enabled); ODINLOG(odinlog,normalDebug) << "parameterMode done" << STD_endl; bool show_tooltip=label_cut; STD_string tooltip=ldrlabel_uncut; STD_string descr=val.get_description(); if(descr!="") { tooltip+=": "+descr; tooltip=justificate(tooltip); show_tooltip=true; } if(show_tooltip) add_tooltip(widget_cache,tooltip.c_str()); grid->add_widget( widget, 0, 0, alignment); widget->show(); } unsigned int JDXwidget::get_sizedfarray_size_and_factor(unsigned int& nx, unsigned int& ny, unsigned int& nz) const { Log odinlog(&val,"get_sizedfarray_size_and_factor"); PixmapProps pixprops=val.get_gui_props().pixmap; int dim=sizedfarray.dim(); nx=sizedfarray.size(dim-1); ny=sizedfarray.size(dim-2); nz=1; if(dim==3) nz=sizedfarray.size(dim-3); unsigned int factor=1; ODINLOG(odinlog,normalDebug) << "ny/nx=" << ny << "/" << nx << STD_endl; ODINLOG(odinlog,normalDebug) << "minsize/maxsize=" << pixprops.minsize << "/" << pixprops.maxsize << STD_endl; if (nx >= ny) factor=(unsigned int)secureDivision(pixprops.minsize,ny); else factor=(unsigned int)secureDivision(pixprops.minsize,nx); if(!factor) factor=1; if( (factor*nx) > pixprops.maxsize) factor=(unsigned int)secureDivision(pixprops.maxsize,nx); if( (factor*ny) > pixprops.maxsize) factor=(unsigned int)secureDivision(pixprops.maxsize,ny); if(!factor) factor=1; return factor; } void JDXwidget::create_or_update_floatArrwidget(const farray& arr, bool initial) { Log odinlog(&val,"create_or_update_floatArrwidget"); rows=2; cols=2; ArrayScale x_axprops=val.get_gui_props().scale[xPlotScale]; ArrayScale y_axprops=val.get_gui_props().scale[yPlotScaleLeft]; sizedfarray=arr; sizedfarray.autosize(); unsigned int newdim=sizedfarray.dim(); unsigned int newsize=sizedfarray.total(); if(newdim==3) newdim=2; // treat 2D and 3D equally if(newsize==0) newdim=0; // treat zero size as zero dim ODINLOG(odinlog,normalDebug) << "newdim/newsize=" << newdim << "/" << newsize << STD_endl; if(!initial) { unsigned int olddim=oldfarraysize.dim(); unsigned int oldsize=oldfarraysize.total(); if(olddim==3) olddim=2; // treat 2D and 3D equally bool delete_old=false; if(newdim!=olddim) delete_old=true; if(newdim==1 && (newsize!=oldsize) && (newsize==1 || oldsize==1)) delete_old=true; if(newdim>1 && sizedfarray.get_extent()!=oldfarraysize) delete_old=true; ODINLOG(odinlog,normalDebug) << "newdim/olddim/newsize/oldsize/delete_old=" << newdim << "/" << olddim << "/" << newsize << "/" << oldsize << "/" << delete_old << STD_endl; if(delete_old) { if(floatArrempty) {floatArrempty->hide(); delete floatArrempty; floatArrempty=0;} if(floatArrwidget1) {floatArrwidget1->hide(); delete floatArrwidget1; floatArrwidget1=0;} if(floatArredit) {floatArredit->hide(); delete floatArredit; floatArredit=0;} if(floatArrwidget2) {floatArrwidget2->hide(); delete floatArrwidget2; floatArrwidget2=0;} } } if(newdim==0) { if(!floatArrempty) { floatArrempty=new QLabel(this); floatArrempty->setText((ldrlabel+"(Empty)").c_str()); set_widget(floatArrempty); } } if(newdim==1) { if(newsize==1) { rows=1; cols=1; if(floatArredit) { emit newfloatval( sizedfarray[0] ); } else { floatArredit=new floatLineBox(sizedfarray[0],_FLOAT_DIGITS_,vport,ldrlabel.c_str()); set_widget(floatArredit); connect(floatArredit,SIGNAL(floatLineBoxValueChanged( float )),this,SLOT(changeJDXfloat( float ))); connect(this,SIGNAL(newfloatval( float )),floatArredit,SLOT(setfloatLineBoxValue( float ))); } } if(newsize>1) { rows=3; ODINLOG(odinlog,normalDebug) << "x_label/unit=" << x_axprops.label << "/" << x_axprops.unit << STD_endl; ODINLOG(odinlog,normalDebug) << "y_label/unit=" << y_axprops.label << "/" << y_axprops.unit << STD_endl; if(floatArrwidget1) { emit newfloatArr1( sizedfarray.c_array(), sizedfarray.length(), x_axprops.minval,x_axprops.maxval ); } else { floatArrwidget1=new floatBox1D(sizedfarray.c_array(),sizedfarray.length(),vport,ldrlabel.c_str(),val.get_gui_props().fixedsize, x_axprops.get_label_with_unit().c_str(),y_axprops.get_label_with_unit().c_str(), x_axprops.minval,x_axprops.maxval,val.get_gui_props().fixedsize); set_widget(floatArrwidget1, GuiGridLayout::Default, true); connect(this,SIGNAL(newfloatArr1( const float*, int, float, float)), floatArrwidget1,SLOT(refresh( const float*, int, float, float))); } } } if(newdim==2) { ArrayScale dispscale=val.get_gui_props().scale[displayScale]; ODINLOG(odinlog,normalDebug) << "dispscale.minval/maxval=" << dispscale.minval << "/" << dispscale.maxval << STD_endl; if(val.get_gui_props().pixmap.autoscale) { dispscale.minval=sizedfarray.minvalue(); dispscale.maxval=sizedfarray.maxvalue(); ODINLOG(odinlog,normalDebug) << "Autoscaling with min/max=" << dispscale.minval << "/" << dispscale.maxval << STD_endl; sizedfarray.normalize(); } if(floatArrwidget2) { ODINLOG(odinlog,normalDebug) << "Emitting new c_array" << STD_endl; emit newfloatArr2( sizedfarray.c_array(),dispscale.minval,dispscale.maxval); mapfarray=val.get_gui_props().pixmap.overlay_map; // mapfarray.normalize(); if(mapfarray.total()) { ODINLOG(odinlog,normalDebug) << "New overlay_map" << STD_endl; float mapmin, mapmax; val.get_gui_props().pixmap.get_overlay_range(mapmin, mapmax); emit newfloatArrMap(mapfarray.c_array(), mapmin, mapmax, val.get_gui_props().pixmap.overlay_rectsize); } } else { unsigned int nx,ny,nz; unsigned int factor=get_sizedfarray_size_and_factor(nx,ny,nz); bool colormap=val.get_gui_props().pixmap.color; overlay_map=val.get_gui_props().pixmap.overlay_map; // create local copy for c_array() bool olm_firescale=val.get_gui_props().pixmap.overlay_firescale; float olm_rectsize=val.get_gui_props().pixmap.overlay_rectsize; const float* olm=0; int olm_x=1; int olm_y=1; int olm_z=1; float olm_upp=0.0; float olm_low=0.0; if(overlay_map.length()) { val.get_gui_props().pixmap.get_overlay_range(olm_low, olm_upp); // olm_upp=overlay_map.maxvalue(); // olm_low=overlay_map.minvalue(); // overlay_map.normalize(); olm=overlay_map.c_array(); int olm_dim=overlay_map.dim(); if(olm_dim>2) olm_z=overlay_map.size(olm_dim-3); if(olm_dim>1) olm_y=overlay_map.size(olm_dim-2); if(olm_dim>0) olm_x=overlay_map.size(olm_dim-1); ODINLOG(odinlog,normalDebug) << "olm/olm_z/olm_y/olm_x=" << olm << "/" << olm_z << "/" << olm_y << "/" << olm_x << STD_endl; } floatArrwidget2=new floatBox3D(sizedfarray.c_array(),dispscale.minval,dispscale.maxval,nx,ny,nz,factor,vport,ldrlabel.c_str(), olm,olm_low,olm_upp,olm_x,olm_y,olm_z,olm_firescale,olm_rectsize,colormap); set_widget(floatArrwidget2, GuiGridLayout::Default, true); connect(floatArrwidget2,SIGNAL(clicked(int,int,int)),this,SLOT(emitClicked(int, int, int))); connect(floatArrwidget2,SIGNAL(newProfile(const float*, int, bool, int)),this,SLOT(emitNewProfile(const float*, int, bool, int))); connect(floatArrwidget2,SIGNAL(newMask(const float*, int)),this,SLOT(emitNewMask(const float*, int))); connect(this,SIGNAL(newfloatArr2( const float*, float, float)),floatArrwidget2,SLOT(refresh( const float*, float, float))); connect(this,SIGNAL(newfloatArrMap( const float*, float, float, float)),floatArrwidget2,SLOT(refreshMap( const float*, float, float, float ))); } } oldfarraysize=sizedfarray.get_extent(); } void JDXwidget::emitValueChanged() { emit valueChanged(); } void JDXwidget::emitDone() { emit doneButtonPressed(); } void JDXwidget::updateWidget() { Log odinlog(&val,"updateWidget"); emit updateSubWidget(); if(blockwidget) blockwidget->updateWidget(); // for all 1D/2D plots, get again, might have been changed ArrayScale x_axprops=val.get_gui_props().scale[xPlotScale]; PixmapProps pixprops=val.get_gui_props().pixmap; if(intslider || intedit) { ODINLOG(odinlog,normalDebug) << "newintval(" << val.get_label() << ")=" << val.printvalstring() << STD_endl; emit newintval( atoi(val.printvalstring().c_str()) ); } if(floatslider || floatedit) { float* dumfloat=val.cast(dumfloat); double* dumdouble=val.cast(dumdouble); float floatval=0.0; if(dumfloat) floatval=(*dumfloat); if(dumdouble) floatval=(*dumdouble); emit newfloatval( floatval ); } if(enumwidget) { JDXenum* dumenum=val.cast(dumenum); if(dumenum) emit newenumval( dumenum->get_item_index() ); } if(boolwidget) { bool* dumbool=val.cast(dumbool); if(dumbool) emit newboolval(*dumbool); } if(complexArrwidget) { carray* dumcarray=val.cast(dumcarray); if(dumcarray) { if(dumcarray->dim()==1) { fvector ampvec=amplitude(*dumcarray); fvector phavec=phase(*dumcarray); emit newcomplexArr( ampvec.c_array(), phavec.c_array(), dumcarray->length(), x_axprops.minval,x_axprops.maxval); } } } if(floatArrempty || floatArrwidget1 || floatArrwidget2 || floatArredit) { farray* dumfarray=val.cast(dumfarray); if(dumfarray) { create_or_update_floatArrwidget(*dumfarray,false); } darray* dumdarray=val.cast(dumdarray); if(dumdarray) { ODINLOG(odinlog,normalDebug) << "dumdarray=" << (void*)dumdarray << "/" << STD_string(dumdarray->get_extent()) << STD_endl; farray farr(dumdarray->get_extent()); for(unsigned int i=0; iget_function_index() ); ODINLOG(odinlog,normalDebug) << "get_function_index()=" << dumfunc->get_function_index() << STD_endl; for(STD_list::iterator it=subdialogs.begin(); it!=subdialogs.end(); ++it) { (*it)->updateWidget(); } } if(stringwidget) { STD_string* dumstring=val.cast(dumstring); if(dumstring) { const char* str=dumstring->c_str(); ODINLOG(odinlog,normalDebug) << "str=" << str << STD_endl; emit newstringval(str); } } if(filenamewidget) { JDXfileName* dumfileName=val.cast(dumfileName); if(dumfileName) emit newfilenameval( dumfileName->c_str() ); } if(formulawidget) { JDXformula* dumformula=val.cast(dumformula); if(dumformula) emit newformulaval( dumformula->c_str() ); } if(triplewidget) { JDXtriple* dumtriple=val.cast(dumtriple); if(dumtriple) emit newtripleval( (*dumtriple)[0],(*dumtriple)[1],(*dumtriple)[2] ); } } void JDXwidget::deleteDialogs() { emit deleteSubDialogs(); for(STD_list::iterator it=subdialogs.begin(); it!=subdialogs.end(); ++it) { (*it)->hide(); // delete (*it); } subdialogs.clear(); } void JDXwidget::changeJDXint( int newval ) { int* dumint=val.cast(dumint); if(dumint) (*dumint)=newval; long* dumlong=val.cast(dumlong); if(dumlong) (*dumlong)=newval; emit valueChanged(); } void JDXwidget::changeJDXfloat( float newval ) { Log odinlog(&val,"changeJDXfloat"); ODINLOG(odinlog,normalDebug) << "newval=" << newval << STD_endl; float* dumfloat=val.cast(dumfloat); if(dumfloat) (*dumfloat)=newval; double* dumdouble=val.cast(dumdouble); if(dumdouble) (*dumdouble)=newval; farray* dumfarray=val.cast(dumfarray); if(dumfarray && dumfarray->length()) dumfarray[0]=newval; darray* dumdarray=val.cast(dumdarray); if(dumdarray && dumdarray->length()) dumdarray[0]=newval; // STD_string dummy=JDXdouble(newval).printvalstring(); // val.parsevalstring(dummy); ODINLOG(odinlog,normalDebug) << "val=" << val.printvalstring() << STD_endl; emit valueChanged(); } void JDXwidget::changeJDXenum( int newval ) { JDXenum* dumenum=val.cast(dumenum); if(dumenum) dumenum->set_item_index(newval); emit valueChanged(); } void JDXwidget::changeJDXbool( bool newval ) { bool* dumbool=val.cast(dumbool); if(dumbool) (*dumbool)=newval; emit valueChanged(); } void JDXwidget::changeJDXaction() { JDXaction* dumaction=val.cast(dumaction); if(dumaction) dumaction->trigger_action(); emit valueChanged(); } void JDXwidget::changeJDXfunction( int newval ) { Log odinlog(&val,"changeJDXfunction"); ODINLOG(odinlog,normalDebug) << "newval=" << newval << STD_endl; deleteDialogs(); JDXfunction* dumfunc=val.cast(dumfunc); if(dumfunc) dumfunc->set_function(newval); emit valueChanged(); } void JDXwidget::changeJDXstring( const char* newval ) { Log odinlog(&val,"changeJDXstring"); ODINLOG(odinlog,normalDebug) << "newval=" << newval << STD_endl; STD_string* dumstring=val.cast(dumstring); if(dumstring) { STD_string newval_str=STD_string(newval); // direct assignment gives bogus results on MacOS 10.4 with GCC4 and std::string (*dumstring)=newval_str; ODINLOG(odinlog,normalDebug) << "newval_str/dumstring=" << newval_str << "/" << (*dumstring) << STD_endl; } emit valueChanged(); } void JDXwidget::changeJDXfileName( const char* newval ) { JDXfileName* dumfilename=val.cast(dumfilename); if(dumfilename) { STD_string newvalstr(newval); (*dumfilename)=newvalstr; } emit valueChanged(); } void JDXwidget::changeJDXformula( const char* newval ) { JDXformula* dumformula=val.cast(dumformula); if(dumformula) (*dumformula)=newval; emit valueChanged(); } void JDXwidget::changeJDXtriple( float xval,float yval,float zval ) { JDXtriple* dumtriple=val.cast(dumtriple); if(dumtriple) { (*dumtriple)[0]=xval; (*dumtriple)[1]=yval; (*dumtriple)[2]=zval; } emit valueChanged(); } void JDXwidget::browseJDXfileName() { Log odinlog(&val,"browseJDXfileName"); JDXfileName* dumfilename=val.cast(dumfilename); if(dumfilename) { STD_string suffix=dumfilename->get_suffix(); ODINLOG(odinlog,normalDebug) << "suffix=" << suffix << STD_endl; if(suffix!="") suffix=STD_string(val.get_label())+" (*."+suffix+")"; STD_string startdir=dumfilename->get_defaultdir(); // local copy for c_str() ODINLOG(odinlog,normalDebug) << "startdir/suffix=" << startdir << "/" << suffix << STD_endl; STD_string fname; if(dumfilename->is_dir()) fname=get_directory("Please select a directory", startdir.c_str(), vport); else fname=get_open_filename("Please select a file", startdir.c_str(), suffix.c_str(), vport); if (fname!="") { (*dumfilename)=fname; filenamewidget->setstringBoxText(fname.c_str()); } } emit valueChanged(); } void JDXwidget::infoJDXformula() { JDXformula* dumformula=val.cast(dumformula); if(dumformula) { message_question((justificate(dumformula->get_syntax(),0,false,_INFOBOX_LINEWIDTH_)).c_str(), val.get_label().c_str(), vport); } emit valueChanged(); } void JDXwidget::editJDXfunction() { JDXfunction* dumfunc=val.cast(dumfunc); if(dumfunc) { JDXwidgetDialog* dlg=new JDXwidgetDialog(*(dumfunc->get_funcpars_block()),1,vport); subdialogs.push_back(dlg); connect(dlg,SIGNAL(valueChanged()), this,SLOT(emitValueChanged())); } emit valueChanged(); } void JDXwidget::infoJDXfunction() { JDXfunction* dumfunc=val.cast(dumfunc); if(dumfunc) { message_question((justificate(dumfunc->get_funcdescription(),0,false,_INFOBOX_LINEWIDTH_)).c_str(), (dumfunc->get_label()+STD_string(" info")).c_str(), vport); } } odin-1.8.5/odinqt/stringbox.h0000644000175000017500000000322511322062347013067 00000000000000/*************************************************************************** intedit.h - description ------------------- begin : Sun Aug 27 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef STRINGBOX_H #define STRINGBOX_H #include #include "odinqt.h" /** * This class contains a QlineEdit to display a string * in a nice box with a label. */ class stringBox : public QGroupBox { Q_OBJECT public: stringBox(const char* text, QWidget *parent, const char *name, const char *buttontext=0); ~stringBox(); public slots: void setstringBoxText( const char* text ); private slots: void reportTextChanged(); void reportButtonClicked(); signals: void stringBoxTextEntered( const char* text ); void stringBoxButtonPressed(); private: GuiGridLayout* grid; GuiLineEdit* le; GuiButton* pb; }; #endif odin-1.8.5/odinqt/Makefile.am0000644000175000017500000000231011322062347012725 00000000000000 libodinqt_la_LDFLAGS = -no-undefined -release $(VERSION) $(GUILIBS) libodinqt_la_LIBADD = ../odinpara/libodinpara.la if GUI_ENABLED INCLUDES = $(all_includes) # Auto-generate any needed moc files %_moc.cpp: %.h $(MOC) -o $@ $< lib_LTLIBRARIES = libodinqt.la library_includedir=$(includedir)/odinqt library_include_HEADERS = \ odinqt.h odinqt_callback.h \ boolbutton.h \ complex1d.h \ enumbox.h \ float1d.h \ float2d.h \ float3d.h \ floatedit.h \ intedit.h \ plot.h \ stringbox.h \ jdxwidget.h \ jdxblockwidget.h libodinqt_la_SOURCES = \ odinqt.h odinqt.cpp odinqt_callback.h 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odin-1.8.5/odinqt/complex1d.h0000644000175000017500000000743111322062347012747 00000000000000/*************************************************************************** complex1d.h - description ------------------- begin : Sun Aug 27 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef COMPLEX1D_H #define COMPLEX1D_H #include #include "odinqt.h" #define SYMBOL_MAX_NUMOF_POINTS 20 class GuiPlot; // forward declaration class DetachedComplexfloatBox1D; // forward declaration /** * QLabel containing a plotted complex array (2 curves) */ class complexfloatBox1D : public QGroupBox { Q_OBJECT public: complexfloatBox1D(const float *data1, const float *data2, int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel=0, const char *yAxisLabelLeft=0, const char *yAxisLabelRight=0, float min_x=0.0, float max_x=0.0, bool detachable=false); complexfloatBox1D(const double *data1,const double *data2,int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel=0, const char *yAxisLabelLeft=0, const char *yAxisLabelRight=0, float min_x=0.0, float max_x=0.0, bool detachable=false); ~complexfloatBox1D(); public slots: void refresh(const float *data1,const float *data2,int n, float min_x, float max_x); void refresh(const float *data1,const float *data2,int n) {refresh(data1,data2,n,0.0,0.0);} void refresh(const double *data1,const double *data2,int n, float min_x, float max_x); void refresh(const double *data1,const double *data2,int n) {refresh(data1,data2,n,0.0,0.0);} private slots: void autoscale(); void detach(); void mousePressedInPlot(const QMouseEvent& qme); void mouseReleasedInPlot(const QMouseEvent& qme); private: void common_init(const char *name, bool fixed_size, bool data1, bool data2, const char *xAxisLabel, const char *yAxisLabelLeft, const char *yAxisLabelRight, bool detachable); void create_x_cache(float min_x, float max_x, int n); long curveid1; long curveid2; dvector data1_cache; dvector data2_cache; dvector x_cache; const double* data1_ptr; const double* data2_ptr; // Use strings to cache labels since original arrays may be outdated STD_string name_cache; STD_string xAxisLabel_cache; STD_string yAxisLabelLeft_cache; STD_string yAxisLabelRight_cache; float min_x_cache; float max_x_cache; int n_cache; bool detachable_cache; GuiGridLayout *grid; GuiPlot* plotter; int x_pressed,y_pressed; DetachedComplexfloatBox1D* detached; }; /////////////////////////////////////////////////////////////////// class DetachedComplexfloatBox1D : public GuiDialog { public: DetachedComplexfloatBox1D(const double *data1,const double *data2,int n,complexfloatBox1D *parent, const char *name, bool fixed_size, const char *xAxisLabel, const char *yAxisLabelLeft, const char *yAxisLabelRight, float min_x, float max_x); ~DetachedComplexfloatBox1D(); void refresh(const double *data1,const double *data2,int n, float min_x, float max_x); private: void create_grid(); GuiGridLayout *grid; complexfloatBox1D* cfb; }; #endif odin-1.8.5/odinqt/float1d.cpp0000644000175000017500000000361411322062347012737 00000000000000/*************************************************************************** float1d.cpp - description ------------------- begin : Tue Jul 11 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #include "float1d.h" floatBox1D::floatBox1D(const float *data,int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel, const char *yAxisLabel, float min_x, float max_x, bool detachable) : complexfloatBox1D(data,0,n,parent,name, fixed_size, xAxisLabel, yAxisLabel, 0, min_x, max_x, detachable ) { } floatBox1D::floatBox1D(const double *data,int n,QWidget *parent, const char *name, bool fixed_size, const char *xAxisLabel, const char *yAxisLabel, float min_x, float max_x, bool detachable) : complexfloatBox1D(data,0,n,parent,name, fixed_size, xAxisLabel, yAxisLabel, 0, min_x, max_x, detachable ) { } void floatBox1D::refresh(const float* data,int n, float min_x, float max_x) { complexfloatBox1D::refresh(data,0,n, min_x, max_x ); } void floatBox1D::refresh(const double* data,int n, float min_x, float max_x) { complexfloatBox1D::refresh(data,0,n, min_x, max_x ); } odin-1.8.5/odinqt/float2d.cpp0000644000175000017500000003721111322062347012740 00000000000000#include // for mouse events #include #include #include "float2d.h" #include #include #define LOGMAP_FACTOR 2 #define LEGEND_DIGITS 3 #define MAX_LOGMAP_HUE 70.0 #define MAX_MAP_HUE 270.0 #define X_ENUM 0 #define Y_ENUM 1 #define CROSSHAIR_SIZE 4 #define MAP_RECT_SIZE 0.8 void floatArray2pixbuff(unsigned char* imagebuff, const float* farray, int nx, int ny, int coarseFactor, int scalespace) { Log odinlog("floatLabel2D","floatArray2pixbuff"); int nx_aligned=((nx*coarseFactor+scalespace+3)/4)*4; // 32-bit aligned lines for QImage ODINLOG(odinlog,normalDebug) << "nx_aligned/nx/ny/coarseFactor/scalespace=" << nx_aligned << "/" << nx << "/" << ny << "/" << coarseFactor << "/" << scalespace << STD_endl; int i,j; // Draw data for (j = 0; j < ny; j++) { int jrev=ny-1-j; for (i = 0; i < nx; i++) { float floatval = farray[j * nx + i]; if (floatval > 1.0) floatval = 1.0; if (floatval < 0.0) floatval = 0.0; unsigned char byteval = (unsigned char) (255.0 * floatval); for (int jj = 0; jj < coarseFactor; jj++) { for (int ii = 0; ii < coarseFactor; ii++) { imagebuff[(jrev * coarseFactor + jj) * nx_aligned + (i * coarseFactor + ii)] = byteval; } } } // Draw scale float floatval = float(j)/float(ny-1); unsigned char byteval = (unsigned char) (255.0 * floatval + 0.5); for (i = (nx*coarseFactor); i < nx_aligned; i++) { for (int jj = 0; jj < coarseFactor; jj++) { imagebuff[(jrev * coarseFactor + jj) * nx_aligned + i] = byteval; } } } } floatLabel2D::floatLabel2D(const float *data, float lowbound, float uppbound, unsigned int nx, unsigned int ny, unsigned int coarseFactor, QWidget *parent, const char *name, const float *overlay_map, float lowbound_map, float uppbound_map, unsigned int nx_map, unsigned int ny_map, bool map_firescale, float map_rectsize, bool colormap) : QLabel(parent ) { Log odinlog("floatLabel2D","floatLabel2D"); ODINLOG(odinlog,normalDebug) << "nx/ny/coarseFactor=" << nx << "/" << ny << "/" << coarseFactor << STD_endl; colormap_cache=colormap; pixmap=0; legend_pixmap=0; nx_cache=nx; ny_cache=ny; nx_map_cache=nx_map; ny_map_cache=ny_map; fire_map_cache=map_firescale; lowbound_map_cache=lowbound_map; uppbound_map_cache=uppbound_map; ODINLOG(odinlog,normalDebug) << "lowbound_map_cache/uppbound_map_cache=" << lowbound_map_cache << "/" << uppbound_map_cache << STD_endl; lowbound_cache=lowbound; uppbound_cache=uppbound; scalespace_cache=0; if(uppbound>lowbound) scalespace_cache=scale_width(lowbound,uppbound); roi_mask=new float[nx_cache*ny_cache]; profile_x=new float[nx_cache]; for(i=0;isetFixedSize( (nx*coarseFactor+scalespace_cache)+this->frameWidth()*2,ny*coarseFactor+this->frameWidth()*2 ); connect(this,SIGNAL(clicked(int,int)),this,SLOT(drawcross(int,int))); refresh(data, lowbound, uppbound); refreshMap(overlay_map, lowbound_map, uppbound_map_cache, map_rectsize); } void floatLabel2D::init_pixmap(bool clear) { Log odinlog("floatLabel2D","init_pixmap"); if(clear || !pixmap) { if(pixmap) delete pixmap; floatArray2pixbuff(imagebuff, data_cache, nx_cache,ny_cache,coarseFactor_cache,scalespace_cache); GuiImage img( imagebuff, nx_cache*coarseFactor_cache+scalespace_cache, ny_cache*coarseFactor_cache, colormap_cache); pixmap = img.create_pixmap(); GuiPainter gp(pixmap); draw_scale_text(gp, 3*_FONT_SIZE_/2, uppbound_cache); draw_scale_text(gp, ny_cache*coarseFactor_cache-_FONT_SIZE_/2, lowbound_cache); gp.end(); } } void floatLabel2D::set_pixmap() { Log odinlog("floatLabel2D","set_pixmap"); // bitBlt( this, 2, 2, pixmap ); ODINLOG(odinlog,normalDebug) << "pixmap=" << (void*)pixmap << STD_endl; this->setPixmap(*pixmap); } int floatLabel2D::scale_width(float lowbound, float uppbound) { return 0.8*STD_max(ftos(lowbound,LEGEND_DIGITS).length(),ftos(uppbound,LEGEND_DIGITS).length())*_FONT_SIZE_; } void floatLabel2D::draw_text(GuiPainter& gp, int xpos, int ypos, const char* txt) const { gp.drawText(xpos+1,ypos+1,txt,"Black"); gp.drawText(xpos, ypos, txt,"White"); } void floatLabel2D::draw_scale_text(GuiPainter& gp, int ypos, float val) const { draw_text(gp, nx_cache*coarseFactor_cache, ypos, ftos(val,LEGEND_DIGITS).c_str()); } void floatLabel2D::refresh(const float* data, float lowbound, float uppbound) { data_cache=data; lowbound_cache=lowbound; uppbound_cache=uppbound; init_pixmap(); set_pixmap(); } void floatLabel2D::write_pixmap(const char* fname, const char* format) const { if(pixmap && fname) pixmap->save (fname,toupperstr(format).c_str()); } int floatLabel2D::get_map_hue(float relval) const { float hue_factor=1.0; if(fire_map_cache) hue_factor=0.25; else relval=1.0-relval; relval=STD_max(float(0.0),relval); relval=STD_min(float(1.0),relval); if (fire_map_cache) { // fmri coloring // adjust balance between red, orange and yellow ... more red, less orange if (relval < 0.25) // more red relval = 0.0; else if ((relval > 0.6) && (relval < 0.7)) // small transition orange to yellow relval = (0.7 - 7.0 / 15.0) / 0.1 * (relval - 0.6) + 7.0 / 15.0; else if (relval > 0.7) relval = relval; else relval = (relval - 0.25) * (4.0 / 3.0); } return MAX_MAP_HUE*hue_factor*relval; } int floatLabel2D::get_map_value(float relval) const { if ((relval < 0.4) && (fire_map_cache)) // darken lower values -> dark red return 255-255*(0.4 - relval); else return 255; } int floatLabel2D::get_map_saturation(float relval) const { if ((relval > 0.8) && (fire_map_cache)) // remove saturation for highest values -> white color return 255-255*(relval-0.8)*5; else return 255; } QLabel* floatLabel2D::get_map_legend(QWidget *parent) const { QLabel* result=new QLabel(parent); int width=6*_FONT_SIZE_; // if(!fire_map_cache) width=scale_width(lowbound_map_cache,uppbound_map_cache); int height=ny_cache*coarseFactor_cache; legend_pixmap = new QPixmap(width,height); GuiPainter *legend_painter = new GuiPainter(legend_pixmap); QColor qc; QColor qc_txt("Black"); for(int iy=0; iyfillRect (0,iy,width,1,qc); draw_text(*legend_painter, 0, 1.5*_FONT_SIZE_, ftos(uppbound_map_cache,LEGEND_DIGITS).c_str()); draw_text(*legend_painter, 0, ny_cache*coarseFactor_cache-_FONT_SIZE_/2, ftos(lowbound_map_cache,LEGEND_DIGITS).c_str()); } result->setPixmap(*legend_pixmap); return result; } void floatLabel2D::write_map_legend(const char* fname, const char* format) const { if(legend_pixmap && fname) legend_pixmap->save(fname, toupperstr(format).c_str()); } void floatLabel2D::refreshMap(const float* map, float map_lowbound, float map_uppbound, float map_rectsize) { Log odinlog("floatLabel2D","refreshMap"); ODINLOG(odinlog,normalDebug) << "map=" << (void*)map << STD_endl; ODINLOG(odinlog,normalDebug) << "map_lowbound/map_uppbound=" << map_lowbound << "/" << map_uppbound << STD_endl; if(!map) return; init_pixmap(); GuiPainter *painter = new GuiPainter(pixmap); float regridfactor_x=float(nx_cache)/float(nx_map_cache); float regridfactor_y=float(ny_cache)/float(ny_map_cache); if(map_rectsize<0.1) map_rectsize=0.1; if(map_rectsize>1.0) map_rectsize=1.0; int width =int(map_rectsize*float(coarseFactor_cache)*regridfactor_x+0.5); if(width<=0) width=1; int height=int(map_rectsize*float(coarseFactor_cache)*regridfactor_y+0.5); if(height<=0) height=1; ODINLOG(odinlog,normalDebug) << "regridfactor_x/regridfactor_y/width/height=" << regridfactor_x << "/" << regridfactor_y << "/" << width << "/" << height << STD_endl; QColor qc; for(unsigned int iym=0; iymmap_lowbound && mapval<=map_uppbound) { float relval=secureDivision(mapval-map_lowbound,map_uppbound-map_lowbound); qc.setHsv(get_map_hue(relval),get_map_saturation(relval),get_map_value(relval)); int lx=int(float(ixm)*regridfactor_x*float(coarseFactor_cache)+0.5); int ly=int(float(ny_map_cache-1-iym)*regridfactor_y*float(coarseFactor_cache)+0.5); painter->fillRect (lx,ly,width,height,qc); } } } painter->end(); set_pixmap(); delete painter; } void floatLabel2D::mousePressEvent(QMouseEvent *e) { Log odinlog("floatLabel2D","mousePressEvent"); if ( left_button(e,false) ) { ODINLOG(odinlog,normalDebug) << "left_button" << STD_endl; roi_polygon.clear(); roi_painter = new GuiPainter(pixmap); roi_painter->moveTo(e->x(),e->y()); mouse_moved=false; } if( middle_button(e,false) ) { ODINLOG(odinlog,normalDebug) << "middle_button" << STD_endl; drawprofil(labelxpos2xpos(e->x()),X_ENUM); } if( right_button(e,false) ) { ODINLOG(odinlog,normalDebug) << "right_button" << STD_endl; drawprofil(labelypos2ypos(e->y()),Y_ENUM); } } void floatLabel2D::mouseReleaseEvent (QMouseEvent *e) { Log odinlog("floatLabel2D","mouseReleaseEvent"); if ( left_button(e,false) ) { ODINLOG(odinlog,normalDebug) << "Qt::LeftButton used" << STD_endl; roi_painter->end(); delete roi_painter; if(mouse_moved) { ODINLOG(odinlog,normalDebug) << "calling drawroi()" << STD_endl; drawroi(); } else { int xcross=labelxpos2xpos(e->x()); int ycross=labelypos2ypos(e->y()); if(xcross>=0 && xcross=0 && ycrossx(),e->y())); roi_painter->lineTo(e->x(),e->y()); roi_painter->repaint(this); mouse_moved=true; } } int floatLabel2D::check_range(int val, int min, int max) { int result=val; if(result=max) result=max-1; return result; } int floatLabel2D::xpos2labelxpos(int pos) { int result=int((float(pos)+0.5)*float(coarseFactor_cache)); return result; // return check_range(result, 0, nx_cache*coarseFactor_cache); // does not work with out-of-FOV slices in geoedit } int floatLabel2D::ypos2labelypos(int pos) { int result=int((float(ny_cache)-1.0-float(pos)+0.5)*float(coarseFactor_cache)); return result; // return check_range(result, 0, ny_cache*coarseFactor_cache); // does not work with out-of-FOV slices in geoedit } int floatLabel2D::labelxpos2xpos(int pos) { int result=(pos/coarseFactor_cache); return check_range(result, 0, nx_cache); } int floatLabel2D::labelypos2ypos(int pos) { int result=(ny_cache-1-pos/coarseFactor_cache); return check_range(result, 0, ny_cache); } int floatLabel2D::xypos2index(int xpos,int ypos) { int result=ypos*nx_cache+xpos; return check_range(result, 0, nx_cache*ny_cache); } void floatLabel2D::drawprofil(int clickpos,int direction) { Log odinlog("floatLabel2D","drawprofil"); unsigned int j; int ix,iy,profpos; init_pixmap(); GuiPainter *painter = new GuiPainter(pixmap); painter->setPen("Green"); switch (direction) { case X_ENUM: painter->moveTo(xpos2labelxpos(clickpos),0);painter->lineTo(xpos2labelxpos(clickpos),ny_cache*coarseFactor_cache); break; case Y_ENUM: painter->moveTo(0,ypos2labelypos(clickpos));painter->lineTo(nx_cache*coarseFactor_cache,ypos2labelypos(clickpos)); break; } ODINLOG(odinlog,normalDebug) << "moveTo done" << STD_endl; painter->setPen("Red"); switch (direction) { case X_ENUM: ODINLOG(odinlog,normalDebug) << "X point" << STD_endl; profpos=int((float)(nx_cache-1)*data_cache[xypos2index(clickpos,0)]); ix=xpos2labelxpos(profpos); iy=ypos2labelypos(0); painter->moveTo(ix,iy); if(ny_cache) profile_y[0]=data_cache[xypos2index(clickpos,0)]; for(j=1; jlineTo(ix,iy); } emit newProfile(profile_y,ny_cache,false,clickpos); break; case Y_ENUM: ODINLOG(odinlog,normalDebug) << "Y point" << STD_endl; ix=xpos2labelxpos(0); profpos=int((float)(ny_cache-1)*data_cache[xypos2index(0,clickpos)]); iy=ypos2labelypos(profpos); ODINLOG(odinlog,normalDebug) << "profpos/iy=" << profpos << "/" << iy << STD_endl; painter->moveTo(ix,iy); if(nx_cache) profile_x[0]=data_cache[xypos2index(0,clickpos)]; for(j=1; jlineTo(ix,iy); } emit newProfile(profile_x,nx_cache,true,clickpos); break; } painter->end(); ODINLOG(odinlog,normalDebug) << "painter done" << STD_endl; set_pixmap(); delete painter; } void floatLabel2D::drawcross(int xpos,int ypos) { Log odinlog("floatLabel2D","drawcross"); ODINLOG(odinlog,normalDebug) << "xpos/ypos=" << xpos << "/" << ypos << STD_endl; // position will be centered on voxel by the transformation functions int centerx=xpos2labelxpos(xpos); int centery=ypos2labelypos(ypos); ODINLOG(odinlog,normalDebug) << "centerx/centery=" << centerx << "/" << centery << STD_endl; init_pixmap(); GuiPainter *painter = new GuiPainter(pixmap); painter->setPen(_ARRAY_SELECTION_COLOR_); painter->moveTo(centerx-CROSSHAIR_SIZE,centery); painter->lineTo(centerx+CROSSHAIR_SIZE,centery); painter->moveTo(centerx,centery-CROSSHAIR_SIZE); painter->lineTo(centerx,centery+CROSSHAIR_SIZE); painter->end(); set_pixmap(); delete painter; } void floatLabel2D::drawroi() { Log odinlog("floatLabel2D","mouseReleaseEvent"); init_pixmap(); GuiPainter *painter = new GuiPainter(pixmap); QRegion* rgn=painter->draw_region(roi_polygon); painter->end(); set_pixmap(); delete painter; if(rgn) { for(unsigned int iy=0; iycontains ( QPoint(xpos2labelxpos(ix),ypos2labelypos(iy)) ) ) roi_mask[iy*nx_cache+ix]=1.0; else roi_mask[iy*nx_cache+ix]=0.0; } } // for(unsigned int i=0; i<(nx_cache*ny_cache); i++) roi_mask[i]=secureDivision(roi_mask[i],double(npoints)); delete rgn; ODINLOG(odinlog,normalDebug) << "emitting newMask" << STD_endl; emit newMask(roi_mask); } } floatLabel2D::~floatLabel2D(){ delete[] imagebuff; // delete[] data_cache; delete[] profile_x; delete[] profile_y; delete[] roi_mask; } odin-1.8.5/odinqt/odinqt_callback.h0000644000175000017500000000554011322062347014164 00000000000000#include #include #include #include #include #include "odinqt.h" #if QT_VERSION > 0x03FFFF #define QT_VERSION_4 #else #if QT_VERSION > 299 #define QT_VERSION_3 #else #define QT_VERSION_PRE3 #endif #endif /** * This class dispatches calls of Qt slots to virtual member functions */ class SlotDispatcher : public QObject { Q_OBJECT public: SlotDispatcher(GuiListView* glv, GuiListViewCallback* glv_cb) { glv_cache=glv; glv_cb_cache=glv_cb; #ifdef QT_VERSION_4 connect(glv->get_widget(), SIGNAL(itemClicked(QTableWidgetItem*)), this, SLOT(qtwi_clicked(QTableWidgetItem*)) ); #else connect(glv->get_widget(), SIGNAL(clicked(QListViewItem*)), this, SLOT(qlvi_clicked(QListViewItem*)) ); #endif } SlotDispatcher(GuiToolButton* gtb, QObject* receiver, const char* member) { if(receiver) connect(gtb->qtb, SIGNAL(clicked()), receiver, member ); } SlotDispatcher(GuiButton* gb, QObject* receiver, const char* member) { if(receiver) connect(gb->qpb, SIGNAL(clicked()), receiver, member ); } SlotDispatcher(GuiLineEdit* gle, QObject* receiver, const char* member) { if(receiver) { #ifdef QT_VERSION_4 connect(gle->qle, SIGNAL(editingFinished()), receiver, member ); #else #ifdef QT_VERSION_3 connect(gle->qle, SIGNAL(lostFocus()), receiver, member ); // only available on Qt3 #endif connect(gle->qle, SIGNAL(returnPressed()), receiver, member ); #endif } } public slots: void qlvi_clicked(QListViewItem* item) { #ifndef QT_VERSION_4 Log odinlog("SlotDispatcher","qlvi_clicked"); ODINLOG(odinlog,normalDebug) << "item=" << item << STD_endl; if(!glv_cb_cache) return; GuiListItem* itemptr=0; GuiListItem(); // create listmap ODINLOG(odinlog,normalDebug) << "GuiListItem(); done" << STD_endl; STD_map::iterator it=GuiListItem::listmap->find(item); if(it!=GuiListItem::listmap->end()) itemptr=it->second; ODINLOG(odinlog,normalDebug) << "itemptr=" << itemptr << STD_endl; glv_cb_cache->clicked(itemptr); #endif } void qtwi_clicked(QTableWidgetItem* item) { #ifdef QT_VERSION_4 Log odinlog("SlotDispatcher","qtwi_clicked"); ODINLOG(odinlog,normalDebug) << "item=" << item << STD_endl; if(!glv_cb_cache) return; GuiListItem* itemptr=0; GuiListItem(); // create tablemap ODINLOG(odinlog,normalDebug) << "GuiListItem(); done" << STD_endl; STD_map::iterator it=GuiListItem::tablemap->find(item); if(it!=GuiListItem::tablemap->end()) itemptr=it->second; ODINLOG(odinlog,normalDebug) << "itemptr=" << itemptr << STD_endl; glv_cb_cache->clicked(itemptr); #endif } private: void common_int() { glv_cache=0; glv_cb_cache=0; } GuiListView* glv_cache; GuiListViewCallback* glv_cb_cache; }; odin-1.8.5/odinqt/float3d.cpp0000644000175000017500000000737311670202077012751 00000000000000#include #include "float3d.h" floatBox3D::floatBox3D(const float *data, float lowbound, float uppbound, long int nx, long int ny, long int nz, int coarseFactor, QWidget *parent, const char *name, const float *overlay_map, float lowbound_map, float uppbound_map, unsigned int nx_map, unsigned int ny_map, unsigned int nz_map, bool map_firescale, float map_rectsize, bool colormap) : QGroupBox(name,parent) { Log odinlog("floatBox3D","floatBox3D"); data_cache=data; oneimagesize=nx*ny; nz_cache=nz; lowbound_cache=lowbound; uppbound_cache=uppbound; map_cache=0; onemapsize=0; lowbound_map_cache=lowbound_map; uppbound_map_cache=uppbound_map; rectsize_map_cache=map_rectsize; if(overlay_map) { if(nz==nz_map) { map_cache=overlay_map; onemapsize=nx_map*ny_map; ODINLOG(odinlog,normalDebug) << "map_cache/onemapsize/nz_map=" << map_cache << "/" << onemapsize << "/" << nz_map << STD_endl; } else { ODINLOG(odinlog,errorLog) << "Cannot handle overlay_map with nz(" << nz_map << ") differing from data's nz(" << nz << ")" << STD_endl; } } int nrow=1; if(nz>1) nrow++; int ncol=2; if(overlay_map) ncol++; grid=new GuiGridLayout( this, nrow, ncol); label = new floatLabel2D(data,lowbound,uppbound,nx,ny,coarseFactor,this,name,overlay_map,lowbound_map,uppbound_map,nx_map,ny_map,map_firescale,map_rectsize,colormap); grid->add_widget( label, 0, 0, GuiGridLayout::Default, 1, 2 ); connect(label,SIGNAL(clicked(int,int)),this,SLOT(emitClicked(int,int))); connect(label,SIGNAL(newProfile(const float *, int, bool, int)),this,SLOT(emitNewProfile(const float *, int, bool, int))); connect(label,SIGNAL(newMask(const float *)),this,SLOT(emitNewMask(const float *))); maplegend=0; if(overlay_map) { maplegend = label->get_map_legend(this); if(maplegend) grid->add_widget( maplegend, 0, 2 ); } zslider=0; zval=0; if(nz>1) { zslider=new GuiSlider(this, 0, nz-1, 1, 0, 1); connect(zslider->get_widget(), SIGNAL(valueChanged(int)), this, SLOT(changez(int))); grid->add_widget( zslider->get_widget(), 1, 0 ); zval=new QLabel(this); grid->add_widget( zval, 1, 1 ); // set size according to max num of digits zval->setMinimumWidth(_FONT_SIZE_*int(log10(nz-1)+1)); zval->setNum(0); } mask3d=new float[nx*ny*nz]; for(int i=0; irefresh(data_cache+iz*oneimagesize,lowbound_cache,uppbound_cache); if(map_cache) label->refreshMap(map_cache+iz*onemapsize,lowbound_map_cache,uppbound_map_cache,rectsize_map_cache); } void floatBox3D::write_pixmap(const char* fname, const char* format, bool dump_all) const { if(dump_all) { for(int iz=0; iz1) onefname+=itos(iz,nz_cache-1); onefname+="."+::tolowerstr(format); label->write_pixmap( onefname.c_str(), format); } repaint_slice(get_current_z()); } else { label->write_pixmap(fname,format); } } void floatBox3D::refresh(const float* data, float lowbound, float uppbound) { data_cache=data; label->refresh(data_cache+oneimagesize*get_current_z(),lowbound,uppbound); lowbound_cache=lowbound; uppbound_cache=uppbound; } void floatBox3D::changez(int iz) { Log odinlog("floatBox3D","changez"); repaint_slice(iz); repaint(); if(zval) zval->setNum(iz); } int floatBox3D::get_current_z() const { if(zslider) return zslider->get_value(); return 0; } floatBox3D::~floatBox3D() { if(zslider) delete zslider; if(zval) delete zval; if(maplegend) delete maplegend; delete label; delete grid; delete[] mask3d; } odin-1.8.5/odinqt/plot.h0000644000175000017500000001051111322062347012022 00000000000000/*************************************************************************** plot.h - description ------------------- begin : Mon Aug 1 2005 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef PLOT_H #define PLOT_H #include // Include Qt stuff first to avoid ambiguities with 'debug' symbol #include "odinqt.h" // forward declarations class QwtPlot; class QwtPlotCurve; class QwtPlotMarker; class QwtPlotGrid; class QRect; class QwtWheel; class QwtScaleDraw; class GuiPlotPicker; // work around different declarations of QwtDoubleRect #if QT_VERSION >= 0x040000 class QRectF; typedef QRectF QwtDoubleRect; #else class QwtDoubleRect; #endif ///////////////////////////////////////////////// /** * Abstraction of a plotting widget */ class GuiPlot : public QObject { Q_OBJECT public: GuiPlot(QWidget *parent, bool fixed_size=false, int width=_ARRAY_WIDGET_WIDTH_-20, int height=_ARRAY_WIDGET_HEIGHT_-20); ~GuiPlot(); void set_x_axis_label(const char *xAxisLabel, bool omit=false); void set_y_axis_label(const char *yAxisLabelLeft, const char *yAxisLabelRight=0); long insert_curve(bool use_right_y_axis=false, bool draw_spikes=false, bool baseline=false); long insert_marker(const char* label, double x, bool outline=false, bool horizontal=false, bool animate=false); void remove_marker(long id); void set_marker_pos(long id, double x); // memory NOT managed by GuiPlot void set_curve_data(long curveid, const double* x, const double* y, int n, bool symbol=false); void replot(); void autoscale(); void autoscale_y(double& maxBound); void rescale_y(double maxBound); void clear(); void remove_markers(); double get_x(int x_pixel) const; double get_y(int y_pixel, bool right_axes=false) const; long closest_curve(int x, int y, int& dist) const; void highlight_curve(long id, bool flag); void set_x_axis_scale(double lbound, double ubound); void set_y_axis_scale(double lbound, double ubound, bool right_axes=false); void set_curve_pen(long id, const char* color, int width=1); void set_rect_outline_style(); void set_line_outline_style(bool horizontal); void enable_axes(bool flag); void enable_grid(bool flag); void print(QPainter* painter, const QRect& rect) const; QWidget* get_widget(); signals: void plotMousePressed(const QMouseEvent&); void plotMouseReleased(const QMouseEvent&); void plotMouseMoved(const QMouseEvent&); private slots: void emit_plotMousePressed(const QMouseEvent& qme); void emit_plotMouseReleased(const QMouseEvent& qme); void emit_plotMouseMoved(const QMouseEvent& qme); private: friend class GuiPlotPicker; void set_axis_label(int axisId, const char* label, bool omit, int alignment); QwtPlot* qwtplotter; GuiPlotPicker* picker; // Use functions with check to access curve_map/marker_map QwtPlotCurve* get_curve(long id); QwtPlotMarker* get_marker(long id); // to emulate Qwt4 behaviour on Qwt5 STD_map curve_map; STD_map marker_map; QwtPlotGrid* plotgrid; int canvas_framewidth; long baseline_id_cache; }; //////////////////////////////////////////////////////////// /** * Abstraction of a slider wheel */ class GuiWheel : public QObject { Q_OBJECT public: GuiWheel(QWidget *parent); ~GuiWheel(); void set_range(double min, double max); void set_value(double newval); QWidget* get_widget(); signals: void valueChanged(double); private slots: void emit_valueChanged(double newval); private: QwtWheel* wheel; }; #endif odin-1.8.5/odinqt/boolbutton.h0000644000175000017500000000325211322062347013237 00000000000000/*************************************************************************** boolbutton.h - description ------------------- begin : Sun Jul 16 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef BOOLBUTTON_H #define BOOLBUTTON_H #include #include "odinqt.h" /** *This class provides a button with a nice frame */ class buttonBox : public QGroupBox { Q_OBJECT public: buttonBox(const char *text, QWidget *parent, const char *buttonlabel); buttonBox(const char *ontext,const char *offtext, bool initstate, QWidget *parent, const char *buttonlabel); ~buttonBox(); bool is_on() const {return gb->is_on();} public slots: void setToggleState(bool); private slots: void reportclicked(); void setButtonState(); signals: void buttonClicked(); void buttonToggled(bool); private: GuiGridLayout* grid; GuiButton* gb; }; #endif odin-1.8.5/odinqt/enumbox.h0000644000175000017500000000323111322062347012522 00000000000000/*************************************************************************** enumbox.h - description ------------------- begin : Tue May 29 2001 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ENUMBOX_H #define ENUMBOX_H #include #include "odinqt.h" /** * This class provides a combobox with a nice frame */ class enumBox : public QGroupBox { Q_OBJECT public: enumBox(const svector& items,QWidget *parent,const char *name,bool editButton=false,bool infoButton=false); ~enumBox(); public slots: void setValue( int val ); signals: void newVal( int val ); void edit(); void info(); private slots: void emitNewVal(int val); void reportEditClicked(); void reportInfoClicked(); private: int old_val; GuiComboBox* cb; GuiButton* pb_edit; GuiButton* pb_info; GuiGridLayout* grid; }; #endif odin-1.8.5/odinqt/intedit.h0000644000175000017500000000557011322062347012515 00000000000000/*************************************************************************** intedit.h - description ------------------- begin : Sun Aug 27 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef INTEDIT_H #define INTEDIT_H #include #include "odinqt.h" /** * This class implements a line edit with int values only. */ class intLineEdit : public QObject { Q_OBJECT public: intLineEdit(int minValue, int maxValue, int value, QWidget *parent, const char *name, int width, int height ); ~intLineEdit(); QWidget* get_widget() {return gle->get_widget();} public slots: void setintLineEditValue( int value ); private slots: void emitSignal( ); signals: void intLineEditValueChanged( int value ); private: void set_value(int value); GuiLineEdit* gle; }; //////////////////////////////////////////////////////////// /** * This class contains a intlineedit to display an int value * in a nice box with a label. */ class intLineBox : public QGroupBox { Q_OBJECT public: intLineBox(int value, QWidget *parent, const char *name); ~intLineBox(); public slots: void setintLineBoxValue( int value ); private slots: void emitSignal( int value ); signals: void intLineBoxValueChanged( int value ); void SignalToChild( int value ); private: GuiGridLayout* grid; intLineEdit *le; }; //////////////////////////////////////////////////////////// /** * This class implements a slider useful for scientific applications * by composing a QSlider(int values) and a intLineEdit into one widget. */ class intScientSlider : public QGroupBox { Q_OBJECT public: intScientSlider(int minValue, int maxValue, int Step, int value, QWidget *parent, const char *name); ~intScientSlider(); public slots: void setintScientSliderValue( int value ); private slots: void emitSignal( int value ); signals: void intScientSliderValueChanged( int value ); private: int value; GuiSlider* slider; GuiGridLayout* grid; intLineEdit *le; }; //////////////////////////////////////////////////////////// #endif odin-1.8.5/odinqt/plot.cpp0000644000175000017500000004573211322062347012372 00000000000000#include // for mouse events #include "plot.h" #ifdef HAVE_QWT_QT4_QWT_GLOBAL_H // For Debian #include #include #include #include #include #include #if QWT_VERSION > 0x04FFFF #include #include #include #include #include #include #else #include #endif #else #include #include #include #include #include #include #if QWT_VERSION > 0x04FFFF #include #include #include #include #include #include #else #include #endif #endif class GuiPlotPrintFilter : public QwtPlotPrintFilter { public: GuiPlotPrintFilter(long baseline_id) : baseline_id_cache(baseline_id) {} private: long baseline_id_cache; // overloading virtual functions from QwtPlotPrintFilter #if QWT_VERSION > 0x04FFFF QColor color(const QColor &c, Item item) const { QColor result=QwtPlotPrintFilter::color(c,item); // default #else QColor color(const QColor &c, Item item, int id = -1) const { QColor result=QwtPlotPrintFilter::color(c,item,id); // default #endif if(item==QwtPlotPrintFilter::Curve) result=QColor("Black"); if(item==QwtPlotPrintFilter::CurveSymbol) result=QColor("Black"); if(item==QwtPlotPrintFilter::Marker) result=QColor("Black"); if(item==QwtPlotPrintFilter::MajorGrid) result=QColor("Gray").light(130); if(item==QwtPlotPrintFilter::MinorGrid) result=QColor("Gray").light(150); #if QWT_VERSION > 041 if(item==QwtPlotPrintFilter::CanvasBackground) result=QColor("White"); #else if(item==QwtPlotPrintFilter::Background) result=QColor("White"); #endif #if QWT_VERSION < 0x04FFFF if(item==QwtPlotPrintFilter::Curve && id==baseline_id_cache) result=QColor("Gray").dark(150); #endif return result; } #if QWT_VERSION > 0x04FFFF QFont font(const QFont &, Item item) const { #else QFont font(const QFont &, Item item, int id = -1) const { #endif return QFont(_FONT_TYPE_, 7); } }; //////////////////////////////////////////////////////////////////////////// struct GuiScaleDraw : QwtScaleDraw { // implementing virtual functions of QwtScaleDraw #if QWT_VERSION < 0x04FFFF QString label (double val) const {return get_str(val);} #else QwtText label (double val) const {return QString(get_str(val));} #endif private: const char* get_str(double val) const { bool vertical=false; #if QWT_VERSION < 0x04FFFF QwtScaleDraw::Orientation ort=orientation(); if(ort==QwtScaleDraw::Left || ort==QwtScaleDraw::Right) vertical=true; #else QwtScaleDraw::Alignment ort=alignment(); if(ort==QwtScaleDraw::LeftScale || ort==QwtScaleDraw::RightScale) vertical=true; #endif if(vertical) result=ftos(val,2,alwaysExp); else result=ftos(val,2,neverExp); return result.c_str(); } mutable STD_string result; }; //////////////////////////////////////////////////////////////////////////// class GuiPlotPicker : public QwtPlotPicker { public: GuiPlotPicker(QwtPlotCanvas* canvas, GuiPlot* plot4feedback) : QwtPlotPicker(canvas), plot(plot4feedback) {} protected: void widgetMousePressEvent(QMouseEvent* qme) { Log odinlog("GuiPlotPicker","widgetMousePressEvent"); QwtPlotPicker::widgetMousePressEvent(qme); plot->emit_plotMousePressed(*qme); ODINLOG(odinlog,normalDebug) << "widgetMousePressEvent" << STD_endl; } void widgetMouseReleaseEvent(QMouseEvent* qme) { Log odinlog("GuiPlotPicker","widgetMouseReleaseEvent"); QwtPlotPicker::widgetMouseReleaseEvent(qme); plot->emit_plotMouseReleased(*qme); ODINLOG(odinlog,normalDebug) << "widgetMouseReleaseEvent" << STD_endl; } void widgetMouseMoveEvent(QMouseEvent* qme) { QwtPlotPicker::widgetMouseMoveEvent(qme); plot->emit_plotMouseMoved(*qme); } private: GuiPlot* plot; }; //////////////////////////////////////////////////////////////////////////// GuiPlot::GuiPlot(QWidget *parent, bool fixed_size, int width, int height) { Log odinlog("GuiPlot","GuiPlot(...)"); baseline_id_cache=0; qwtplotter = new QwtPlot(parent); if(fixed_size) qwtplotter->setFixedSize (width,height); else qwtplotter->setMinimumSize(width,height); qwtplotter->resize(width,height); qwtplotter->plotLayout()->setAlignCanvasToScales(true); // to get mouse-move events qwtplotter->canvas()->setMouseTracking(true); // set default axis titles set_x_axis_label(0); set_y_axis_label(0,0); #if QWT_VERSION < 0x04FFFF qwtplotter->setAxisTitleFont(QwtPlot::xBottom,QFont(_FONT_TYPE_, _FONT_SIZE_)); qwtplotter->setAxisTitleFont(QwtPlot::yLeft, QFont(_FONT_TYPE_, _FONT_SIZE_)); qwtplotter->setAxisTitleFont(QwtPlot::yRight, QFont(_FONT_TYPE_, _FONT_SIZE_)); #endif qwtplotter->enableAxis(QwtPlot::xBottom,true); /* qwtplotter->setAxisLabelFormat(QwtPlot::yLeft,'e',1,10); qwtplotter->setAxisLabelFormat(QwtPlot::xBottom,'f',2); */ qwtplotter->setAxisScaleDraw(QwtPlot::yLeft, new GuiScaleDraw()); qwtplotter->setAxisScaleDraw(QwtPlot::xBottom, new GuiScaleDraw()); qwtplotter->setCanvasBackground(_ARRAY_BACKGROUND_COLOR_); #if QWT_VERSION > 0x04FFFF plotgrid=new QwtPlotGrid(); plotgrid->attach(qwtplotter); ODINLOG(odinlog,normalDebug) << "plotgrid=" << plotgrid << STD_endl; #endif enable_grid(true); #if QWT_VERSION < 0x04FFFF qwtplotter->enableLegend(false); qwtplotter->enableOutline(false); #endif canvas_framewidth=qwtplotter->canvas()->lineWidth(); picker=new GuiPlotPicker(qwtplotter->canvas(),this); picker->setRubberBandPen(QColor(_ARRAY_SELECTION_COLOR_)); set_rect_outline_style(); // do this after picker was initialized } void GuiPlot::set_axis_label(int axisId, const char* label, bool omit, int alignment) { Log odinlog("GuiPlot","set_axis_label"); ODINLOG(odinlog,normalDebug) << "axisId/label/omit/alignment=" << axisId << "/" << label << "/" << omit << "/" << alignment << STD_endl; if(!label || STD_string(label)=="") omit=true; if(omit) { #if QWT_VERSION > 0x04FFFF QwtText txt(""); txt.setFont(QFont(_FONT_TYPE_, 1)); qwtplotter->setAxisTitle(axisId,txt); #else qwtplotter->setAxisTitle(axisId,""); qwtplotter->setAxisTitleFont(axisId,QFont(_FONT_TYPE_, 1)); // make font zero size to save space in widget #endif } else { #if QWT_VERSION > 0x04FFFF QwtText txt(label); txt.setRenderFlags(alignment); qwtplotter->setAxisTitle(axisId,txt); #else qwtplotter->setAxisTitle(axisId,label); qwtplotter->setAxisTitleAlignment(axisId,alignment); #endif } } void GuiPlot::set_x_axis_label(const char *xAxisLabel, bool omit) { set_axis_label(QwtPlot::xBottom,xAxisLabel,omit,Qt::AlignRight); } void GuiPlot::set_y_axis_label(const char *yAxisLabelLeft, const char *yAxisLabelRight) { if(yAxisLabelLeft) set_axis_label(QwtPlot::yLeft, yAxisLabelLeft, false,Qt::AlignCenter); if(yAxisLabelRight) set_axis_label(QwtPlot::yRight,yAxisLabelRight,false,Qt::AlignCenter); if(yAxisLabelLeft) qwtplotter->enableAxis(QwtPlot::yLeft,true); if(yAxisLabelRight) qwtplotter->enableAxis(QwtPlot::yRight,true); } long GuiPlot::insert_curve(bool use_right_y_axis, bool draw_spikes, bool baseline) { Log odinlog("GuiPlot","insert_curve"); long result=0; int yaxis=QwtPlot::yLeft; if(use_right_y_axis) yaxis=QwtPlot::yRight; QPen curvepen(QColor(_ARRAY_FOREGROUND_COLOR1_)); if(use_right_y_axis || baseline) { curvepen=QColor(_ARRAY_FOREGROUND_COLOR2_); } #if QWT_VERSION > 0x04FFFF QwtPlotCurve* curve=new QwtPlotCurve(); curve->setAxis(QwtPlot::xBottom, yaxis); curve->setPen(curvepen); curve->attach(qwtplotter); result=curve_map.size()+1; curve_map[result]=curve; #else result=qwtplotter->insertCurve("",QwtPlot::xBottom,yaxis); qwtplotter->setCurvePen(result,curvepen); #endif if(draw_spikes) { #if QWT_VERSION > 0x04FFFF curve->setBaseline(0.0); curve->setStyle(QwtPlotCurve::Sticks); #else qwtplotter->setCurveBaseline(result,0.0); qwtplotter->setCurveStyle(result,QwtCurve::Sticks); #endif } if(baseline) baseline_id_cache=result; ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } long GuiPlot::insert_marker(const char* label, double x, bool outline, bool horizontal, bool animate) { Log odinlog("GuiPlot","insert_marker"); long result=0; ODINLOG(odinlog,normalDebug) << "label/x/outline/horizontal/animate=" << label << "/" << x << "/" << outline << "/" << horizontal << "/" << animate << STD_endl; int axis=QwtPlot::xBottom; if(horizontal) axis=QwtPlot::yLeft; QColor markcolor(QColor(_ARRAY_MARKER_COLOR_).light(_ARRAY_MARKER_BRIGHT_FACTOR_)); if(animate) markcolor=QColor("red"); if(outline) markcolor=QColor(_ARRAY_SELECTION_COLOR_); #if QWT_VERSION > 0x04FFFF QwtPlotMarker* marker=new QwtPlotMarker(); if(horizontal) { marker->setLineStyle(QwtPlotMarker::HLine); marker->setYValue(x); } else { marker->setLineStyle(QwtPlotMarker::VLine); marker->setXValue(x); } marker->setLinePen(QPen(markcolor)); #if QWT_VERSION > 0x04FFFF QwtText txt(label); txt.setColor(markcolor); txt.setRenderFlags(Qt::AlignTop); marker->setLabel(txt); #else marker->setLabelPen(QPen(markcolor)); marker->setLabelAlignment(Qt::AlignTop); marker->setLabel(QString(label)); #endif marker->attach(qwtplotter); result=marker_map.size()+1; marker_map[result]=marker; #else result=qwtplotter->insertLineMarker(label, axis); qwtplotter->setMarkerPen(result,QPen(markcolor)); if(horizontal) qwtplotter->setMarkerYPos(result,x); else qwtplotter->setMarkerXPos(result,x); #endif ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } void GuiPlot::remove_marker(long id) { Log odinlog("GuiPlot","remove_marker"); ODINLOG(odinlog,normalDebug) << "id=" << id << STD_endl; #if QWT_VERSION > 0x04FFFF QwtPlotMarker* qpm=get_marker(id); if(qpm) qpm->detach(); #else qwtplotter->removeMarker(id); #endif } void GuiPlot::set_marker_pos(long id, double x) { Log odinlog("GuiPlot","remove_marker"); ODINLOG(odinlog,normalDebug) << "id/x=" << id << "/" << x << STD_endl; #if QWT_VERSION > 0x04FFFF QwtPlotMarker* qpm=get_marker(id); if(qpm) qpm->setXValue(x); #else qwtplotter->setMarkerXPos(id,x); #endif } void GuiPlot::set_curve_data(long curveid, const double* x, const double* y, int n, bool symbol) { Log odinlog("GuiPlot","set_curve_data"); ODINLOG(odinlog,normalDebug) << "curveid/x/y/symbol=" << curveid << "/" << x << "/" << y << "/" << symbol << STD_endl; #if QWT_VERSION > 0x04FFFF QwtSymbol::Style symbstyle=QwtSymbol::NoSymbol; #else QwtSymbol::Style symbstyle=QwtSymbol::None; #endif if(symbol) { symbstyle=QwtSymbol::Ellipse; } QwtSymbol symb(symbstyle,QBrush(),QColor(_ARRAY_FOREGROUND_COLOR1_),QSize(PLOT_SYMBOLS_SIZE,PLOT_SYMBOLS_SIZE)); if(n) ODINLOG(odinlog,normalDebug) << "y[" << n/2 << "]=" << y[n/2] << STD_endl; #if QWT_VERSION > 0x04FFFF QwtPlotCurve* qpc=get_curve(curveid); if(qpc) { qpc->setSymbol(symb); qpc->setRawData(x, y, n); } #else qwtplotter->setCurveSymbol(curveid,symb); qwtplotter->setCurveRawData(curveid, x, y, n); #endif } void GuiPlot::replot() { Log odinlog("GuiPlot","replot"); ODINLOG(odinlog,normalDebug) << "replotting " << curve_map.size() << " curves and " << marker_map.size() << " markers" << STD_endl; qwtplotter->replot(); // qwtzoomer->setZoomBase(); } void GuiPlot::autoscale() { qwtplotter->setAxisAutoScale(QwtPlot::xBottom); qwtplotter->setAxisAutoScale(QwtPlot::yLeft); qwtplotter->setAxisAutoScale(QwtPlot::yRight); replot(); } void GuiPlot::autoscale_y(double& maxBound) { qwtplotter->setAxisAutoScale(QwtPlot::yLeft); qwtplotter->replot(); // seems to be neccessary for correct autoscaling, even if the curve is already added #if QWT_VERSION > 0x04FFFF #if QWT_VERSION > 0x0501FF double new_lbound=qwtplotter->axisScaleDiv(QwtPlot::yLeft)->lowerBound(); double new_hbound=qwtplotter->axisScaleDiv(QwtPlot::yLeft)->upperBound(); #else double new_lbound=qwtplotter->axisScaleDiv(QwtPlot::yLeft)->lBound(); double new_hbound=qwtplotter->axisScaleDiv(QwtPlot::yLeft)->hBound(); #endif #else double new_lbound=qwtplotter->axisScale(QwtPlot::yLeft)->lBound(); double new_hbound=qwtplotter->axisScale(QwtPlot::yLeft)->hBound(); #endif // symmetrical adjustment maxBound=STD_max(fabs(new_lbound),fabs(new_hbound)); new_lbound=-maxBound; new_hbound= maxBound; qwtplotter->setAxisScale(QwtPlot::yLeft, new_lbound, new_hbound); // switch back to manual scaling for scrolling replot(); } void GuiPlot::rescale_y(double maxBound) { qwtplotter->setAxisScale(QwtPlot::yLeft, -maxBound, maxBound); replot(); } void GuiPlot::clear() { Log odinlog("GuiPlot","clear()"); #if QWT_VERSION > 0x04FFFF for(STD_map::const_iterator curvit=curve_map.begin(); curvit!=curve_map.end(); ++curvit) { ODINLOG(odinlog,normalDebug) << "Detaching curve #" << curvit->first << STD_endl; curvit->second->detach(); ODINLOG(odinlog,normalDebug) << "Deleting curve #" << curvit->first << STD_endl; delete curvit->second; } ODINLOG(odinlog,normalDebug) << "Clearing curve cache" << STD_endl; curve_map.clear(); ODINLOG(odinlog,normalDebug) << "Removing markers" << STD_endl; remove_markers(); #endif qwtplotter->clear(); // do this after detaching curves } void GuiPlot::remove_markers() { #if QWT_VERSION > 0x04FFFF for(STD_map::const_iterator markit=marker_map.begin(); markit!=marker_map.end(); ++markit) { markit->second->detach(); delete markit->second; } marker_map.clear(); #else qwtplotter->removeMarkers(); #endif } double GuiPlot::get_x(int x_pixel) const { Log odinlog("GuiPlot","get_x"); double result=qwtplotter->invTransform(QwtPlot::xBottom,x_pixel+canvas_framewidth); ODINLOG(odinlog,normalDebug) << "result/x_pixel=" << result << "/" << x_pixel << STD_endl; return result;; } double GuiPlot::get_y(int y_pixel, bool right_axes) const { if(right_axes) return qwtplotter->invTransform(QwtPlot::yRight, y_pixel+canvas_framewidth); else return qwtplotter->invTransform(QwtPlot::yLeft, y_pixel+canvas_framewidth); } long GuiPlot::closest_curve(int x, int y, int& dist) const { #if QWT_VERSION > 0x04FFFF Log odinlog("GuiPlot","closest_curve"); long result=-1; double dmin = 1.0e10; double curvedist; QPoint pos(x,y); for(STD_map::const_iterator curvit=curve_map.begin(); curvit!=curve_map.end(); ++curvit) { curvit->second->closestPoint(pos,&curvedist); if(curvedistfirst; dist=int(curvedist); dmin=curvedist; } } ODINLOG(odinlog,normalDebug) << "result/dist" << result << "/" << dist << STD_endl; return result; #else return qwtplotter->closestCurve(x,y,dist); #endif } void GuiPlot::highlight_curve(long id, bool flag) { const char* color=_ARRAY_FOREGROUND_COLOR1_; if(flag) color=_ARRAY_HIGHLIGHT_COLOR_; set_curve_pen(id,color); } void GuiPlot::set_x_axis_scale(double lbound, double ubound) { Log odinlog("GuiPlot","set_x_axis_scale"); ODINLOG(odinlog,normalDebug) << "lbound/ubound=" << lbound << "/" << ubound << STD_endl; qwtplotter->setAxisScale(QwtPlot::xBottom,lbound,ubound); } void GuiPlot::set_y_axis_scale(double lbound, double ubound, bool right_axes) { if(right_axes) qwtplotter->setAxisScale(QwtPlot::yRight,lbound,ubound); else qwtplotter->setAxisScale(QwtPlot::yLeft, lbound,ubound); } void GuiPlot::set_curve_pen(long id, const char* color, int width) { QPen qp; qp.setColor(color); qp.setWidth(width); #if QWT_VERSION > 0x04FFFF QwtPlotCurve* qpc=get_curve(id); if(qpc) qpc->setPen(qp); #else qwtplotter->setCurvePen(id,qp); #endif } void GuiPlot::set_rect_outline_style() { picker->setSelectionFlags(QwtPicker::RectSelection | QwtPicker::CornerToCorner | QwtPicker::DragSelection); picker->setRubberBand(QwtPicker::RectRubberBand); } void GuiPlot::set_line_outline_style(bool horizontal) { picker->setSelectionFlags(QwtPicker::PointSelection | QwtPicker::DragSelection); if(horizontal) picker->setRubberBand(QwtPicker::HLineRubberBand); else picker->setRubberBand(QwtPicker::VLineRubberBand); } void GuiPlot::enable_axes(bool flag) { qwtplotter->enableAxis(QwtPlot::xBottom,flag); qwtplotter->enableAxis(QwtPlot::yLeft,flag); } void GuiPlot::enable_grid(bool flag) { Log odinlog("GuiPlot","enable_grid"); if(flag) { QPen gridpen(QColor(_ARRAY_GRID_COLOR_).dark(_ARRAY_GRID_DARK_FACTOR_)); #if QWT_VERSION > 0x04FFFF ODINLOG(odinlog,normalDebug) << "plotgrid=" << plotgrid << STD_endl; plotgrid->setPen(gridpen); plotgrid->setMajPen(gridpen); plotgrid->setMinPen(gridpen); #else qwtplotter->setGridPen(gridpen); qwtplotter->setGridMajPen(gridpen); qwtplotter->setGridMinPen(gridpen); #endif } #if QWT_VERSION > 0x04FFFF plotgrid->enableX(flag); plotgrid->enableY(flag); #else qwtplotter->enableGridX(flag); qwtplotter->enableGridY(flag); #endif } void GuiPlot::print(QPainter* painter, const QRect& rect) const { GuiPlotPrintFilter pfilter(baseline_id_cache); qwtplotter->print(painter,rect,pfilter); } QWidget* GuiPlot::get_widget() {return qwtplotter;} void GuiPlot::emit_plotMousePressed(const QMouseEvent& qme) { emit plotMousePressed(qme); } void GuiPlot::emit_plotMouseReleased(const QMouseEvent& qme) { emit plotMouseReleased(qme); } void GuiPlot::emit_plotMouseMoved(const QMouseEvent& qme) { emit plotMouseMoved(qme); } QwtPlotCurve* GuiPlot::get_curve(long id) { STD_map::iterator it=curve_map.find(id); if(it==curve_map.end()) return 0; return it->second; } QwtPlotMarker* GuiPlot::get_marker(long id) { STD_map::iterator it=marker_map.find(id); if(it==marker_map.end()) return 0; return it->second; } GuiPlot::~GuiPlot() { Log odinlog("GuiPlot","~GuiPlot()"); clear(); #if QWT_VERSION > 0x04FFFF delete plotgrid; #endif delete picker; delete qwtplotter; } //////////////////////////////////////////////////////////////////////////// GuiWheel::GuiWheel(QWidget *parent) { wheel=new QwtWheel(parent); wheel->setOrientation(Qt::Vertical); connect( wheel, SIGNAL(valueChanged(double)), SLOT(emit_valueChanged(double)) ); } void GuiWheel::set_range(double min, double max) { wheel->setRange(min,max); } void GuiWheel::set_value(double newval) { wheel->fitValue(newval); } QWidget* GuiWheel::get_widget() {return wheel;} void GuiWheel::emit_valueChanged(double newval) {emit valueChanged(newval);} GuiWheel::~GuiWheel() { delete wheel; } odin-1.8.5/odinqt/floatedit.cpp0000644000175000017500000001424611322062347013363 00000000000000#include #include "floatedit.h" #include // for ftos #include floatLineEdit::floatLineEdit(float minValue, float maxValue, float value,int digits, QWidget *parent, const char *name, int width, int height ) { gle = new GuiLineEdit(parent, this, SLOT(emitSignal()), width, height); // minValue & maxValue unused so far: minValue=maxValue=0.0; digits_cache=digits; set_value(value); } floatLineEdit::~floatLineEdit() { delete gle; } void floatLineEdit::setfloatLineEditValue( float newValue ) { set_value(newValue); } void floatLineEdit::emitSignal() { if(gle->is_modified()) { value_cache=atof(gle->get_text()); set_value(value_cache); emit floatLineEditValueChanged(value_cache); } } void floatLineEdit::set_value(float value) { value_cache=value; gle->set_text( ftos(value_cache,digits_cache).c_str() ); } ////////////////////////////////////////////////////////////////////////// floatSlider::floatSlider(float minValue, float maxValue, float step, float value, QWidget *parent, const char *name ) { int nsteps=int((maxValue-minValue)/step+0.5); int ival=int((value-minValue)/step+0.5); gs=new GuiSlider( parent, 0, nsteps , 1, ival, nsteps/20); minValue_cache=minValue; step_cache=step; connect(gs->get_widget(),SIGNAL(valueChanged( int )),this,SLOT(emitSignal( int ))); } void floatSlider::setfloatSliderValue( float newValue ) { oldPosition=int((newValue-minValue_cache)/step_cache+0.5); gs->set_value(oldPosition); } void floatSlider::emitSignal( int newintvalue ) { Log odinlog("floatSlider","emitSignal"); ODINLOG(odinlog,normalDebug) << "newintvalue/oldPosition=" << newintvalue << "/" << oldPosition << STD_endl; if (!(newintvalue==oldPosition)) { float newfloatval=minValue_cache+newintvalue*step_cache; emit floatSliderValueChanged(newfloatval); } } QWidget* floatSlider::get_widget() {return gs->get_widget();} floatSlider::~floatSlider() { delete gs; } ////////////////////////////////////////////////////////////////////////// floatLineBox::floatLineBox(float value, int digits,QWidget *parent, const char *name ) : QGroupBox(name,parent) { grid=new GuiGridLayout( this, 1, 1); // Create connected floatSlider and floatLineEdit le = new floatLineEdit( 0.0, 0.0, value,digits, this, "LineEdit", TEXTEDIT_WIDTH, TEXTEDIT_HEIGHT); grid->add_widget(le->get_widget(), 0, 0); connect(le,SIGNAL(floatLineEditValueChanged( float )), this,SLOT(emitSignal( float ))); } void floatLineBox::setfloatLineBoxValue( float newvalue ) { le->setfloatLineEditValue(newvalue); } void floatLineBox::emitSignal( float newvalue ) { emit floatLineBoxValueChanged(newvalue); } floatLineBox::~floatLineBox(){ delete le; delete grid; } ////////////////////////////////////////////////////////////////////////// floatScientSlider::floatScientSlider(float minValue, float maxValue, float Step, float value, int digits, QWidget *parent, const char *name ) : QGroupBox(name, parent ) { grid=new GuiGridLayout(this, 1, 4); slider = new floatSlider( minValue, maxValue, Step, value, this, "Slider" ); le = new floatLineEdit( minValue, maxValue, value,digits, this, "LineEdit", SLIDER_CELL_WIDTH, SLIDER_CELL_HEIGHT ); grid->add_widget(slider->get_widget(), 0, 0, GuiGridLayout::Default, 1, 3 ); grid->add_widget(le->get_widget(), 0, 3); // connect slider and lineedit connect(slider, SIGNAL(floatSliderValueChanged( float )),le, SLOT(setfloatLineEditValue( float))); connect(le, SIGNAL(floatLineEditValueChanged( float )),slider, SLOT(setfloatSliderValue( float))); // Emit signal 'floatScientSliderValueChanged' to outer world connect(slider,SIGNAL(floatSliderValueChanged( float )),this,SLOT(emitSignal( float ))); connect(le,SIGNAL(floatLineEditValueChanged( float )),this,SLOT(emitSignal( float ))); } void floatScientSlider::setfloatScientSliderValue( float newvalue ) { slider->setfloatSliderValue(newvalue); le->setfloatLineEditValue(newvalue); } void floatScientSlider::emitSignal( float newvalue ) { emit floatScientSliderValueChanged(newvalue); } floatScientSlider::~floatScientSlider(){ delete le; delete slider; delete grid; } //////////////////////////////////////////////////////////////////// floatLineBox3D::floatLineBox3D(float xval, float yval, float zval, int digits,QWidget *parent, const char *name ) : QGroupBox(name,parent) { grid=new GuiGridLayout(this, 1, 3); xcache=xval; ycache=yval; zcache=zval; lex = new floatLineEdit( 0.0, 0.0, xval,digits,this, "lex", TEXTEDIT_WIDTH, TEXTEDIT_HEIGHT ); ley = new floatLineEdit( 0.0, 0.0, yval,digits,this, "ley", TEXTEDIT_WIDTH, TEXTEDIT_HEIGHT ); lez = new floatLineEdit( 0.0, 0.0, zval,digits,this, "lez", TEXTEDIT_WIDTH, TEXTEDIT_HEIGHT ); grid->add_widget( lex->get_widget(), 0, 0 ); grid->add_widget( ley->get_widget(), 0, 1 ); grid->add_widget( lez->get_widget(), 0, 2 ); connect(lex,SIGNAL(floatLineEditValueChanged( float )),this,SLOT(emitSignal_x( float ))); connect(ley,SIGNAL(floatLineEditValueChanged( float )),this,SLOT(emitSignal_y( float ))); connect(lez,SIGNAL(floatLineEditValueChanged( float )),this,SLOT(emitSignal_z( float ))); connect(this,SIGNAL(SignalToChild_x( float )),lex, SLOT(setfloatLineEditValue( float))); connect(this,SIGNAL(SignalToChild_y( float )),ley, SLOT(setfloatLineEditValue( float))); connect(this,SIGNAL(SignalToChild_z( float )),lez, SLOT(setfloatLineEditValue( float))); } void floatLineBox3D::setfloatLineBox3DValue( float xval, float yval, float zval ) { xcache=xval; ycache=yval; zcache=zval; emit SignalToChild_x( xval ); emit SignalToChild_y( yval ); emit SignalToChild_z( zval ); } void floatLineBox3D::emitSignal_x( float newvalue ) {xcache=newvalue; emit floatLineBox3DValueChanged(newvalue,ycache,zcache);} void floatLineBox3D::emitSignal_y( float newvalue ) {ycache=newvalue; emit floatLineBox3DValueChanged(xcache,newvalue,zcache);} void floatLineBox3D::emitSignal_z( float newvalue ) {zcache=newvalue; emit floatLineBox3DValueChanged(xcache,ycache,newvalue);} floatLineBox3D::~floatLineBox3D(){ delete lex; delete ley; delete lez; delete grid; } odin-1.8.5/odinqt/stringbox.cpp0000644000175000017500000000204511322062347013421 00000000000000#include "stringbox.h" stringBox::stringBox(const char* text,QWidget *parent, const char *name, const char *buttontext ) : QGroupBox(name,parent) { unsigned int ncol=1; if(buttontext) ncol++; grid=new GuiGridLayout( this, 1, ncol); le = new GuiLineEdit(this, this, SLOT(reportTextChanged())); grid->add_widget( le->get_widget(), 0, 0 ); // Create a push button pb=0; if(buttontext) { pb = new GuiButton( this, this, SLOT(reportButtonClicked()), buttontext ); grid->add_widget( pb->get_widget(), 0, 1, GuiGridLayout::VCenter ); } setstringBoxText(text); } void stringBox::reportButtonClicked() { emit stringBoxButtonPressed(); } void stringBox::reportTextChanged() { if(le->is_modified()) { emit stringBoxTextEntered(le->get_text()); } } void stringBox::setstringBoxText( const char* text ) { Log odinlog("stringBox","setstringBoxText"); ODINLOG(odinlog,normalDebug) << "text=" << text << STD_endl; le->set_text(text); } stringBox::~stringBox() { if(pb) delete pb; delete le; delete grid; } odin-1.8.5/odinqt/odinqt.h0000644000175000017500000003452411363773557012375 00000000000000/*************************************************************************** odinqt.h - description ------------------- begin : Sun Aug 27 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINQT_H #define ODINQT_H #include #include #include // for svector // global configuration #define _FONT_TYPE_ "helvetica" #define _ARRAY_WIDGET_WIDTH_ 270 #define _ARRAY_WIDGET_HEIGHT_ 180 #define _ARRAY_BACKGROUND_COLOR_ "Black" #define _ARRAY_FOREGROUND_COLOR1_ "White" #define _ARRAY_FOREGROUND_COLOR2_ "Grey" #define _ARRAY_GRID_COLOR_ "Green" #define _ARRAY_GRID_DARK_FACTOR_ 250 #define _ARRAY_SELECTION_COLOR_ "Yellow" #define _ARRAY_HIGHLIGHT_COLOR_ "Orange" #define _ARRAY_MARKER_COLOR_ "Blue" #define _ARRAY_MARKER_BRIGHT_FACTOR_ 180 #define _LAYOUT_STRETCH_FACTOR_ 1 #define SLIDER_CELL_WIDTH 75 #define SLIDER_CELL_HEIGHT 25 #define TEXTEDIT_WIDTH 75 #define TEXTEDIT_HEIGHT 25 #define PLOT_SYMBOLS_SIZE 5 // platform-specific configuration #ifdef USING_WIN32 #define _FONT_SIZE_ 8 #else #define _FONT_SIZE_ 10 #endif ///////////////////////////////////////////////// // forward declarations class QObject; class QWidget; class QString; class QGridLayout; class QPushButton; class QLineEdit; class QPopupMenu; class QMenu; class QKeySequence; class QPoint; class QSlider; class QComboBox; class QLabel; class QPainter; class QPixmap; class QMouseEvent; class QColor; class QString; class QRegion; class QApplication; class QScrollView; class QScrollArea; class QDialog; class QMainWindow; class QProgressDialog; class QImage; class QListView; class QListViewItem; class QCheckListItem; class QTableWidget; class QTableWidgetItem; class QTreeWidget; class QTreeWidgetItem; class QProgressBar; class QScrollBar; class QToolBar; class QToolButton; class QPrinter; class QPaintDevice; class QWizard; class QTextEdit; class QTextView; class SlotDispatcher; ///////////////////////////////////////////////// /** * Helper classfor debugging the OdinQt component */ class OdinQt { public: static const char* get_compName(); }; ///////////////////////////////////////////////// // Helper functions for Qt portability const char* c_str(const QString& qs); int layout_border_size(); void init_label(QLabel* ql); bool left_button(const QMouseEvent* qme, bool return_current_state); bool right_button(const QMouseEvent* qme, bool return_current_state); bool middle_button(const QMouseEvent* qme, bool return_current_state); void add_tooltip(QWidget* w, const char* txt); void set_platform_defaults(QWidget* w, bool enable=true); STD_string get_save_filename(const char* caption=0, const char* startwith="", const char* filter="", QWidget* parent=0); STD_string get_open_filename(const char* caption=0, const char* startwith="", const char* filter="", QWidget* parent=0); STD_string get_directory(const char* caption=0, const char* startwith="", QWidget* parent=0); bool message_question(const char* text, const char* caption, QWidget* parent, bool ask=false, bool error=false); int paintdevice_height(const QPaintDevice* qpd); int paintdevice_width(const QPaintDevice* qpd); svector get_possible_image_fileformats(); ///////////////////////////////////////////////// // Helper classes for Qt portability /** * Abstraction of a grid layout */ class GuiGridLayout { public: GuiGridLayout(QWidget *parent, int rows, int columns, bool margin=true); ~GuiGridLayout(); enum Alignment {Default, VCenter, Center}; void add_widget(QWidget *w, int row, int column, Alignment alignment=Default, int rowSpan=1, int columnSpan=1 ); void set_col_stretch(int col, int factor); void set_row_stretch(int row, int factor); void set_col_minsize(int col, int minsize); void set_row_minsize(int row, int minsize); private: QGridLayout* qgl; }; ///////////////////////////////////////////////// /** * Abstraction of a push button */ class GuiButton { public: GuiButton(QWidget *parent, QObject* receiver, const char* member, const char *onlabel, const char *offlabel=0, bool initstate=false); ~GuiButton(); void set_toggled(bool state); void set_text(bool state); void set_default(bool state); bool is_on() const; QWidget* get_widget(); private: friend class SlotDispatcher; QPushButton* qpb; SlotDispatcher* sd; const char* ontext; const char* offtext; }; ///////////////////////////////////////////////// /** * Abstraction of a text editing field */ class GuiLineEdit { public: GuiLineEdit(QWidget *parent, QObject* receiver, const char* member, int width=-1, int height=-1); ~GuiLineEdit(); void set_text(const char* txt); const char* get_text() const; bool is_modified(); QWidget* get_widget(); private: friend class SlotDispatcher; QLineEdit* qle; SlotDispatcher* sd; }; ///////////////////////////////////////////////// /** * Abstraction of a popup menu */ class GuiPopupMenu { public: GuiPopupMenu(QWidget *parent); ~GuiPopupMenu(); void insert_item(const char* text, const QObject* receiver, const char* member, int accel=0); void insert_separator(); void popup(const QPoint& p); private: friend class GuiMainWindow; QPopupMenu* qpm; // for Qt pre4 QMenu* qm; // for Qt4 int id; }; ///////////////////////////////////////////////// /** * Abstraction of a slider */ class GuiSlider { public: GuiSlider(QWidget *parent, int minValue, int maxValue, int pageStep, int value, int tickInterval); ~GuiSlider(); int get_value() const; void set_value(int val); bool modified_externally() const {bool result=modified; modified=false; return result;} QSlider* get_widget() {return qs;} private: QSlider* qs; mutable bool modified; }; ///////////////////////////////////////////////// class GuiToolBar; // forward declarion /** * Abstraction of a combo box */ class GuiComboBox { public: GuiComboBox(QWidget* parent, const svector& names); GuiComboBox(GuiToolBar* parent, const svector& names); ~GuiComboBox(); void set_names(const svector& names); void set_current_item(int index); int get_current_item() const; QComboBox* get_widget() {return qcb;} private: void common_init(QWidget* parent, const svector& names); QComboBox* qcb; }; ///////////////////////////////////////////////// /** * Abstraction of a painter */ class GuiPainter { public: GuiPainter(QPixmap* qpm); ~GuiPainter(); // forwarding functions to QPainter void moveTo(int x, int y); void lineTo(int x, int y); bool begin(QPixmap* qpm); bool end(); void setPen(const char* pencolor, int linewidth=1, bool dotted=false, float lightdark=0.0); void fillRect( int x, int y, int w, int h, const QColor& col); void drawRect(int x, int y, int w, int h); void drawText( int x, int y, const QString& txt, const QColor& col); QRegion* draw_region(const STD_list& plist); QPainter* get_painter() {return qp;} void repaint(QLabel* dst); private: QPainter* qp; QPixmap* qpm_cache; int x_cache, y_cache; }; ///////////////////////////////////////////////// /** * Abstraction of a GUI application */ class GuiApplication { public: GuiApplication(int argc=0, char *argv[]=0); ~GuiApplication(); int start(QWidget* mainwidget); QObject* get_object(); static void quit(); static int argc(); static char** argv(); static void process_events(); private: QApplication* qa; // Cache cmdline args separately for Qt and for later use static int argc_cache; static char** argv_cache; static int argc4qt; static char** argv4qt; }; ///////////////////////////////////////////////// /** * Abstraction of a GUI main window */ class GuiMainWindow { public: GuiMainWindow(QWidget* parent = 0); ~GuiMainWindow(); void show(QWidget* central_widget, bool show_toolbutton_text=false); void set_caption(const char* text); void set_status_message(const char* text, int timeout_ms=0); void set_status_xpm(const char** xpm); QWidget* get_widget(); void insert_menu( const char* text, GuiPopupMenu * gpm); void insert_menu_separator(); void close(); private: friend class GuiToolBar; QMainWindow* qmw; QLabel* statusIcon; QLabel* statusText; }; ///////////////////////////////////////////////// /** * Abstraction of a scrollable window/area */ class GuiScroll { public: GuiScroll(QWidget* child, QWidget* parent); ~GuiScroll(); QWidget* get_widget(); private: QScrollView* qsv; // for Qt pre4 QScrollArea* qsa; // for Qt4 }; ///////////////////////////////////////////////// class QDialogDerived; // to overload paintEvent /** * Abstraction of a dialog */ class GuiDialog { public: GuiDialog(QWidget *parent, const char* caption, bool modal=false); virtual ~GuiDialog(); QWidget* get_widget(); virtual void repaint() {} // overload to repaint dialog virtual void close() {} // overload to perform additional stuff when closing dialog void show(); void cancel(); void done(); void hide(); int exec(); private: QDialogDerived* qd; }; ///////////////////////////////////////////////// /** * Abstraction of a progress dialog */ class GuiProgressDialog { public: GuiProgressDialog(QWidget *parent, bool modal, int total_steps); ~GuiProgressDialog(); void set_progress(int progr); int get_progress() const; void set_total_steps(int steps); bool was_cancelled() const; void reset(); void set_text(const char* txt); void show(); void hide(); private: QProgressDialog* qpd; }; ///////////////////////////////////////////////// /** * Abstraction of an image class */ class GuiImage { public: GuiImage(unsigned char* data, int width, int height, bool colormap); ~GuiImage(); QPixmap* create_pixmap() const; private: QImage* qi; }; ///////////////////////////////////////////////// class GuiListItem; // forward declaration class GuiListViewCallback { public: virtual void clicked(GuiListItem* item) = 0; protected: GuiListViewCallback() {} }; /** * Abstraction of a list/tree view class */ class GuiListView { public: GuiListView(QWidget *parent, const svector& column_labels, int first_column_width=-1, int min_height=-1, GuiListViewCallback* callback=0, bool tree=false); ~GuiListView(); QWidget* get_widget(); private: friend class GuiListItem; QListView* qlv; // for Qt pre4 QTableWidget* qtw; // for Qt4 QTreeWidget* qtrw; // for Qt4 SlotDispatcher* sd; }; ///////////////////////////////////////////////// /** * Abstraction of a list/tree view item */ class GuiListItem : public StaticHandler { public: GuiListItem() {common_init();} // used for constructing listmap GuiListItem(GuiListView *parent, const svector& column_entries, bool checkable=false, bool initstate=false); GuiListItem(GuiListItem *parent, GuiListItem *after, const svector& column_entries); ~GuiListItem(); bool is_checked() const; const char* get_text() const; // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); private: friend class SlotDispatcher; void common_init(); QListViewItem* qlvi; // for Qt pre4 QCheckListItem* qcli; // for Qt pre4 QTableWidgetItem* qtwi; // for Qt4 QTreeWidgetItem* qtrwi; // for Qt4 QTreeWidget* parent_qtrw; // for Qt4 // global map to retrieve GuiListItem from QListViewItem static STD_map* listmap; // for Qt pre4 static STD_map* tablemap; // for Qt4 }; ///////////////////////////////////////////////// /** * Abstraction of a progress bar */ class GuiProgressBar { public: GuiProgressBar(QWidget *parent, int total_steps); ~GuiProgressBar(); void set_progress(int progr); void set_min_width(int w); QWidget* get_widget(); private: QProgressBar* qpb; }; ///////////////////////////////////////////////// /** * Abstraction of a scroll bar */ class GuiScrollBar { public: GuiScrollBar(QWidget* parent); ~GuiScrollBar(); void set_values(int min, int max, int linestep, int pagestep, int value); QScrollBar* get_widget(); private: QScrollBar* qsb; }; ///////////////////////////////////////////////// /** * Abstraction of a tool bar */ class GuiToolBar { public: GuiToolBar(GuiMainWindow* parent, const char* label); ~GuiToolBar(); QWidget* get_widget(); void add_separator(); private: friend class GuiToolButton; friend class GuiComboBox; QToolBar* qtb; }; ///////////////////////////////////////////////// /** * Abstraction of a tool button */ class GuiToolButton { public: GuiToolButton(GuiToolBar* parent, const char** xpm, const char* label, QObject* receiver, const char* member, bool checkable=false, bool initstate=false ); ~GuiToolButton(); bool is_on() const; void set_on(bool flag); void set_enabled(bool flag); void set_label(const char* text); void set_tooltip(const char* text); private: friend class SlotDispatcher; QToolButton* qtb; SlotDispatcher* sd; }; ///////////////////////////////////////////////// /** * Abstraction of a printer driver */ class GuiPrinter { public: GuiPrinter(); ~GuiPrinter(); bool setup(QWidget* parent); QPaintDevice* get_device(); private: QPrinter* qp; }; ///////////////////////////////////////////////// /** * Abstraction of a text viewer */ class GuiTextView { public: GuiTextView(QWidget* parent, int minwidth, int minheight); ~GuiTextView(); void set_text(const char* txt); void append_text(const char* txt); QWidget* get_widget(); private: void scroll_end(); QTextEdit* qte; }; #endif odin-1.8.5/odinseq/0000755000175000017500000000000011735135551011127 500000000000000odin-1.8.5/odinseq/seqacqread.h0000644000175000017500000001011011455553540013323 00000000000000/*************************************************************************** seqacqread.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQACQREAD_H #define SEQACQREAD_H #include #include #include #include #include /** * @addtogroup odinseq * @{ */ /** * \brief Acquisition + readout gradient * * This class represents an acquisition window with a read gradient. */ class SeqAcqRead : public virtual SeqAcqInterface, public SeqParallel { // virtual functions of SeqFreqChanInterface are marhshalled to acq public: /** * Constructs an acquisition window with a simultaneous read gradient labeled 'object_label' and the * following properties: * - sweepwidth: The sampling frequency * - read_size: The desired matrix size in read direction * - fov: The Field of View * - gradchannel: The channel where the read gradient will be placed * - os_factor: See class 'SeqAcq' for explanation * - partial_fourier: The amount of partial Fourier undersampling (0=no undersampling, 1=half fourier) * - partial_fourier_at_end: If set to 'true', partial Fourier will omit data at the end of the readout * - nucleus: See class 'SeqAcq' for explanation * - phaselist: See class 'SeqAcq' for explanation * - freqlist: See class 'SeqAcq' for explanation * - timestep: The time resolution for the digitised ramps, the default is to * take minimum time step the scanner is capable of. * - rampmode: This parameter determines the shape of the ramp waveform */ SeqAcqRead(const STD_string& object_label,double sweepwidth,unsigned int read_size, float fov, direction gradchannel, float os_factor=1.0, float partial_fourier=0.0, bool partial_fourier_at_end=false, const STD_string& nucleus="", const dvector& phaselist=0, const dvector& freqlist=0, float timestep = 0.0, rampType rampmode = linear); /** * Constructs an acquisition window with read gradient which is a copy of 'sar' */ SeqAcqRead(const SeqAcqRead& sar); /** * Constructs an empty acquisition window with read gradient with the given label. */ SeqAcqRead(const STD_string& object_label="unnamedSeqAcqRead"); /** * This assignment operator will make this object become an exact copy of 'sar'. */ SeqAcqRead& operator = (const SeqAcqRead& sar); /** * Returns reference to read gradient. */ const SeqGradTrapez& get_readgrad() const {return read;} // marshalling virtual functions of SeqAcqInterface to acq, except: double get_acquisition_center() const; double get_acquisition_start() const; SeqAcqInterface& set_sweepwidth(double sw, float os_factor); // produce warning private: friend class SeqGradEcho; // overloaded for SeqAcqDeph const SeqVector* get_dephgrad(SeqGradChanParallel& dephobj, bool rephase) const; void build_seq(); void common_init(); float corrected_partfour; // helper during construction SeqAcq acq; SeqGradTrapez read; SeqDelay middelay; SeqGradDelay midgrad; SeqDelay tozero; SeqGradTrapez readdephgrad; SeqGradTrapez readrephgrad; }; /** @} */ #endif odin-1.8.5/odinseq/seqplot.h0000644000175000017500000001657311363773555012734 00000000000000/*************************************************************************** seqplot.h - description ------------------- begin : Sat Sep 25 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPLOT_H #define SEQPLOT_H #include // for units class RotMatrix; // forward declaration /** * @addtogroup odinseq_internals * @{ */ enum plotChannel {B1re_plotchan=0, B1im_plotchan, rec_plotchan, signal_plotchan, freq_plotchan, phase_plotchan, Gread_plotchan, Gphase_plotchan, Gslice_plotchan, numof_plotchan}; enum markType {no_marker=0, exttrigger_marker, halttrigger_marker, snapshot_marker, reset_marker, acquisition_marker, endacq_marker, excitation_marker, refocusing_marker, storeMagn_marker, recallMagn_marker, inversion_marker, saturation_marker, numof_markers }; static const char* markLabel[]={"none", "exttrigger", "halttrigger", "snapshot", "reset", "acquisition", "endacq", "excitation", "refocusing", "storeMagn", "recallMagn", "inversion", "saturation" }; enum timecourseMode {tcmode_curves=0, tcmode_plain, tcmode_slew_rate, tcmode_kspace, tcmode_M1, tcmode_M2, tcmode_b_trace, tcmode_backgr_kspace, tcmode_backgr_crossterm, tcmode_eddy_currents, numof_tcmodes}; static const char* timecourseLabel[]= {"Curves", "Plain", "Slew Rate", "k-Space", "1st Grad. Moment", "2nd Grad. Moment", "b-Value Trace", "Backgr. k-Space", "Backgr. Crossterm", "Eddy Currents"}; static const char* timecoursePrefix[]={"G", "G", "dG", "k", "M1", "M2", "b", "k", "c", "G"}; static const char* timecourseUnit[]= {ODIN_GRAD_UNIT, ODIN_GRAD_UNIT, ODIN_GRAD_UNIT"/"ODIN_TIME_UNIT, "rad/"ODIN_SPAT_UNIT, "rad*"ODIN_TIME_UNIT"/"ODIN_SPAT_UNIT, "rad*"ODIN_TIME_UNIT"^2/"ODIN_SPAT_UNIT, ODIN_TIME_UNIT"/"ODIN_SPAT_UNIT"^2", "rad/"ODIN_SPAT_UNIT, ODIN_TIME_UNIT"/"ODIN_SPAT_UNIT"^2", ODIN_GRAD_UNIT}; //////////////////////////////////////////////////////////////////// /** * Special data structure suitable to display a single curve in QwtPlot */ struct Curve4Qwt { Curve4Qwt() : size(0), x(0), y(0), spikes(false), has_freq_phase(false), gradmatrix(0) {} bool operator == (const Curve4Qwt&) const {return false;} // dummy operator bool operator < (const Curve4Qwt&) const {return false;} // dummy operator double get_bounds(bool endpoint) const {if(!size) return 0.0; if(endpoint) return x[size-1]; else return x[0];} const char* label; plotChannel channel; int size; double* x; double* y; bool spikes; // values will not be interpolated between points, draw sticks instead bool has_freq_phase; double freq; double phase; const RotMatrix* gradmatrix; }; //////////////////////////////////////////////////////////////////// /** * Special data structure suitable to display a simple marker in QwtPlot */ struct Marker4Qwt { bool operator == (const Marker4Qwt&) const {return false;} // dummy operator bool operator < (const Marker4Qwt&) const {return false;} // dummy operator double get_bounds(bool) const {return x;} const char* label; double x; markType type; }; //////////////////////////////////////////////////////////////////// /** * Special data structure suitable to display a marker with stored values in QwtPlot */ struct TimecourseMarker4Qwt { bool operator == (const TimecourseMarker4Qwt&) const {return false;} // dummy operator bool operator < (const TimecourseMarker4Qwt&) const {return false;} // dummy operator double get_bounds(bool) const {return x;} double x; double y[numof_plotchan]; markType type; }; //////////////////////////////////////////////////////////////////// /** * Special data structure suitable to hold digitized timecourses */ struct SeqTimecourseData { SeqTimecourseData() : size(0), x(0), n_rec_points(0) {for(int i=0; i::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime, double max_highres_interval ) const = 0; virtual void get_signal_curves(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const = 0; virtual void get_markers(STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const = 0; virtual bool timecourse_created(timecourseMode type) const = 0; virtual bool create_timecourses(timecourseMode type, const STD_string& nucleus, ProgressMeter* progmeter) const = 0; virtual const SeqTimecourseData* get_timecourse(timecourseMode type) const = 0; virtual const SeqTimecourseData* get_subtimecourse(timecourseMode type, double starttime, double endtime) const = 0; virtual void get_timecourse_markers(timecourseMode type, STD_list::const_iterator& result_begin, STD_list::const_iterator& result_end, double starttime, double endtime ) const = 0; virtual double get_total_duration() const = 0; virtual unsigned int n_frames() const = 0; virtual JcampDxBlock& get_opts(bool timecourse_opts, bool simulation_opts) const = 0; virtual void set_coilsdir(const STD_string& coilsdir) const = 0; virtual void add_signal_curve(const Curve4Qwt& signal_curve) const = 0; virtual bool monitor_simulation() const = 0; virtual bool simulate(const STD_string& fidfile, const STD_string& samplefile, ProgressMeter* progmeter, SeqSimFeedbackAbstract* feedback) const = 0; virtual bool has_curves_on_channel(plotChannel chan) const = 0; }; /** @} */ #endif odin-1.8.5/odinseq/seqpuls.h0000644000175000017500000003166611322062345012720 00000000000000/*************************************************************************** seqpuls.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPULS_H #define SEQPULS_H #include #include #include #include #define _MAX_PULSE_ATTENUATION_ 120.0 /** * @ingroup odinseq * Enum to specify the type of a pulse.It is essential for the calculation of k-space trajectories * and other stuff to specify this correctly for each object derived from 'SeqPulsInterface' * - excitation: An excitation pulse. * - refocusing: A refocusing pulse. * - storeMagn: Stores the magnetization in longitudinal direction (stimulated echo) * - recallMagn: Recalls the magnetization from the longitudinal direction (stimulated echo) * - inversion: An inversion pulse * - saturation: A saturation pulse */ enum pulseType {excitation=0, refocusing, storeMagn, recallMagn, inversion, saturation, numof_pulseTypes}; static const char* pulseTypeLabel[]={"excitation", "refocusing","storeMagn","recallMagn","inversion","saturation"}; /////////////////////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * This is the abstract base class for all objects that have the * property of a generating an RF field */ class SeqPulsInterface : public virtual SeqTreeObj, public virtual SeqFreqChanInterface { public: /** * Sets the duration of the pulse. In case of a more complex pulse * that needs some extra commands before and after the actual pulse * will be played out, this function still sets the effective * duration, i.e. when the RF-field is non-zero */ virtual SeqPulsInterface& set_pulsduration(float pulsduration) {if(marshall) marshall->set_pulsduration(pulsduration); else marshall_error(); return *this;} /** * Returns the duration of the pulse. In case of a more complex pulse * that needs some extra commands before and after the actual pulse * will be played out, this function still returns the effective * duration, i.e. when the RF-field is applied */ virtual double get_pulsduration() const {if(marshall) return marshall->get_pulsduration(); else marshall_error(); return 0.0;} /** * Returns the flip angle of the pulse */ virtual float get_flipangle() const {if(marshall) return marshall->get_flipangle(); else marshall_error(); return 0.0;} /** * Sets the flip angle of the pulse */ virtual SeqPulsInterface& set_flipangle(float flipangle) {if(marshall) marshall->set_flipangle(flipangle); else marshall_error(); return *this;} /** * Sets a list of flip angles which can be iterated through by a loop * and the get_flipangle_vector() function */ SeqPulsInterface& set_flipangles(const fvector& flipangles); /** * Returns the list of actual flip angles which will be iterated * through by a loop in combination with the get_flipangle_vector() function */ fvector get_flipangles() const {return get_flipangle()*get_flipscales();} /** * Sets the power deposition (or pulse attenuation on Bruker) of the pulse */ virtual SeqPulsInterface& set_power(float pulspower) {if(marshall) marshall->set_power(pulspower); else marshall_error(); return *this;} /** * Returns the power deposition (or pulse attenuation on Bruker) of the pulse */ virtual float get_power() const {if(marshall) return marshall->get_power(); else marshall_error(); return 0.0;} /** * Sets the relative center of the pulse */ virtual SeqPulsInterface& set_rel_magnetic_center(float center) {if(marshall) marshall->set_rel_magnetic_center(center); else marshall_error(); return *this;} /** * Returns the relative center of the pulse */ virtual float get_rel_magnetic_center() const {if(marshall) return marshall->get_rel_magnetic_center(); else marshall_error(); return 0.0;} /** * Returns the absolute center of the pulse */ virtual float get_magnetic_center() const {if(marshall) return marshall->get_magnetic_center(); else marshall_error(); return 0.0;} /** * Sets the type of the pulse */ virtual SeqPulsInterface& set_pulse_type(pulseType type) {if(marshall) marshall->set_pulse_type(type); else marshall_error(); return *this;} /** * Returns the type of the pulse */ virtual pulseType get_pulse_type() const {if(marshall) return marshall->get_pulse_type(); else marshall_error(); return pulseType(0);} /** * Sets the reordering scheme of the flipangle vector */ virtual SeqPulsInterface& set_flipangle_reorder_scheme(reorderScheme scheme,unsigned int nsegments) {if(marshall) marshall->set_flipangle_reorder_scheme(scheme,nsegments); else marshall_error(); return *this;} /** * Returns a sequence vector to iterate over flipangles */ virtual const SeqVector& get_flipangle_vector() const {if(marshall) return marshall->get_flipangle_vector(); else marshall_error(); return get_dummyvec();} /** * Returns the reorder vector for flipangles */ virtual const SeqVector& get_flipangle_reorder_vector() const {if(marshall) return marshall->get_flipangle_vector(); else marshall_error(); return get_dummyvec();} protected: SeqPulsInterface() : marshall(0) {} virtual ~SeqPulsInterface() {} virtual void set_flipscales(const fvector& flipscales) {if(marshall) marshall->set_flipscales(flipscales); else marshall_error();} virtual fvector get_flipscales() const {if(marshall) return marshall->get_flipscales(); else marshall_error(); return fvector();} void set_marshall(SeqPulsInterface* mymarshall) {marshall=mymarshall;} // to be used in constructor code private: SeqPulsInterface* marshall; // for marshalling member functions to a sub-object }; /////////////////////////////////////////////////////////////////////////////////////// class SeqPuls; // forward declaration /** * @ingroup odinseq_internals * A vector class to iterate through a list of flip angles, only to be used by SeqPuls */ class SeqFlipAngVector : public SeqVector { public: SeqFlipAngVector(const STD_string& object_label, SeqPuls* flipangvec_user ) : SeqVector(object_label), user(flipangvec_user) {} // overloading virtual functions from SeqVector unsigned int get_vectorsize() const {return flipanglescale.size();} bool needs_unrolling_check() const {return true;} bool prep_iteration() const; svector get_vector_commands(const STD_string& iterator) const; fvector flipanglescale; private: // disable copying SeqFlipAngVector(const SeqFlipAngVector&) {} SeqFlipAngVector& operator = (const SeqFlipAngVector&) {return *this;} SeqPuls* user; }; /////////////////////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The base class for platform specific drivers of RF pulses */ class SeqPulsDriver : public SeqDriverBase { public: SeqPulsDriver() {} virtual ~SeqPulsDriver() {} virtual bool prep_driver(const cvector& wave, double pulsduration, double pulscenter, float b1max, float power, float flipangle, const fvector& flipscales, pulseType plstype) = 0; virtual void event(eventContext& context, double start) const = 0; virtual double get_rf_energy() const = 0; virtual bool prep_flipangle_iteration(unsigned int count) = 0; virtual double get_predelay() const = 0; virtual double get_postdelay() const = 0; virtual STD_string get_program(programContext& context, unsigned int phaselistindex, int channel, const STD_string& iteratorcommand) const = 0; virtual STD_string get_instr_label() const = 0; virtual svector get_flipvector_commands(const STD_string& iterator) const =0; // virtual svector get_phase_commands(const STD_string& iterator) const =0; virtual void new_freq(double newfreq) const = 0; virtual bool has_new_freq() const = 0; virtual SeqPulsDriver* clone_driver() const = 0; }; /////////////////////////////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * * \brief RF pulse * * This class represents a shaped RF-pulse with a complex waveform */ class SeqPuls : public virtual SeqPulsInterface, public SeqObjBase, public SeqFreqChan, public SeqDur { public: /** * Constructs a pulse labeled 'object_label' with the following properties: * - wave: The complex waveform that will be played out * - pulsduration: The duration of the pulse * - pulspower: The power of the pulse in dB * - nucleus: This parameter determines the frequency at which the pulse will * be played out to be the resonance frequency of the specified nucleus * - phaselist: This is an array of phases at which the acquired pulse will be * modulated. Use the get_phaselist_vector() function to attach it to a loop. * - freqlist: This is an array of frequency offsets at which the pulse waveform * will be modulated. * - rel_magnetic_center: This parameter specifies the point in time that will be used * as the center of the pulse for timing calculations, e.g. for a spin-echo */ SeqPuls(const STD_string& object_label,const cvector& waveform,float pulsduration, float pulspower, const STD_string& nucleus="",const dvector& phaselist=0, const dvector& freqlist=0,float rel_magnetic_center=0.5); /** * Constructs an empty pulse with the given label. */ SeqPuls(const STD_string& object_label = "unnamedSeqPuls"); /** * Constructs a pulse which is a copy of 'sp' */ SeqPuls(const SeqPuls& sp); /** * This assignment operator will make this pulse become an exact copy of 'sp'. */ SeqPuls& operator = (const SeqPuls& sp); /** * Sets the complex waveform of the pulse */ SeqPuls& set_wave(const cvector& waveform); /** * Returns the complex RF waveform */ cvector get_wave() const {return wave;} /** * Returns the time offset within this object where the RF starts */ double get_pulsstart() const {return pulsdriver->get_predelay();} // overloading virtual functions from SeqPulsInterface SeqPulsInterface& set_pulsduration(float pulsduration); double get_pulsduration() const; float get_flipangle() const {return system_flipangle;} SeqPulsInterface& set_flipangle(float flipangle) {return set_system_flipangle(flipangle);} float get_power() const {return power;} SeqPulsInterface& set_power(float pulspower) {power=pulspower; return *this;} SeqPulsInterface& set_rel_magnetic_center(float center) {relmagcent=center; return *this;} float get_rel_magnetic_center() const {return relmagcent;} float get_magnetic_center() const; SeqPulsInterface& set_pulse_type(pulseType type); pulseType get_pulse_type() const; const SeqVector& get_flipangle_vector() const {return flipvec;} void set_flipscales(const fvector& flipscales) {flipvec.flipanglescale=flipscales;} fvector get_flipscales() const {return flipvec.flipanglescale;} SeqPulsInterface& set_flipangle_reorder_scheme(reorderScheme scheme,unsigned int nsegments) {flipvec.set_reorder_scheme(scheme,nsegments); return *this;} const SeqVector& get_flipangle_reorder_vector() const {return flipvec.get_reorder_vector();} // overloading virtual function from SeqTreeObj double get_duration() const; STD_string get_program(programContext& context) const; double get_rf_energy() const; STD_string get_properties() const; unsigned int event(eventContext& context) const; SeqValList get_freqvallist(freqlistAction action) const; // some helper functions to use SeqPulse together with OdinPulse/Pulsar SeqPuls& set_system_flipangle(float angle); SeqPuls& set_B1max(float b1max); float get_B1max() const {return B1max_mT;} private: friend class SeqFlipAngVector; // overloading virtual functions from SeqFreqChan double get_freqchan_duration() const {return get_pulsduration();} STD_string get_driver_instr_label() const {return pulsdriver->get_instr_label();} // overwriting virtual functions from SeqClass bool prep(); mutable SeqDriverInterface pulsdriver; cvector wave; float power; float system_flipangle; float B1max_mT; float relmagcent; pulseType plstype; SeqFlipAngVector flipvec; }; /** @} */ #endif odin-1.8.5/odinseq/seqobjvec.h0000644000175000017500000000732511322062345013200 00000000000000/*************************************************************************** seqobjvec.h - description ------------------- begin : Mon Aug 9 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQOBJVEC_H #define SEQOBJVEC_H #include #include class SeqGradObjInterface; // forward declaration /** * @ingroup odinseq * * \brief Vector to loop over sequence objects * * This vector class is used to iterate over a list of other sequence objects. * To make use of it, append other sequence objects to this via the += operator and use it together with a loop: * \verbatim SeqObjVector objvec; SeqPuls alpha; // excitation pulse SeqDelay delay; // delay objvec+=alpha; // put alpha into the vector objvec+=delay; // put delay into the vector SeqObjLoop loop; loop ( objvec ) [objvec]; // plays out alpha first and then delay \endverbatim * */ class SeqObjVector : public SeqVector, public SeqObjBase, public List { public: /** * Construct an empty vector of sequence objects with the given label */ SeqObjVector(const STD_string& object_label="unnamedSeqObjVector"); /** * Constructs a copy of 'sov' */ SeqObjVector(const SeqObjVector& sov); /** * Assignment operator that makes this sequence container become a copy of 'sov' */ SeqObjVector& operator = (const SeqObjVector& sov); /** * Appends soa to the list of elements in this vector of sequence objects */ SeqObjVector& operator += (const SeqObjBase& soa); /** * Appends sgoa to the list of elements in this vector of sequence objects */ SeqObjVector& operator += (SeqGradObjInterface& sgoa); /** * Appends sgcl to the list of elements in this vector of sequence objects */ SeqObjVector& operator += (SeqGradChanList& sgcl); // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; double get_duration() const; unsigned int event(eventContext& context) const; void query(queryContext& context) const; RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const; SeqValList get_freqvallist(freqlistAction action) const; SeqValList get_delayvallist() const; double get_rf_energy() const; // implemented virtual functions from SeqClass void clear_container(); // implemented virtual functions from SeqVector unsigned int get_vectorsize() const {return List::size();} bool needs_unrolling_check() const {return true;} bool is_obj_vector() const {return true;} bool is_acq_vector() const {return true;} // this vector may contain vectors which are relevant for acquisition bool is_qualvector() const {return true;} // timing may change private: constiter get_current() const; }; #endif odin-1.8.5/odinseq/seqgradvec.cpp0000644000175000017500000000714011322062345013671 00000000000000#include "seqgradvec.h" #include "seqgradconst.h" #include "seqloop.h" SeqGradVector::SeqGradVector(const STD_string& object_label,direction gradchannel, float maxgradstrength,const fvector& trimarray, double gradduration) : SeqGradChan(object_label,gradchannel,maxgradstrength,gradduration), SeqVector(object_label) { parent=0; set_trims(trimarray); } SeqGradVector::SeqGradVector(const SeqGradVector& sgv) { parent=0; SeqGradVector::operator = (sgv); } SeqGradVector::SeqGradVector(const STD_string& object_label) : SeqGradChan(object_label), SeqVector(object_label) { parent=0; } SeqGradVector& SeqGradVector::set_trims(const fvector& trims) { trimvals=trims; return *this; } unsigned int SeqGradVector::get_vectorsize() const {return trimvals.size();} svector SeqGradVector::get_vector_commands(const STD_string& iterator) const { return graddriver->get_vector_commands(iterator); } SeqGradVector& SeqGradVector::operator = (const SeqGradVector& sgv) { Log odinlog(this,"SeqGradVector::operator = "); SeqGradChan::operator = (sgv); SeqVector::operator = (sgv); trimvals=sgv.trimvals; return *this; } STD_string SeqGradVector::get_grdpart(float matrixfactor) const { Log odinlog(this,"get_grdpart"); ODINLOG(odinlog,normalDebug) << "matrixfactor=" << matrixfactor << STD_endl; if(parent) { ODINLOG(odinlog,normalDebug) << "has parent " << parent->get_label() << STD_endl; return parent->get_grdpart(matrixfactor); } if(SeqVector::is_handled()) { return graddriver->get_vector_program(get_strength(),matrixfactor,get_current_reord_index()); } return graddriver->get_const_program(get_current_strength(),matrixfactor); // Generate const-gradient entry if vector not handled (for Bruker) } float SeqGradVector::get_current_strength() const { unsigned int count=get_current_index(); if(parent) count=parent->get_current_index(); float trim=1.0; if(count odinlog(this,"prep"); if(!SeqGradChan::prep()) return false; bool result=graddriver->prep_vector(get_strength(),get_grdfactors_norot(),get_gradduration(),trimvals,get_index_matrix(),get_nesting_relation()); return result; } svector SeqGradVector::get_reord_vector_commands(const STD_string& iterator) const { Log odinlog(this,"get_reord_vector_commands"); svector result=SeqVector::get_reord_vector_commands(iterator); unsigned int result_size=result.size(); svector reordvec=graddriver->get_reord_commands(); ODINLOG(odinlog,normalDebug) << "reordvec=" << reordvec.printbody() << STD_endl; if(reordvec.size()) { if(!result_size) return reordvec; svector newresult; newresult.resize(result_size+reordvec.size()); unsigned int i; for(i=0; iset_label(STD_string(get_label())+"_("+ftos(starttime)+"-"+ftos(endtime)+")"); sgv->set_duration(endtime-starttime); sgv->set_temporary(); sgv->parent=this; return *sgv; } bool SeqGradVector::prep_iteration() const { Log odinlog(this,"prep_iteration"); int count=get_current_index(); if(parent) count=parent->get_current_index(); ODINLOG(odinlog,normalDebug) << "count/vectorsize=" << count << "/" << get_vectorsize() << STD_endl; return graddriver->prep_vector_iteration(count); } odin-1.8.5/odinseq/seqacqspiral.cpp0000644000175000017500000001345711322062345014245 00000000000000#include "seqacqspiral.h" void SeqAcqSpiral::common_init() { SeqAcqInterface::set_marshall(&acq); SeqFreqChanInterface::set_marshall(&acq); } SeqAcqSpiral::SeqAcqSpiral(const STD_string& object_label,double sweepwidth, float fov, unsigned int sizeRadial, unsigned int numofSegments, JDXtrajectory& traj, bool inout, bool optimize, const STD_string& nucleus, const dvector& phaselist) : SeqObjList(object_label), par(object_label+"_par"), spirgrad_in(object_label+"_spirgrad_in",traj,secureInv(sweepwidth),secureDivision(fov,sizeRadial),sizeRadial/(1+int(inout)),numofSegments/(1+int(inout)),true,optimize,nucleus), spirgrad_out(object_label+"_spirgrad_out",traj,secureInv(sweepwidth),secureDivision(fov,sizeRadial),sizeRadial/(1+int(inout)),numofSegments/(1+int(inout)),false,optimize,nucleus), preacq(object_label+"_preacq"), acq(object_label+"_acq", int(inout)*spirgrad_in.spiral_size()+spirgrad_out.spiral_size(), sweepwidth, 1.0, nucleus, phaselist), inout_traj(inout) { Log odinlog(this,"SeqAcqSpiral(...)"); common_init(); // set the rotation matrices for the spiral interleaves rotvec.set_label(STD_string(get_label())+"_rotvec"); unsigned int nrot=numofSegments; if(inout) nrot/=2; if(!nrot) nrot=1; rotvec.create_inplane_rotation(nrot); acq.set_rel_center(0.0); if(inout) acq.set_rel_center(0.5); gbalance=SeqGradTrapezParallel(object_label+"_gbalance", -spirgrad_in.get_gradintegral()[readDirection], -spirgrad_in.get_gradintegral()[phaseDirection], 0.0, 0.5*systemInfo->get_max_grad()); build_seq(); } SeqAcqSpiral::SeqAcqSpiral(const SeqAcqSpiral& sas) { common_init(); SeqAcqSpiral::operator = (sas); } SeqAcqSpiral::SeqAcqSpiral(const STD_string& object_label) : SeqObjList(object_label) { common_init(); } SeqAcqSpiral& SeqAcqSpiral::operator = (const SeqAcqSpiral& sas) { SeqObjList::operator = (sas); par=sas.par; spirgrad_in=sas.spirgrad_in; spirgrad_out=sas.spirgrad_out; preacq=sas.preacq; acq=sas.acq; gbalance=sas.gbalance; rotvec=sas.rotvec; inout_traj=sas.inout_traj; build_seq(); return *this; } fvector SeqAcqSpiral::get_ktraj(unsigned int iseg, direction channel) const { Log odinlog(this,"get_ktraj"); const RotMatrix& rotmatrix=rotvec[iseg]; ODINLOG(odinlog,normalDebug) << "rotmatrix=" << rotmatrix.print() << STD_endl; fvector kx_in(spirgrad_in.get_ktraj(readDirection)); fvector ky_in(spirgrad_in.get_ktraj(phaseDirection)); fvector kx_out(spirgrad_out.get_ktraj(readDirection)); fvector ky_out(spirgrad_out.get_ktraj(phaseDirection)); unsigned int size=kx_out.length(); if(inout_traj) size+=kx_in.length(); fvector result(size); dvector kvec(3); dvector kvec_rot(3); kvec=0; unsigned int offset=0; if(inout_traj) offset=kx_in.length(); for(unsigned int i=0; i odinlog(this,"get_denscomp"); fvector denscomp_in(spirgrad_in.get_denscomp()); fvector denscomp_out(spirgrad_out.get_denscomp()); unsigned int size=denscomp_out.length(); if(inout_traj) size+=denscomp_in.length(); fvector result(size); unsigned int offset=0; if(inout_traj) offset=denscomp_in.length(); for(unsigned int i=0; i odinlog(this,"set_sweepwidth"); ODINLOG(odinlog,warningLog) << "Ignoring request to change sweepwidth after construction" << STD_endl; return *this; } bool SeqAcqSpiral::prep() { Log odinlog(this,"prep"); if(!SeqObjList::prep()) return false; unsigned int acqsize= get_ktraj(0,readDirection).length(); unsigned int segsize=rotvec.get_vectorsize(); unsigned int gradsize=3; ODINLOG(odinlog,normalDebug) << "acqsize/segsize=" << acqsize << "/" << segsize << STD_endl; farray ktrajs(segsize,acqsize,gradsize); for(unsigned int iseg=0; iseg odinlog(this,"build_seq"); par.clear(); SeqObjList::clear(); double acqcent=par.get_pulprogduration()+acq.get_acquisition_start(); double shift=systemInfo->get_grad_shift_delay()-acqcent; if(inout_traj) shift += gbalance.get_gradduration()+spirgrad_in.get_ramp_duration(); ODINLOG(odinlog,normalDebug) << "acqcent/shift=" << acqcent << "/" << shift << STD_endl; if(shift>=systemInfo->get_min_duration(delayObj)) { ODINLOG(odinlog,normalDebug) << "acq is played out later, because gradient switching is delayed" << STD_endl; preacq.set_duration(shift); if(inout_traj) par /= (gbalance + spirgrad_in + spirgrad_out); else par /= spirgrad_out; par /= (preacq + acq); } else { ODINLOG(odinlog,normalDebug) << "gradients are played out later, because acq is delayed" << STD_endl; if(inout_traj) { par /= (gbalance + spirgrad_in + spirgrad_out); spirgrad_in.set_predelay_duration(-shift); } else { par /= spirgrad_out; spirgrad_out.set_predelay_duration(-shift); } par /= acq; } (*this)+=par; SeqObjList::set_gradrotmatrixvector(rotvec); } odin-1.8.5/odinseq/seqtree.h0000644000175000017500000002123611455553540012675 00000000000000/*************************************************************************** seqtree.h - description ------------------- begin : Fri Oct 17 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQTREE_H #define SEQTREE_H #include #include #include /** * @addtogroup odinseq_internals * @{ */ /////////////////////////////////////////////////////////////////////////// /** * Callback to display tree-like structures */ class SeqTreeCallbackAbstract { public: virtual void display_node(const SeqClass* thisnode, const SeqClass* parentnode, int treelevel, const svector& columntext) = 0; }; /////////////////////////////////////////////////////////////////////////// class ProgressMeter; // forward declaration /** * This enum is used to specify the behaviour for an event: * - seqRun: trigger the hardware events * - printEvent: Print all events to the console * - countEvents: Returns the number of events without actually executing them */ enum eventAction {seqRun=0, printEvent, countEvents}; /** * Structure that holds the context in which the event of a sequence object is requested */ struct eventContext { eventContext() : action(seqRun), noflush(false), seqcheck(false), elapsed(0.0), event_display(0), event_progmeter(0) {} // the action to be performed eventAction action; // do not flush eventblock bool noflush; // just a test run (e.g. fSEQCheck on Idea) bool seqcheck; // counter for time elapsed since start of the sequence double elapsed; // callback pointers to display events in GUI/console SeqTreeCallbackAbstract* event_display; // pointer for progess meter ProgressMeter* event_progmeter; }; /////////////////////////////////////////////////////////////////////////// /** * This enum is used to specify the behaviour for a call to get_freqvallist: * - calcDeps: Calculates dependencies between consecutive pulse frequency events * - calcList: Creates the gloabal pulse frequency list * - calcAcqList: Creates the gloabal acquisition frequency list * - calcDecList: Creates the gloabal decoupling frequency list */ enum freqlistAction {calcDeps=0,calcList,calcAcqList,calcDecList}; /////////////////////////////////////////////////////////////////////////// /** * This enum is used to specify the behaviour for program printing: * - brukerPpg: create Bruker pulse program * - brukerGpg: create Bruker gradient program * - brukerParx: create Bruker parx interface file (to set ACQP parameters) * - epicCode: Sequence source code for the EPIC framework * - epicPg: Code for the pulsegen section (EPIC) */ enum programMode {brukerPpg=0, brukerGpg, brukerParx, epicCode, epicPg, epicScan, epicPreScan, epicPreScanDummy, numOfProgModes}; /** * Structure that holds the context the sequence program is (recursively) generated with, i.e. type of program or formatting */ struct programContext { programContext() : mode(programMode(0)), formatted(true), nestlevel(0), neststatus(false) {} // the type of program to generate programMode mode; // whether code is nicely formatted (indention, comments), the main // use of this flag is to decide whether to blocks of code are the // same (despite formatting) and whether they can be wrapped in a loop bool formatted; // counter for indention if generating pulse programs int nestlevel; // whether indention is currently enabled bool neststatus; }; /////////////////////////////////////////////////////////////////////////// class SeqTreeObj; //forward declaration /** * This enum is used to specify the behaviour for a call to query: * - count_acqs: Count the number of acquisition objects * - checkoccur: Check the occurence of a particular sequence object in this branch of the tree * - check_acq_iter: Check for an iterator in subtree which is relevant for reco indicies * - tag_toplevel_reploop: Identify and tag outermost repetition loop * - display_tree: Display sequence tree */ enum queryAction {count_acqs, checkoccur, check_acq_iter, tag_toplevel_reploop, display_tree}; /** * Structure that holds the context the sequence tree is (recursively) queried with */ struct queryContext { queryContext() : action(count_acqs), numof_acqs(0), checkoccur_sto(0), checkoccur_result(false), check_acq_iter_result(false), tree_display(0), parentnode(0), treelevel(0), repetitions_prot(0) {} // the action requested queryAction action; // stuff for action 'count_acqs' unsigned int numof_acqs; // stuff for action 'checkoccur' const SeqTreeObj* checkoccur_sto; bool checkoccur_result; bool check_acq_iter_result; // stuff for action 'display_tree' SeqTreeCallbackAbstract* tree_display; const SeqTreeObj* parentnode; int treelevel; // stuff for action 'tag_toplevel_reploop' int repetitions_prot; // the number of reps in the protocol }; /////////////////////////////////////////////////////////////////////////// /** * Instantiation of value list (SeqValList) with double. * It is used in sequence trees to retrieve frequency lists, delay lists, etc. */ struct SeqValList : public ValList { SeqValList(const STD_string& object_label="unnamedSeqValList", unsigned int repetitions=1) : ValList(object_label,repetitions) {} }; /////////////////////////////////////////////////////////////////////////// /** * This is the base class for all objects that can be part of the sequence tree */ class SeqTreeObj : public virtual SeqClass { public: /** * Returns the duration of the sequence object. */ virtual double get_duration() const = 0; /** * Returns the part in the pulse/gradient program of this sequence object. * 'context' holds data about how the program should be generated, e.g. type * of program and formatting. */ virtual STD_string get_program(programContext& context) const {return "";} /** * Returns a string describing the object */ virtual STD_string get_properties() const {return "";} /** * Queries the sequence tree for events, returns the number of events executed */ virtual unsigned int event(eventContext& context) const { // make inline to speed up event execution if(context.action==printEvent) display_event(context); context.elapsed+=get_duration(); return 0; // no real hardware events played out } /** * Appends the k-space coordinates in this branch of the sequence tree to 'coords' * and returns their ordering */ virtual RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const {return RecoValList();} /** * Returns true if 'sto' can be found in the objects branch of the sequence tree */ bool contains(const SeqTreeObj* sto) const; /** * Generates a graphical representation of the sequence tree using 'display' */ void tree(SeqTreeCallbackAbstract* display) const; /** * Returns the list of frequency values in the objects branch of the sequence tree */ virtual SeqValList get_freqvallist(freqlistAction action) const {return SeqValList();} /** * Returns the list of delay values in the objects branch of the sequence tree */ virtual SeqValList get_delayvallist() const {return SeqValList();} /** * Returns the RF power deposition in the objects branch of the sequence tree. * The physical unit is unspecified, it depends on the current platform. */ virtual double get_rf_energy() const {return 0.0;} protected: friend class SeqObjList; friend class SeqObjVector; friend class SeqParallel; SeqTreeObj(); virtual ~SeqTreeObj() {} SeqTreeObj& operator = (const SeqTreeObj& sto) { SeqClass::operator =(sto); return *this; } /** * Query the sequence tree recursively */ virtual void query(queryContext& context) const; static int looplevel; private: void display_event(eventContext& context) const; }; /** @} */ #endif odin-1.8.5/odinseq/odinpulse_trajectories.cpp0000644000175000017500000002340011322062345016322 00000000000000#include "odinpulse.h" #include ///////////////////////////////////////////////////////////////////////// // 1D trajectories: class Const : public JDXfunctionPlugIn { JDXdouble lower; JDXdouble upper; public: Const() : JDXfunctionPlugIn("Const") { lower=0.0; lower.set_minmaxval(0.0,1.0); upper=1.0; upper.set_minmaxval(0.0,1.0); append_member(lower,"lowerBoundary"); append_member(upper,"upperBoundary"); set_description("A trajectory with a linear stepping in k-space (for slice-selective pulses) or in the time domain (for frequency-selective pulses)." "With the parameters lowerBoundary and upperBoundary, a subarea of the pulse can be specified."); } const kspace_coord& calculate_traj(float s) const { double l=lower; double u=upper; if( l <0.0 ) l=0.0; if( l >1.0 ) l=1.0; if( u <0.0 ) u=0.0; if( u >1.0 ) u=1.0; double offset=l; double slew=u-l; coord_retval.traj_s=offset+slew*s; coord_retval.kz = 2.0 * coord_retval.traj_s - 1.0; coord_retval.Gz = 2.0 * slew; coord_retval.denscomp = 1.0; return coord_retval; } const traj_info& get_traj_properties() const { double l=lower; double u=upper; if( l <0.0 ) l=0.0; if( l >1.0 ) l=1.0; if( u <0.0 ) u=0.0; if( u >1.0 ) u=1.0; traj_info_retval.rel_center=secureDivision((0.5-l),(u-l)); if(traj_info_retval.rel_center<0.0) traj_info_retval.rel_center=0.0; if(traj_info_retval.rel_center>1.0) traj_info_retval.rel_center=1.0; return traj_info_retval; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Const;} }; ///////////////////////////////////////////////////////////////////////// class Sinus : public JDXfunctionPlugIn { JDXint cycles; JDXfilter spectfilter; public: Sinus() : JDXfunctionPlugIn("Sinus"), spectfilter("spectfilter") { cycles=8; cycles.set_minmaxval(1,20); append_member(cycles,"NumPulses"); spectfilter.set_function(0); append_member(spectfilter,"SpectralFilter"); set_description("This is a trajectory with a sinus-shaped gradient waveform. The NumPulses\n" "parameter specifies the number of times the trajectory passes the k-space origin. This trajectory may be used for spectral-spatial\n" "selective pulses."); } const kspace_coord& calculate_traj(float s) const { coord_retval.traj_s=s; float phi = PII * float(cycles) * (s - 1.0); coord_retval.kz = -cos (phi); coord_retval.Gz = PII * cycles * sin (phi); coord_retval.denscomp = fabs(coord_retval.Gz) * spectfilter.calculate (fabs(s-0.5)*2.0); // Quick hack: Apply filter in spectral dimension via denscomp return coord_retval; } const traj_info& get_traj_properties() const { traj_info_retval.rel_center=1.0-1.0/(float(cycles)*2.0); return traj_info_retval; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Sinus;} }; ///////////////////////////////////////////////////////////////////////// // 2D trajectories: // Base class for all Archimedian spirals, c.f. Block and Frahm, JMRI 21:657-668(2005) class ArchimedianSpiral : public JDXfunctionPlugIn { JDXint cycles; virtual void calc_theta(float& theta, float& dtheta, float s) const = 0; public: ArchimedianSpiral(const STD_string& label) : JDXfunctionPlugIn(label) { cycles=16; cycles.set_minmaxval(1,64); append_member(cycles,"NumCycles"); } const kspace_coord& calculate_traj(float s) const { coord_retval.traj_s=s; float theta, dtheta; calc_theta(theta, dtheta, s); float phi = -2.0 * PII * (float)cycles * theta; float dphi = -2.0 * PII * (float)cycles * dtheta; coord_retval.kx = theta * cos (phi); coord_retval.ky = theta * sin (phi); coord_retval.Gx = dtheta * cos (phi) - theta * sin (phi) * dphi; coord_retval.Gy = dtheta * sin (phi) + theta * cos (phi) * dphi; coord_retval.denscomp = fabs(phi*dphi); //radius / sqrt (phi * phi + 1.0); return coord_retval; } const traj_info& get_traj_properties() const { traj_info_retval.rel_center=1.0; traj_info_retval.max_kspace_step=secureInv(2.0*cycles); return traj_info_retval; } }; /////////////////////////////////////////////////////////////////////////// class ConstSpiral : public ArchimedianSpiral { public: ConstSpiral() : ArchimedianSpiral("ConstSpiral") { set_description("An Archimedian spiral where the radius increases linearly with time."); } // implementing virtual function of ArchimedianSpiral void calc_theta(float& theta, float& dtheta, float s) const { // Spiral is out->in theta=1.0-s; dtheta=-1.0; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new ConstSpiral;} }; ///////////////////////////////////////////////////////////////////////// class WrapSpiral : public ArchimedianSpiral { JDXfloat switchpoint; public: WrapSpiral() : ArchimedianSpiral("WrapSpiral") { switchpoint=0.5; switchpoint.set_minmaxval(0.0,1.0); append_member(switchpoint,_TRAJ_OPTIMIZE_PARLABEL_); set_description("An Archimedian spiral.\n" "In the inner part of k-space the radius increases linerly with time,\n" "while in the outer part the distance between adjacent sampling points along the\n" "trajectory in k-space is kept constant.\n" "The "_TRAJ_OPTIMIZE_PARLABEL_" parameter determines the relative point in time (between\n" "0.0 and 1.0) where the switching between these two modes occurs."); } // implementing virtual function of ArchimedianSpiral void calc_theta(float& theta, float& dtheta, float s) const { if (s < switchpoint) { // const sampling density theta = sqrt (1.0 - 2.0 * s / (switchpoint + 1.0)); dtheta = -1.0 / ((switchpoint + 1.0) * theta); } else { // const spiral if(switchpoint>=1.0) { // take radius/dradius of const spiral theta = 1.0-s; dtheta = -1.0; } else { float denominator=sqrt (1.0 - switchpoint*switchpoint); theta = secureDivision(1.0-s, denominator); dtheta = secureDivision(-1.0, denominator); } } } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new WrapSpiral;} }; ///////////////////////////////////////////////////////////////////////// class BoernertSpiral : public ArchimedianSpiral { JDXfloat alpha; public: BoernertSpiral() : ArchimedianSpiral("BoernertSpiral") { alpha=0.5; alpha.set_minmaxval(0.0,1.0); append_member(alpha,_TRAJ_OPTIMIZE_PARLABEL_); set_description("An Archimedian spiral as described in Boernert et al, MAGMA 9:29-41(1999)."); } // implementing virtual function of ArchimedianSpiral void calc_theta(float& theta, float& dtheta, float s) const { float f=1.0-s; float df=-1.0; float g=sqrt(alpha+(1.0-alpha)*(1.0-s)); float dg=secureDivision(alpha-1.0, 2.0*g); theta=secureDivision(f,g); dtheta=secureDivision(df*g-f*dg,g*g); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new BoernertSpiral;} }; ///////////////////////////////////////////////////////////////////////// class SegmentedRotation : public JDXfunctionPlugIn { JDXtrajectory Trajectory; JDXint Segment; JDXint Nsegments; mutable kspace_coord tds; // mutable -> member function calculate_traj defined as const mutable traj_info ti; RotMatrix rot_matrix; float deltaphi; mutable dvector vec; mutable dvector rot_vec; public: SegmentedRotation() : JDXfunctionPlugIn("SegmentedRotation") { Nsegments=8; Nsegments.set_minmaxval(1,30); Segment=1; Segment.set_minmaxval(1,30); vec.resize(3); rot_vec.resize(3); append_member(Trajectory,"Trajectory"); append_member(Nsegments,"NumSegments"); append_member(Segment,"CurrSegment"); set_description("This is a segmented trajectory, which can be used to rotate the other 2D-trajectories."); Trajectory.set_function_mode(twoDeeMode); } void init_trajectory(OdinPulse* pls=0) { if (Nsegments < 1) Nsegments = 1; if (Segment >= Nsegments) Segment = int (Nsegments); if (Segment < 1) Segment = 1; Trajectory.init_trajectory(pls); float phi= float(Segment-1) * 2.0 * PII / float(Nsegments); rot_matrix.set_inplane_rotation(phi); } const kspace_coord& calculate_traj(float s) const { tds=Trajectory.calculate(s); vec[0]=tds.kx; vec[1]=tds.ky; vec[2]=0.0; rot_vec=rot_matrix*vec; tds.kx=rot_vec[0]; tds.ky=rot_vec[1]; tds.kz=0.0; // calculate gradient vector vec[0]=tds.Gx; vec[1]=tds.Gy; vec[2]=0.0; rot_vec=rot_matrix*vec; tds.Gx=rot_vec[0]; tds.Gy=rot_vec[1]; tds.Gz=0.0; return tds; } const traj_info& get_traj_properties() const { ti=Trajectory.get_traj_info(); ti.max_kspace_step/=float(Nsegments); return ti; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new SegmentedRotation;} }; ///////////////////////////////////////////////////////////////////////// // allocating plugins void JDXtrajectory::init_static() { (new Const)->register_function(trajFunc,zeroDeeMode).register_function(trajFunc,oneDeeMode); (new Sinus)->register_function(trajFunc,oneDeeMode); (new ConstSpiral)->register_function(trajFunc,twoDeeMode); (new WrapSpiral)->register_function(trajFunc,twoDeeMode); (new BoernertSpiral)->register_function(trajFunc,twoDeeMode); (new SegmentedRotation)->register_function(trajFunc,twoDeeMode); } void JDXtrajectory::destroy_static() { // pulgins will be deleted by JDXfunction } EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/odinseq/seqveciter.h0000644000175000017500000000473111455553540013400 00000000000000/*************************************************************************** seqveciter.h - description ------------------- begin : Fri Jan 19 2007 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQVECITER_H #define SEQVECITER_H #include #include /** * @addtogroup odinseq * @{ */ /** * \brief Iterator for vectors * * Iterator to step manually through vectors. * Each occurence of this iterator in the sequence tree will * increment actual value of the vector by one. If the end of * the vector is reached, iteration starts again at the beginning, * i.e. the iteration is cyclical. * Use add_vector() to append vectors which should be controlled * by this iterator. */ class SeqVecIter : public SeqCounter, public SeqObjBase { public: /** * Construct an empty iterator with the given label. * Iteration will start at index 'start'. */ SeqVecIter(const STD_string& object_label = "unnamedSeqVecIter", unsigned int start=0); /** * Copy constructor */ SeqVecIter(const SeqVecIter& svi); /** * Assignment operator */ SeqVecIter& operator = (const SeqVecIter& svi); // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; double get_duration() const; unsigned int event(eventContext& context) const; STD_string get_properties() const; void query(queryContext& context) const; RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const; private: bool is_acq_iterator() const; // overwriting virtual functions from SeqClass bool prep(); unsigned int startindex; }; /** @} */ #endif odin-1.8.5/odinseq/seqgradecho.cpp0000644000175000017500000002245111455553540014045 00000000000000#include "seqgradecho.h" void SeqGradEcho::common_init(const STD_string& objlabel) { SeqAcqInterface::set_marshall(&acqread); SeqFreqChanInterface::set_marshall(&acqread); postexcpart.set_label(objlabel+"_postexcpart"); postacqpart.set_label(objlabel+"_postacqpart"); phasesim.set_label(objlabel+"_phasesim"); phasesim3d.set_label(objlabel+"_phasesim3d"); phasereordsim.set_label(objlabel+"_phasereordsim"); midpart.set_label(objlabel+"_midpart"); mode=slicepack; balanced_grads=false; } SeqGradEcho::SeqGradEcho(const STD_string& object_label, SeqPulsar& exc, double sweepwidth, unsigned int readnpts, float FOVread, unsigned int phasenpts, float FOVphase, encodingScheme scheme, reorderScheme reorder, unsigned int nsegments, unsigned int reduction, unsigned int acl_bands, bool balanced, float partial_fourier_phase, float partial_fourier_read, bool partial_fourier_read_at_end, float os_factor, const STD_string& nucleus) : SeqObjList(object_label), pls_reph(object_label+"_exc_reph",exc), acqread(object_label+"_acqread", sweepwidth, readnpts, FOVread, readDirection, os_factor, partial_fourier_read, partial_fourier_read_at_end, nucleus) { Log odinlog(this,"SeqGradEcho"); common_init(object_label); mode=slicepack; balanced_grads=balanced; pulsptr.set_handled(&exc); // use duration of on-ramp and constant part of pls_reph as duration of constant part of the other trapezoids double constdur=pls_reph.get_constgrad_duration()+pls_reph.get_onramp_duration(); // use SeqGradPhaseEnc to initialize phase encoding SeqGradPhaseEnc pedummy(object_label+"_phase", phasenpts, FOVphase, constdur, phaseDirection, scheme, reorder, nsegments, reduction, acl_bands, partial_fourier_phase, nucleus); phase=pedummy.vectorgrad; if(balanced_grads) { phase_rew=phase; phase_rew.set_label("phase_rew"); phase_rew.invert_strength(); } // the same for read-dephase float readdeph_strengh=secureDivision(acqread.readdephgrad.get_integral(),constdur); readdeph=SeqGradConst(object_label+"_readdeph",acqread.read.get_channel(),readdeph_strengh,constdur); build_seq(); } SeqGradEcho::SeqGradEcho(const STD_string& object_label, unsigned int readnpts, float FOVread, unsigned int phasenpts, float FOVphase, unsigned int slicenpts, float FOVslice, SeqPulsar& exc, double sweepwidth, unsigned int reduction, unsigned int acl_bands, bool balanced, float partial_fourier_phase, float partial_fourier_read, bool partial_fourier_read_at_end, float os_factor, const STD_string& nucleus) : SeqObjList(object_label), pls_reph(object_label+"_exc_reph",exc), acqread(object_label+"_acqread", sweepwidth, readnpts, FOVread, readDirection, os_factor, partial_fourier_read, partial_fourier_read_at_end, nucleus) { Log odinlog(this,"SeqGradEcho"); common_init(object_label); mode=voxel_3d; balanced_grads=balanced; pulsptr.set_handled(&exc); // use duration of on-ramp and constant part of pls_reph as duration of constant part of the other trapezoids double constdur=pls_reph.get_constgrad_duration()+pls_reph.get_onramp_duration(); // use SeqGradPhaseEnc to initialize phase encoding SeqGradPhaseEnc pedummy(object_label+"_phase", phasenpts, FOVphase, constdur, phaseDirection, linearEncoding, noReorder, 1, reduction, acl_bands, partial_fourier_phase, nucleus); phase=pedummy.vectorgrad; // use SeqGradPhaseEnc to initialize phase encoding SeqGradPhaseEnc pedummy3d(object_label+"_phase3d", slicenpts, FOVslice, constdur, sliceDirection, linearEncoding, noReorder, 1, reduction, acl_bands, 0.0, nucleus); phase3d=pedummy3d.vectorgrad; // Merge slice rephaser and 2nd phase encoding float integral_phase3d=phase3d.get_strength()*phase3d.get_gradduration(); float integral_reph=pls_reph.get_gradintegral()[sliceDirection]; fvector integrals_slice = phase3d.get_trims()*integral_phase3d + integral_reph; ODINLOG(odinlog,normalDebug) << "integrals_slice=" << integrals_slice << STD_endl; float maxabsintegral_slice=integrals_slice.maxabs(); float strength_slice=secureDivision(maxabsintegral_slice, constdur); fvector trims_slice(integrals_slice/maxabsintegral_slice); phase3d=SeqGradVector("phase3d", sliceDirection, strength_slice, trims_slice, constdur); if(balanced_grads) { phase_rew=phase; phase_rew.set_label("phase_rew"); phase_rew.invert_strength(); phase3d_rew=phase3d; phase3d_rew.set_label("phase3d_rew"); phase3d_rew.invert_strength(); } // the same for read-dephase float readdeph_strengh=secureDivision(acqread.readdephgrad.get_integral(),constdur); readdeph=SeqGradConst(object_label+"_readdeph",acqread.read.get_channel(),readdeph_strengh,constdur); build_seq(); } SeqGradEcho::SeqGradEcho(const STD_string& object_label) : SeqObjList(object_label) { common_init(object_label); } SeqGradEcho::SeqGradEcho(const SeqGradEcho& sge) { SeqGradEcho::operator = (sge); common_init(sge.get_label()); } SeqGradEcho& SeqGradEcho::operator = (const SeqGradEcho& sge) { SeqObjList::operator = (sge); pulsptr=sge.pulsptr; pls_reph=sge.pls_reph; phase=sge.phase; phase3d=sge.phase3d; phase_rew=sge.phase_rew; phase3d_rew=sge.phase3d_rew; acqread=sge.acqread; readdeph=sge.readdeph; midpart=sge.midpart; mode=sge.mode; balanced_grads=sge.balanced_grads; build_seq(); return *this; } SeqGradEcho& SeqGradEcho::set_pe_reorder_scheme(reorderScheme scheme,unsigned int nsegments) { phase.set_reorder_scheme(scheme,nsegments); if(balanced_grads) phase_rew.set_reorder_scheme(scheme,nsegments); return *this; } SeqVector& SeqGradEcho::get_pe_vector() { if(balanced_grads) return phasesim; return phase; } SeqVector& SeqGradEcho::get_pe3d_vector() { if(balanced_grads) return phasesim3d; return phase3d; } const SeqVector& SeqGradEcho::get_pe_reorder_vector() const { if(balanced_grads) return phasereordsim; return phase.get_reorder_vector(); } double SeqGradEcho::get_echo_time() const { Log odinlog(this,"get_echo_time"); double result=0.0; if(pulsptr.get_handled()) { double magcenter=(pulsptr.get_handled()->get_duration()) - (pulsptr.get_handled()->get_magnetic_center()); ODINLOG(odinlog,normalDebug) << "magcenter=" << magcenter << STD_endl; result+=magcenter; } double middur=midpart.get_duration(); double postexcdur=postexcpart.get_duration(); double acqcenter=acqread.get_acquisition_center(); ODINLOG(odinlog,normalDebug) << "middur/postexcdur/acqcenter=" << middur << "/" << postexcdur << "/" << acqcenter << STD_endl; result += middur + postexcdur + acqcenter; return result; } SeqGradEcho& SeqGradEcho::set_midpart(const SeqObjBase& soa) { midpart=soa; build_seq(); // Has to be re-built so that objects of midpart are copied to this return *this; } SeqAcqInterface& SeqGradEcho::set_template_type(templateType type) { acqread.set_template_type(type); if(type==phasecorr_template) phase.set_strength(0.0); return *this; } double SeqGradEcho::get_preacq() const { double result=0.0; if(pulsptr.get_handled()) result+=pulsptr.get_handled()->get_duration(); result+=midpart.get_duration(); result+=postexcpart.get_duration(); return result; } SeqGradInterface& SeqGradEcho::set_gradrotmatrix(const RotMatrix& matrix) { if(pulsptr.get_handled()) pulsptr.get_handled()->set_gradrotmatrix(matrix); postexcpart.set_gradrotmatrix(matrix); acqread.set_gradrotmatrix(matrix); postacqpart.set_gradrotmatrix(matrix); return *this; } SeqGradInterface& SeqGradEcho::invert_strength() { if(pulsptr.get_handled()) pulsptr.get_handled()->invert_strength(); postexcpart.invert_strength(); acqread.invert_strength(); postacqpart.invert_strength(); return *this; } fvector SeqGradEcho::get_gradintegral() const { fvector result(3); result=0.0; if(pulsptr.get_handled()) result+=pulsptr.get_handled()->get_gradintegral(); result+=postexcpart.get_gradintegral(); result+=acqread.get_gradintegral(); result+=postacqpart.get_gradintegral(); return result; } void SeqGradEcho::build_seq() { Log odinlog(this,"build_seq"); clear(); postexcpart.clear(); postacqpart.clear(); phasesim.clear(); phasesim3d.clear(); phasereordsim.clear(); if(balanced_grads) { phasesim+=phase; phasesim+=phase_rew; phasereordsim+=phase.get_reorder_vector(); phasereordsim+=phase_rew.get_reorder_vector(); if(mode==voxel_3d) { phasesim3d+=phase3d; phasesim3d+=phase3d_rew; } } if(mode==voxel_3d) { postexcpart /= phase3d / phase / readdeph ; if(balanced_grads) postacqpart /= phase3d_rew / phase_rew / readdeph ; } else { postexcpart /= pls_reph / phase / readdeph ; if(balanced_grads) postacqpart /= pls_reph / phase_rew / readdeph ; } if(pulsptr.get_handled()) { (*this)+=(*pulsptr.get_handled()) + midpart + postexcpart + acqread; if(balanced_grads) (*this) += postacqpart; } else { ODINLOG(odinlog,warningLog) << "No pulse specified for gradient echo module" << STD_endl; } // reco stuff acqread.set_reco_vector(line,phase); if(mode==voxel_3d) acqread.set_reco_vector(line3d,phase3d); if(pulsptr.get_handled()) acqread.set_reco_vector(slice,*pulsptr.get_handled()); } odin-1.8.5/odinseq/seqdelayvec.cpp0000644000175000017500000000352711322062345014057 00000000000000#include "seqdelayvec.h" SeqDelayVector::SeqDelayVector(const STD_string& object_label,const dvector& delaylist) : SeqObjBase(object_label), SeqVector(object_label), delayvecdriver(object_label), delayvec(delaylist) { } SeqDelayVector::SeqDelayVector(const STD_string& object_label) : SeqObjBase(object_label), SeqVector(object_label), delayvecdriver(object_label) { } SeqDelayVector::SeqDelayVector(const SeqDelayVector& sdv) { SeqDelayVector::operator = (sdv); } SeqDelayVector& SeqDelayVector::operator = (const SeqDelayVector& sdv) { SeqObjBase::operator = (sdv); SeqVector::operator = (sdv); delayvecdriver=sdv.delayvecdriver; delayvec=sdv.delayvec; return *this; } SeqDelayVector& SeqDelayVector::set_delayvector(const dvector& delays) { delayvec=delays; return *this; } dvector SeqDelayVector::get_delayvector() const {return delayvec;} double SeqDelayVector::get_duration() const { double result=systemInfo->get_min_duration(delayObj); double value=0.0; if(get_vectorsize()) { value=delayvec[get_current_index()]; } if(value>result) result=value; return result; } STD_string SeqDelayVector::get_program(programContext& context) const { Log odinlog(this,"get_program"); double delaydur=0.0; if(get_vectorsize()) { delaydur=delayvec[get_current_index()]; } ODINLOG(odinlog,normalDebug) << "context.mode/delaydur=" << context.mode << "/" << delaydur << STD_endl; return delayvecdriver->get_program(context,delaydur); } SeqValList SeqDelayVector::get_delayvallist() const { Log odinlog(this,"get_delayvallist"); SeqValList result(get_label()); result.set_value(get_duration()); return result; } unsigned int SeqDelayVector::get_vectorsize() const {return delayvec.size();} bool SeqDelayVector::prep() { if(!SeqObjBase::prep()) return false; return delayvecdriver->prep_driver(); } odin-1.8.5/odinseq/00seqtest.cpp0000644000175000017500000000432111322062345013373 00000000000000#include "seqall.h" #ifdef ODIN_DEBUG int seqtestfunc() { SeqGradConst constgrad; SeqGradConstPulse constgradpulse; SeqPulsar pulsar; SeqObjList list; SeqDelay delay; SeqObjLoop loop; SeqDecoupling dec; SeqGradEcho grech; SeqAcqEPI epi; SeqAcqSpiral spiral; SeqDiffWeight dw; SeqSat sat; SeqFieldMap fmap; // Testing + operator constgrad + constgrad; constgrad + constgradpulse; constgrad + pulsar; constgrad + list; constgrad + delay; constgrad + loop; constgrad + dec; constgradpulse + constgrad; constgradpulse + constgradpulse; constgradpulse + pulsar; constgradpulse + list; constgradpulse + delay; constgradpulse + loop; constgradpulse + dec; pulsar + constgrad; pulsar + constgradpulse; pulsar + pulsar; pulsar + list; pulsar + delay; pulsar + loop; pulsar + dec; list + constgrad; list + constgradpulse; list + pulsar; list + list; list + delay; list + loop; list + dec; delay + constgrad; delay + constgradpulse; delay + pulsar; delay + list; delay + delay; delay + loop; delay + dec; loop + constgrad; loop + constgradpulse; loop + pulsar; loop + list; loop + delay; loop + loop; loop + dec; dec + constgrad; dec + constgradpulse; dec + pulsar; dec + list; dec + delay; dec + loop; dec + dec; // Testing / operator constgrad / constgrad; constgrad / constgradpulse; constgrad / list; constgrad / delay; constgrad / loop; constgrad / dec; constgradpulse / constgrad; constgradpulse / constgradpulse; constgradpulse / list; constgradpulse / delay; constgradpulse / loop; constgradpulse / dec; list / constgrad; list / constgradpulse; delay / constgrad; delay / constgradpulse; loop / constgrad; loop / constgradpulse; dec / constgrad; dec / constgradpulse; // Testing += operator list += constgrad; list += constgradpulse; list += pulsar; list += list; list += delay; list += loop; list += dec; constgradpulse += constgrad; constgradpulse += constgradpulse; // Testing = operator list = constgrad; list = constgradpulse; list = pulsar; list = list; list = delay; list = loop; list = dec; return 0; } #endif odin-1.8.5/odinseq/seqrotmatrixvector.h0000644000175000017500000000670311322062345015203 00000000000000/*************************************************************************** seqrotmatrixvector.h - description ------------------- begin : Wed Jul 30 2003 copyright : (C) 2003 by Thies H. Jochimsen and Michael v. Mengershausen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQROTMATRIXVECTOR_H #define SEQROTMATRIXVECTOR_H #include class SeqGradChanList; // forward declaration /** * @ingroup odinseq * * \brief Vector of SeqRotMatrix's * * This class keeps an arry of rotation matrices. * It can be used consecutively by a gradient object within a loop * via the function SeqObjList::set_gradrotmatrixvector(). */ class SeqRotMatrixVector : public SeqVector, public Handled { public: /** * default constructor */ SeqRotMatrixVector(const STD_string& object_label = "unnamedSeqRotMatrixVector"); /** * constructs a rot-matrix vector from an existing rot-matrix vector */ SeqRotMatrixVector(const SeqRotMatrixVector& srmv); /** * Destructor */ ~SeqRotMatrixVector(); /** * assignment operator */ SeqRotMatrixVector& operator = (const SeqRotMatrixVector& srmv); /** * returns the index'th matrix */ const RotMatrix& operator [] (unsigned long index) const; /** * returns the currently active matrix when used inside a loop */ const RotMatrix& get_current_matrix () const; /** * Makes this a vector of 'nsegments' matrices that * rotate the first and second dimension (read, phase) with * a constant angle increment of 2*PI/nsegments. */ SeqRotMatrixVector& create_inplane_rotation(unsigned int nsegments); /** * clears the list of rotation matrices */ SeqRotMatrixVector& clear() { rotMatrixList.clear(); return *this; }; /** * adds a new rotation matrix at the end of the vector */ SeqRotMatrixVector& append(const RotMatrix& srm) { // srm.check_and_correct(); rotMatrixList.push_back(srm); return *this; }; /** * returns values with max. absolute values for each element of the matrix vector */ RotMatrix get_maxMatrix () const; // implemented virtual from SeqVector unsigned int get_vectorsize() const {return rotMatrixList.size();}; bool needs_unrolling_check() const {return get_vectorsize()>1;} bool is_qualvector() const {return false;} bool prep_iteration() const; svector get_vector_commands(const STD_string& iterator) const {iterator_cache=iterator; return svector();} // return stored iterator, quick hack for EPIC rotmats const STD_string& get_iterator() const {return iterator_cache;} private: friend class SeqGradChan; mutable STD_string iterator_cache; STD_list rotMatrixList; RotMatrix dummyrotmat; }; #endif odin-1.8.5/odinseq/seqrotmatrixvector.cpp0000644000175000017500000000442411322062345015534 00000000000000#include "seqrotmatrixvector.h" #include "seqloop.h" #include "seqgradchan.h" #include SeqRotMatrixVector::SeqRotMatrixVector(const STD_string& object_label): SeqVector(object_label){ Log odinlog(this,"SeqRotMatrixVector(const STD_string&)"); set_label(object_label); } SeqRotMatrixVector::SeqRotMatrixVector(const SeqRotMatrixVector& srmv) { Log odinlog(this,"SeqRotMatrixVector(SeqRotMatrixVector)"); SeqRotMatrixVector::operator = (srmv); } SeqRotMatrixVector& SeqRotMatrixVector::operator = (const SeqRotMatrixVector& srmv){ Log odinlog(this,"operator ="); SeqVector::operator = (srmv); rotMatrixList=srmv.rotMatrixList; return *this; }; SeqRotMatrixVector::~SeqRotMatrixVector() { Log odinlog(this,"~SeqRotMatrixVector"); } const RotMatrix& SeqRotMatrixVector::operator [] (unsigned long index) const{ unsigned long i=0; STD_list::const_iterator it; for ( it=rotMatrixList.begin(); it !=rotMatrixList.end();++it){ if(i==index) return *it; i++; } return dummyrotmat; }; const RotMatrix& SeqRotMatrixVector::get_current_matrix () const{ if(get_vectorsize()) return (*this)[get_current_index()]; return dummyrotmat; } SeqRotMatrixVector& SeqRotMatrixVector::create_inplane_rotation(unsigned int nsegments) { Log odinlog(this,"create_inplane_rotation"); clear(); for(unsigned int i=0; i; odin-1.8.5/odinseq/seqphase.h0000644000175000017500000000641511322062345013027 00000000000000/*************************************************************************** seqphase.h - description ------------------- begin : Sun Apr 4 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPHASE_H #define SEQPHASE_H #include #include #include /////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The base class for platform specific drivers of phase lists */ class SeqPhaseDriver : public SeqDriverBase { public: SeqPhaseDriver() {} virtual ~SeqPhaseDriver() {} virtual void prep_driver(const dvector& phaselist) = 0; virtual unsigned int get_phaselistindex(const dvector& phaselist) const = 0; virtual STD_string get_loopcommand(const dvector& phaselist) const = 0; virtual svector get_phasevec_commands(const STD_string& iterator, const STD_string& instr) const = 0; virtual SeqPhaseDriver* clone_driver() const = 0; }; /////////////////////////////////////////////////////////////////// class SeqFreqChan; // forward declaration /** * @ingroup odinseq_internals * A vector class for managing phase lists */ class SeqPhaseListVector : public SeqVector, public virtual SeqClass { private: //make everything private so that only SeqFreqChan can use it SeqPhaseListVector(const STD_string& object_label = "unnamedSeqPhaseListVector", const dvector& phase_list=0 ); SeqPhaseListVector(const SeqPhaseListVector& spl); SeqPhaseListVector& operator = (const SeqPhaseListVector& spl); /** * Specifies the phaselist */ SeqPhaseListVector& set_phaselist(const dvector& pl); /** * Returns the phaselist */ dvector get_phaselist() const {return phaselist;} /** * Return the index for the phaselist */ unsigned int get_phaselistindex() const; /** * Returns the current phase in deg */ double get_phase() const; // overloaded functions of SeqVector unsigned int get_vectorsize() const {return phaselist.size();} STD_string get_loopcommand() const; svector get_vector_commands(const STD_string& iterator) const; bool prep_iteration() const; bool is_qualvector() const {return false;} private: friend class SeqFreqChan; // overwriting virtual functions from SeqClass bool prep(); // the hardware driver mutable SeqDriverInterface phasedriver; dvector phaselist; // in deg // the frequency object in which this object is embedded SeqFreqChan* user; }; #endif odin-1.8.5/odinseq/seqsimvec.cpp0000644000175000017500000001276611322062345013556 00000000000000#include "seqsimvec.h" SeqSimultanVector::SeqSimultanVector(const SeqSimultanVector& ssv) { SeqSimultanVector::operator = (ssv); } SeqSimultanVector& SeqSimultanVector::operator = (const SeqSimultanVector& ssv) { SeqVector::operator = (ssv); SeqClass::operator = (ssv); List::operator = (ssv); return *this; } SeqSimultanVector& SeqSimultanVector::operator += (const SeqVector& sv) { Log odinlog(this,"+="); if(&sv==this) ODINLOG(odinlog,errorLog) << "refusing to manage myself" << STD_endl; else { append(sv); sv.simhandler.set_handled(this); } return *this; } svector SeqSimultanVector::get_vector_commands(const STD_string& iterator) const { Log odinlog(this,"get_vector_commands"); STD_list labels; STD_list::const_iterator veciter; // using local iterator because member functions may be nested for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { svector veclabels=(*veciter)->get_vector_commands(iterator); for(unsigned int i=0; i::const_iterator it=labels.begin(); it!=labels.end(); ++it) { result[index]=*it; index++; } return result; } unsigned int SeqSimultanVector::get_vectorsize() const { Log odinlog(this,"get_vectorsize"); unsigned int result=0; STD_list::const_iterator veciter; // using local iterator because member functions may be nested if(size()) { result=(*get_const_begin())->get_vectorsize(); for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { if((*veciter)->get_vectorsize()!=result) ODINLOG(odinlog,errorLog) << "vector size mismatch" << STD_endl; } } return result; } unsigned int SeqSimultanVector::get_numof_iterations() const { Log odinlog(this,"get_numof_iterations"); unsigned int result=0; STD_list::const_iterator veciter; // using local iterator because member functions may be nested if(size()) { result=(*get_const_begin())->get_numof_iterations(); for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { if((*veciter)->get_numof_iterations()!=result) ODINLOG(odinlog,errorLog) << "numof_iterations mismatch" << STD_endl; } } return result; } STD_string SeqSimultanVector::get_loopcommand() const { Log odinlog(this,"get_loopcommand"); STD_string result; STD_list::const_iterator veciter; // using local iterator because member functions may be nested if(size()) { result=(*get_const_begin())->get_loopcommand(); for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { if((*veciter)->get_loopcommand()!=result) ODINLOG(odinlog,errorLog) << "loopcommand mismatch" << STD_endl; } } return result; } nestingRelation SeqSimultanVector::get_nesting_relation() const { Log odinlog(this,"get_nesting_relation"); nestingRelation result=noRelation; STD_list::const_iterator veciter; // using local iterator because member functions may be nested if(size()) { result=(*get_const_begin())->get_nesting_relation(); for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { if((*veciter)->get_nesting_relation()!=result) ODINLOG(odinlog,errorLog) << "nesting_relation mismatch" << STD_endl; } } return result; } bool SeqSimultanVector::needs_unrolling_check() const { Log odinlog(this,"needs_unrolling_check"); bool result=false; STD_list::const_iterator veciter; // using local iterator because member functions may be nested for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { if((*veciter)->needs_unrolling_check()) result=true; } return result; } bool SeqSimultanVector::prep_iteration() const { Log odinlog(this,"prep_iteration"); bool result=true; ODINLOG(odinlog,normalDebug) << "managing " << size() << " vectors" << STD_endl; STD_list::const_iterator veciter; // using local iterator because member functions may be nested for(veciter=get_const_begin(); veciter!=get_const_end(); ++veciter) { ODINLOG(odinlog,normalDebug) << "prep_iteration of " << (*veciter)->get_label() << STD_endl; if(!(*veciter)->prep_iteration()) { ODINLOG(odinlog,errorLog) << (*veciter)->get_label() << ".prep_iteration() failed" << STD_endl; return false; } } return result; } /* bool SeqSimultanVector::is_acq_vector() const { Log odinlog(this,"SeqSimultanVector::is_acq_vector"); return SeqVector::is_acq_vector(); } */ const SeqVector& SeqSimultanVector::set_vechandler(const SeqCounter* sc) const { Log odinlog(this,"set_vechandler"); SeqVector::set_vechandler(sc); STD_list::const_iterator veciter; // using local iterator because member functions may be nested for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { (*veciter)->set_vechandler(sc); } return *this; } bool SeqSimultanVector::is_qualvector() const { Log odinlog(this,"is_qualvector"); STD_list::const_iterator veciter; // using local iterator because member functions may be nested for(veciter=get_const_begin();veciter!=get_const_end();++veciter) { if((*veciter)->is_qualvector()) return true; } return false; } void SeqSimultanVector::clear_container() { List::clear(); } odin-1.8.5/odinseq/seqcmdline.h0000644000175000017500000000423611322062345013341 00000000000000/*************************************************************************** seqcmdline.h - description ------------------- begin : Tue Jan 18 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQCMDLINE_H #define SEQCMDLINE_H #include #define USAGE_INDENTION_FACTOR 2 ///////////////////////////////////////////////////////// #ifdef NO_CMDLINE struct SeqCmdlineActionList {}; // dummy class #else struct SeqCmdlineAction { SeqCmdlineAction(const STD_string& act, const STD_string& descr) : action(act), description(descr) {} void add_req_arg(const STD_string& opt, const STD_string& descr) {req_args[opt]=descr;} void add_opt_arg(const STD_string& opt, const STD_string& descr) {opt_args[opt]=descr;} STD_string action; STD_string description; STD_map req_args; STD_map opt_args; }; typedef STD_list SeqCmdlineActionList; #endif ///////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Helper class to deal with command line arguments */ class SeqCmdLine : public SeqClass { public: static int process(int argc, char *argv[]); static STD_string format_actions(const SeqCmdlineActionList& actions); private: static STD_string usage(const STD_string& meth, const STD_string& description); }; #endif odin-1.8.5/odinseq/seqdriver.cpp0000644000175000017500000000442111322062345013550 00000000000000#include "seqdriver.h" #include "seqplatform.h" #ifdef PARAVISION_PLUGIN #include "../platforms/Paravision/odinseq_paravision/seqparavision.h" #endif #ifdef IDEA_PLUGIN #include "../platforms/IDEA_n4/odinseq_idea/seqidea.h" #endif #ifdef STANDALONE_PLUGIN #include "../platforms/StandAlone/odinseq_standalone/seqstandalone.h" #endif #ifdef EPIC_PLUGIN #include "../platforms/EPIC/odinseq_epic/seqepic.h" #endif ///////////////////////////////////////////////////////////////////// SeqPlatformInstances::SeqPlatformInstances() { Log odinlog("SeqPlatformInstances","SeqPlatformInstances"); PlatformRegistration da; int i; for(i=0; i #include "seqdiffweight.h" #include "seqgradchanparallel.h" float* get_dti_dirarr(unsigned int ndir); // forward declaration void calc_dw_grads(fvector& gradtrims, double& delta, const fvector& bvals, float maxgradstrength, float middur, float gamma) { Log odinlog("SeqDiffWeight","calc_grads"); float maxbval=bvals.maxabs(); // solve cubic equation for delta double a=3.0/2.0*middur; double c=-3.0/2.0*secureDivision(maxbval,gamma*gamma*maxgradstrength*maxgradstrength); ODINLOG(odinlog,normalDebug) << "a/c=" << a << "/" << c << STD_endl; double x0=0.0; double x1=0.0; double x2=0.0; int nroots=solve_cubic (a,0.0,c,&x0,&x1,&x2); ODINLOG(odinlog,normalDebug) << "nroots/x0/x1/x2=" << nroots << "/" << x0 << "/" << x1 << "/" << x2 << STD_endl; delta=maxof3(x0,x1,x2); ODINLOG(odinlog,normalDebug) << "delta=" << delta << STD_endl; unsigned int ntrims=bvals.length(); gradtrims.resize(ntrims); for(unsigned int i=0; i odinlog(this,"SeqDiffWeight(...)"); middle_part=midpart; fvector gradtrims1; double delta; calc_dw_grads(gradtrims1, delta, bvals, maxgradstrength, middle_part.get_duration(), systemInfo->get_gamma(nucleus)); fvector gradtrims2(gradtrims1); if(!stejskalTanner) gradtrims2=-gradtrims1; // reset for(int idim=0; idim odinlog(this,"SeqDiffWeight(...)"); float* arr=get_dti_dirarr(ndir); if(!arr) { ODINLOG(odinlog,errorLog) << "array not available for ndir=" << ndir << STD_endl; return; } middle_part=midpart; STD_list blist[n_directions]; unsigned int idim; // single declaration for MSVC6 for(idim=0; idim=baseline_rep && idir<(ndir-1)) { repcounter=0; for(idim=0; idimget_gamma(nucleus)); fvector gradtrims2(gradtrims1); if(!stejskalTanner) gradtrims2=-gradtrims1; ODINLOG(odinlog,normalDebug) << "gradtrims1[" << idim << "]=" << gradtrims1 << STD_endl; ODINLOG(odinlog,normalDebug) << "gradtrims2[" << idim << "]=" << gradtrims2 << STD_endl; pfg1[idim]=SeqGradVectorPulse(object_label+"_pfg1_"+directionLabel[idim],direction(idim),maxgradstrength,gradtrims1,delta); pfg2[idim]=SeqGradVectorPulse(object_label+"_pfg2_"+directionLabel[idim],direction(idim),maxgradstrength,gradtrims2,delta); } build_seq(); } SeqDiffWeight::SeqDiffWeight(const STD_string& object_label ) : SeqObjList(object_label), SeqSimultanVector(object_label) { } SeqDiffWeight& SeqDiffWeight::operator = (const SeqDiffWeight& sgdw) { SeqSimultanVector::operator = (sgdw); SeqObjList::operator = (sgdw); for(int idim=0; idimset_temporary(); SeqGradChanParallel* sgcp2=new SeqGradChanParallel(get_label()+"_sgcp2"); sgcp2->set_temporary(); SeqSimultanVector::clear(); for(int idim=0; idim odinlog(this,"SeqDiffWeightFlowComp()"); fvector gradtrims; double delta; calc_dw_grads(gradtrims, delta, 0.5*bvals, maxgradstrength, 0.0, systemInfo->get_gamma(nucleus)); pfg1=SeqGradVectorPulse(object_label+"_pfg1",chan,maxgradstrength, gradtrims,delta); pfg2=SeqGradVectorPulse(object_label+"_pfg2",chan,-maxgradstrength,gradtrims,2.0*delta); pfg3=SeqGradVectorPulse(object_label+"_pfg3",chan,maxgradstrength, gradtrims,delta); build_seq(); } SeqDiffWeightFlowComp::SeqDiffWeightFlowComp(const STD_string& object_label) : SeqGradChanList(object_label), SeqSimultanVector(object_label) {} SeqDiffWeightFlowComp& SeqDiffWeightFlowComp::operator = (const SeqDiffWeightFlowComp& sgdwfc) { SeqSimultanVector::operator = (sgdwfc); SeqGradChanList::operator = (sgdwfc); pfg1=sgdwfc.pfg1; pfg2=sgdwfc.pfg2; pfg3=sgdwfc.pfg3; delay=sgdwfc.delay; build_seq(); return *this; } void SeqDiffWeightFlowComp::build_seq() { SeqSimultanVector::clear(); SeqSimultanVector::operator += (pfg1); SeqSimultanVector::operator += (pfg2); SeqSimultanVector::operator += (pfg3); SeqGradChanList::clear(); SeqGradChanList::operator += (pfg1); SeqGradChanList::operator += (delay); SeqGradChanList::operator += (pfg2); SeqGradChanList::operator += (delay); SeqGradChanList::operator += (pfg3); } ////////////////////////////////////////////////////////////////////////////////////////// static float ps3 [9] = { 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; //static float ps3 [9] = { -0.100796, 0.994902, 0.003109, -0.994900, -0.100783, -0.004049, -0.003715, -0.003501, 0.999987}; static float ps4 [12] = { -0.021560, -0.304929, 0.952131, -0.949220, -0.064610, 0.307906, 0.491865, 0.656790, 0.571572, 0.435796, -0.897109, 0.072653}; static float ps5 [15] = { -0.810867, -0.496465, 0.309866, 0.307318, -0.931254, 0.195761, -0.171601, -0.145829, 0.974314, -0.894745, 0.169209, -0.413280, 0.139610, 0.736549, 0.661819}; static float ps6 [18] = { -0.006226, -0.064447, 0.997902, 0.636679, -0.653135, 0.409945, -0.399917, -0.828419, 0.392157, 0.789559, 0.384929, 0.477940, -0.887689, 0.101313, 0.449159, 0.152552, -0.851204, -0.502175}; static float ps7 [21] = { 0.055396, -0.824375, 0.563326, 0.811301, -0.575497, 0.102927, -0.229063, 0.783589, 0.577511, -0.881413, -0.159849, 0.444477, 0.564952, 0.817041, 0.115211, 0.707747, 0.119062, 0.696361, -0.150399, -0.035322, 0.987994}; static float ps8 [24] = { -0.590425, -0.804665, -0.062549, 0.027408, -0.732319, -0.680410, 0.756064, -0.645224, 0.109787, 0.952343, 0.144115, 0.268837, 0.391908, -0.032990, 0.919413, 0.101437, -0.919831, 0.378974, -0.389232, -0.418658, 0.820502, -0.751151, 0.241893, 0.614215}; static float ps9 [27] = { 0.393918, -0.259108, 0.881868, 0.625857, 0.591521, 0.508337, 0.517317, -0.817156, 0.254244, -0.758341, 0.441699, 0.479396, -0.234181, 0.114957, 0.965373, 0.958459, -0.080740, 0.273564, -0.041437, 0.894887, 0.444364, -0.237557, -0.849808, 0.470524, 0.818447, 0.402205, -0.410335}; static float ps10 [30] = { 0.557836, 0.789965, 0.254507, 0.569859, -0.258762, -0.779937, -0.195499, -0.880727, 0.431393, 0.932196, -0.349524, -0.094038, 0.549517, -0.660507, 0.511627, -0.015038, -0.296982, 0.954765, 0.818590, 0.095700, 0.566350, -0.833628, -0.392682, 0.388415, 0.175157, 0.478983, 0.860172, -0.299722, 0.912303, 0.279053}; static float ps11 [33] = { 0.511351, 0.804163, 0.303054, -0.794769, -0.503466, 0.338916, 0.174571, 0.221229, 0.959470, -0.234636, -0.431883, 0.870875, 0.815945, 0.188147, 0.546657, -0.981514, 0.181966, 0.059311, -0.599540, 0.800343, 0.001858, -0.081149, -0.946839, 0.311306, -0.636726, 0.218439, 0.739503, 0.517936, -0.498952, 0.694830, -0.161200, 0.795247, 0.584462}; static float ps12 [36] = { 0.425180, 0.315653, 0.848284, 0.185196, -0.382898, 0.905037, -0.480267, -0.117082, 0.869273, -0.477164, -0.715637, 0.510077, -0.702985, 0.558424, -0.440426, -0.707505, -0.690260, -0.151584, 0.944077, 0.041899, -0.327051, -0.264785, 0.510148, 0.818314, 0.918467, 0.068806, 0.389467, 0.085525, 0.922253, 0.377009, -0.144817, 0.947629, -0.284652, -0.704094, 0.656651, 0.270298}; static float ps13 [39] = { 0.608489, 0.354732, 0.709863, 0.840005, 0.542193, 0.020474, -0.380743, -0.814648, 0.437474, 0.207531, -0.233095, 0.950051, -0.789643, 0.613015, -0.025996, -0.937460, -0.021576, 0.347425, 0.304986, -0.753712, 0.582152, 0.873326, -0.161334, 0.459645, 0.321048, 0.871575, 0.370521, -0.486692, -0.248656, 0.837437, -0.041337, 0.427363, 0.903135, -0.582926, 0.527413, 0.618088, -0.220542, 0.971625, 0.085473}; static float ps14 [42] = { -0.529230, -0.838809, 0.127733, -0.502637, 0.855008, -0.127741, -0.313344, 0.635274, 0.705864, -0.000007, 0.000003, 1.000000, 0.601859, 0.028092, -0.798108, -0.333120, -0.625125, -0.705868, 0.923984, 0.258254, -0.282062, 0.301096, -0.657339, 0.690830, 0.821113, -0.458657, -0.339715, 0.835101, 0.432657, 0.339727, -0.015439, -0.983550, -0.179977, 0.915418, -0.287130, 0.282075, 0.321591, 0.647564, -0.690826, 0.600669, -0.046970, 0.798117}; static float ps15 [45] = { 0.957387, -0.187071, 0.220034, 0.190618, 0.585245, 0.788133, 0.325492, -0.844583, -0.425129, 0.022796, -0.678409, 0.734331, -0.596977, -0.258722, 0.759395, -0.416250, 0.343103, 0.842031, 0.734448, 0.292307, 0.612489, 0.581881, -0.362502, 0.728016, 0.928822, 0.354407, -0.108098, -0.861661, 0.322776, 0.391608, 0.525770, 0.761172, -0.379714, -0.034273, 0.991162, -0.128153, 0.084508, -0.056169, 0.994838, 0.630413, -0.756662, 0.173326, 0.491239, 0.826626, 0.274542}; static float ps16 [48] = { 0.554077, 0.486008, 0.675866, -0.495011, 0.455826, 0.739721, 0.944451, 0.224351, 0.240166, -0.818498, -0.461979, 0.341521, 0.629291, -0.144331, 0.763650, -0.302298, -0.787745, 0.536725, 0.011914, 0.814134, 0.580555, 0.030663, -0.999031, 0.031565, 0.589202, -0.783569, -0.197131, 0.562891, 0.816715, 0.127007, 0.052951, 0.220175, 0.974022, 0.067168, -0.416946, 0.906446, 0.878961, -0.413143, 0.238202, -0.522802, -0.177477, 0.833775, 0.409735, -0.767260, 0.493386, -0.919674, 0.170720, 0.353630}; static float ps17 [51] = { -0.084677, -0.798978, 0.595368, -0.285378, 0.382557, 0.878755, 0.239575, -0.008537, 0.970840, -0.826274, 0.479411, -0.295697, -0.933600, 0.272403, 0.232780, -0.585702, 0.695361, 0.416445, 0.348167, 0.536125, 0.768993, 0.687326, 0.597291, -0.413312, -0.788627, -0.069187, -0.610967, 0.672858, 0.682522, 0.285353, -0.729422, -0.025495, 0.683588, -0.028902, 0.887279, 0.460327, 0.432026, -0.525413, 0.733004, -0.386679, 0.910660, -0.145523, -0.269733, -0.320655, 0.907978, -0.266447, -0.962145, 0.057290, -0.969994, -0.241445, -0.028553}; static float ps18 [54] = { -0.358616, 0.232844, 0.903979, 0.990653, -0.112342, 0.077367, -0.282930, 0.716688, 0.637423, -0.891249, -0.417614, 0.176844, -0.733882, -0.178601, 0.655377, 0.579701, -0.807043, -0.112374, 0.000650, 0.985575, 0.169239, 0.319924, -0.498679, 0.805586, -0.822530, 0.367692, 0.433874, -0.412439, -0.753502, 0.511984, 0.153276, -0.903274, 0.400754, 0.228998, 0.150756, 0.961682, 0.720077, -0.052737, 0.691887, 0.530172, 0.845386, 0.065124, 0.737068, -0.568030, 0.366160, 0.309857, 0.667672, 0.676907, -0.209598, -0.358489, 0.909700, 0.795763, 0.431108, 0.425331}; static float ps19 [57] = { -0.506190, -0.182434, 0.842905, -0.353038, -0.682139, 0.640352, 0.416262, 0.804302, 0.424057, -0.364266, -0.916701, 0.164226, 0.265893, -0.875818, 0.402794, -0.788937, -0.296829, -0.538025, -0.635112, 0.742750, 0.212027, -0.853341, -0.307549, 0.420979, 0.000000, 0.000000, 1.000000, -0.170383, 0.527122, -0.832533, 0.617996, -0.195486, 0.761490, -0.126832, 0.982490, 0.136478, 0.755313, -0.565523, 0.331189, -0.890859, 0.267459, 0.367200, 0.987215, -0.062418, 0.146668, 0.317816, 0.401218, 0.859079, -0.500303, 0.374591, 0.780627, 0.131853, -0.737897, -0.661909, -0.813935, -0.580022, -0.032945}; static float ps20 [60] = { -0.947965, 0.033315, 0.316625, -0.399719, -0.680997, 0.613570, -0.224707, 0.635190, 0.738945, -0.625805, -0.223904, 0.747152, 0.664622, 0.112881, 0.738604, -0.855031, -0.480158, 0.195886, -0.256130, 0.083729, 0.963009, -0.198427, 0.183236, -0.962835, 0.168344, 0.896561, 0.409682, -0.505636, -0.860974, 0.055276, 0.690315, -0.403910, 0.600269, -0.002786, -0.980688, 0.195559, -0.966326, -0.047679, -0.252866, -0.428878, 0.867093, 0.253402, 0.490998, -0.811800, 0.316073, 0.109684, -0.655863, 0.746869, 0.701264, 0.583572, 0.409477, -0.862283, 0.506426, 0.000331, -0.688646, 0.405965, 0.600798, 0.266429, 0.453089, 0.850721}; static float ps21 [63] = { 0.281102, 0.664650, 0.692259, 0.912517, 0.330300, -0.241279, -0.523441, -0.498410, 0.691084, 0.959417, -0.211461, -0.186559, -0.737697, -0.614913, -0.278721, -0.671940, 0.628624, 0.391572, -0.593050, -0.773400, 0.223929, 0.214257, 0.116502, 0.969805, 0.409038, -0.735521, 0.540090, 0.953042, 0.036026, 0.300687, -0.738786, 0.080476, 0.669118, 0.629538, -0.272009, 0.727800, -0.348436, 0.936659, -0.035541, -0.297481, -0.074546, 0.951813, -0.282864, 0.460513, 0.841377, 0.065572, -0.476145, 0.876918, 0.240577, 0.958924, 0.150293, -0.804358, 0.556622, -0.207800, 0.661996, 0.272751, 0.698118, -0.108159, -0.886921, 0.449079, -0.183756, 0.858018, 0.479623}; static float ps22 [66] = { -0.882341, 0.332209, -0.333333, -0.352361, -0.935864, 0.000000, 0.986663, 0.162779, 0.000000, 0.341948, 0.773385, 0.533805, -0.498797, 0.682828, -0.533805, 0.728872, 0.598025, -0.333333, -0.000000, -0.000000, 1.000000, 0.634302, -0.773086, 0.000000, 0.158690, -0.961879, 0.222724, 0.087078, -0.527812, 0.844886, 0.413560, 0.339318, 0.844886, -0.840745, -0.090557, 0.533805, 0.446341, 0.366214, -0.816497, -0.540321, 0.203436, -0.816497, -0.825279, -0.184302, -0.533805, 0.912357, -0.343510, -0.222724, -0.753667, -0.618369, -0.222724, 0.253029, 0.806863, -0.533805, -0.572250, 0.622562, 0.533805, -0.153469, 0.930234, 0.333333, -0.093980, 0.569650, 0.816497, 0.500637, -0.188494, -0.844886}; static float ps23 [69] = { 0.461401, -0.470194, 0.752347, -0.001035, -0.702076, 0.712101, 0.335322, 0.027683, 0.941697, -0.165846, 0.814522, 0.555922, 0.663968, 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-0.6391536013183533, 0.5055166536557195, 0.5795995055195465, -0.6391536013183533, 0.5079130747973478, -0.8458982251124606, -0.1627283048565699, 0.5079130747973478, 0.8458982251124606, -0.1627283048565699, 0.5124456619994747, -0.22338814004068744, 0.8291544985025905, 0.5124456619994747, 0.22338814004068744, 0.8291544985025905, 0.5211280929865946, -0.6214809875527959, 0.5849674288458774, 0.5211280929865946, 0.6214809875527959, 0.5849674288458774, 0.5214714469128553, 0, -0.853268732612776, 0.5242037314217923, -0.07617126084340645, 0.8481794544699813, 0.5242037314217923, 0.07617126084340645, 0.8481794544699813, 0.5336572156169057, -0.8447522275830474, -0.04004560167472076, 0.5336572156169057, 0.8447522275830474, -0.04004560167472076, 0.5411354630743502, -0.7660410837037032, 0.34691997446293676, 0.5411354630743502, 0.7660410837037032, 0.34691997446293676, 0.5414703706287629, -0.6755251623335724, -0.5004753668117451, 0.541470370628763, 0.6755251623335724, -0.5004753668117451, 0.5450795306789344, -0.8345416736796134, 0.08017792792821428, 0.5450795306789344, 0.8345416736796134, 0.08017792792821428, 0.545881503504257, -0.12048320108981789, -0.8291544985025905, 0.545881503504257, 0.12048320108981789, -0.8291544985025905, 0.5483907441273382, -0.809100088223958, 0.21124544726797653, 0.5483907441273382, 0.809100088223958, 0.21124544726797653, 0.5541093394289913, -0.5176080003344399, 0.6519545980720968, 0.5541093394289913, 0.5176080003344399, 0.6519545980720968, 0.5613283100572769, -0.7513701216091022, -0.3469199744629367, 0.5613283100572769, 0.7513701216091022, -0.3469199744629367, 0.574516613769574, -0.3065132259869937, 0.7589336616581113, 0.574516613769574, 0.3065132259869937, 0.7589336616581113, 0.5755224857007215, -0.22165711242617026, -0.7871734198788439, 0.5755224857007215, 0.22165711242617026, -0.7871734198788439, 0.5757874293000979, -0.418334054477401, 0.7024709639013442, 0.5757874293000979, 0.418334054477401, 0.7024709639013442, 0.5925026402964927, 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0.7525262214051114, 0.0930563708211101, -0.6519545980720968, 0.7609618011718721, 0, 0.6487966839906476, 0.7658127312019672, -0.5563955177061672, 0.32242036009760555, 0.7658127312019672, 0.5563955177061672, 0.32242036009760555, 0.7699505391839694, -0.5594018111778118, -0.3069947570583225, 0.7699505391839695, 0.5594018111778118, -0.3069947570583225, 0.7868988425360585, -0.19647727299831622, -0.5849674288458774, 0.7868988425360585, 0.19647727299831622, -0.5849674288458774, 0.794654472291766, -0.5773502691896257, 0.1875924740850802, 0.794654472291766, 0.5773502691896257, 0.1875924740850802, 0.7977502805111361, 0.5795995055195465, -0.16630966041063483, 0.7977502805111362, -0.5795995055195466, -0.16630966041063486, 0.7987224860367548, -0.46528185410555045, 0.38151695445860245, 0.7987224860367548, 0.46528185410555045, 0.38151695445860245, 0.8061011971354436, -0.585666801594933, 0.08482486360947541, 0.8061011971354436, 0.585666801594933, 0.08482486360947541, 0.8081338527952605, 0, -0.5889988760314302, 0.8085531618609739, 0.5874482582451998, -0.033857470804871996, 0.808553161860974, -0.5874482582451999, -0.033857470804872, 0.8097861540334745, -0.30622016907826805, -0.5004753668117452, 0.8097861540334745, 0.306220169078268, -0.5004753668117451, 0.816622529093059, -0.41576019618739724, -0.4003387368765019, 0.8166225290930591, 0.41576019618739724, -0.4003387368765019, 0.8234755272545975, -0.35543072586240004, 0.4422183342260814, 0.8234755272545975, 0.35543072586240004, 0.4422183342260814, 0.8295223498394129, -0.08877540026300262, 0.5513724688674999, 0.8295223498394129, 0.08877540026300262, 0.5513724688674999, 0.8351224597613233, -0.22824303804682877, 0.5004753668117452, 0.8351224597613233, 0.22824303804682877, 0.5004753668117452, 0.8352523372260013, -0.4959488176483333, 0.2374622147452561, 0.8352523372260013, 0.4959488176483333, 0.2374622147452561, 0.8468638011056542, -0.09425480719114633, -0.5233906129252252, 0.8468638011056542, 0.09425480719114633, -0.5233906129252252, 0.8556199616698322, -0.44728212428674363, -0.2604864343601271, 0.8556199616698322, 0.44728212428674363, -0.2604864343601271, 0.8683018636018623, -0.48193280435927155, 0.1174420952978156, 0.8683018636018623, 0.48193280435927155, 0.1174420952978156, 0.8706672771858278, -0.39628066808369156, 0.2913762593983249, 0.8706672771858278, 0.39628066808369156, 0.2913762593983249, 0.875122634874367, -0.4680021862650972, -0.12302165492966767, 0.875122634874367, -0.19647727299831622, -0.4422183342260814, 0.875122634874367, 0.19647727299831622, -0.4422183342260814, 0.875122634874367, 0.4680021862650972, -0.12302165492966767, 0.8778809630980393, -0.47885859563629063, 0.004411350734000925, 0.8778809630980393, 0.47885859563629063, 0.004411350734000925, 0.8880554375372868, -0.30166881041813615, -0.3469199744629367, 0.8880554375372868, 0.3016688104181361, -0.34691997446293665, 0.8882250561447018, 0, -0.45940858681215474, 0.8882250561447018, 0, -0.45940858681215463, 0.8944271909999159, 0, 0.447213595499958, 0.895768418755139, -0.2779306951014105, 0.3469199744629367, 0.895768418755139, 0.2779306951014105, 0.3469199744629367, 0.905039215834912, -0.14364161499041464, 0.4003387368765019, 0.905039215834912, 0.14364161499041464, 0.4003387368765019, 0.9081168108377711, -0.38580222481518056, 0.1627283048565699, 0.9081168108377711, 0.38580222481518056, 0.1627283048565699, 0.9192345310435216, -0.3322397296317068, -0.21124544726797656, 0.9192345310435216, 0.3322397296317068, -0.21124544726797656, 0.9196658769956818, -0.0930563708211101, -0.38151695445860245, 0.9196658769956819, 0.0930563708211101, -0.38151695445860245, 0.9282706578194226, -0.36974306703169696, 0.040045601674720765, 0.9282706578194226, 0.36974306703169696, 0.040045601674720765, 0.931509891817533, 0.35476868706133874, -0.0801779279282143, 0.9315098918175331, -0.3547686870613388, -0.08017792792821432, 0.9373125561577, -0.19116759016150822, -0.2913762593983249, 0.9373125561577, 0.19116759016150822, -0.2913762593983249, 0.9389619707336497, -0.271524913266781, 0.21124544726797656, 0.9389619707336497, 0.271524913266781, 0.21124544726797656, 0.9465965938004058, 0, -0.32242036009760555, 0.9517112057440018, 0, 0.3069947570583225, 0.9551169259871324, -0.14106195520847561, 0.2604864343601271, 0.9551169259871324, 0.14106195520847561, 0.2604864343601271, 0.9614507908933246, -0.22165711242617028, -0.16272830485656992, 0.9614507908933246, 0.22165711242617028, -0.16272830485656992, 0.9621351351385714, -0.2605138798701924, 0.0801779279282143, 0.9621351351385714, 0.2605138798701924, 0.0801779279282143, 0.967244736312809, -0.08971798394659967, -0.2374622147452561, 0.967244736312809, 0.08971798394659967, -0.2374622147452561, 0.9683162594941432, -0.24649537802113122, -0.04004560167472076, 0.9683162594941432, 0.24649537802113122, -0.04004560167472076, 0.9822469463768458, 0, -0.1875924740850802, 0.9830738669028043, -0.13576245663339054, 0.1230216549296677, 0.9830738669028043, 0.13576245663339054, 0.1230216549296677, 0.9857439588996775, -0.12048320108981783, -0.11744209529781555, 0.9857439588996775, 0.12048320108981783, -0.11744209529781555, 0.98607357578129, 0, 0.16630966041063486, 0.9916866386330564, -0.12860074160506021, -0.004411350734000926, 0.9916866386330564, 0.12860074160506021, -0.004411350734000926, 0.9963958764033671, 0, -0.08482486360947544, 0.9994266714825543, 0, 0.033857470804872}; float* get_dti_dirarr(unsigned int ndir) { if(ndir==3) return ps3; if(ndir==4) return ps4; if(ndir==5) return ps5; if(ndir==6) return ps6; if(ndir==7) return ps7; if(ndir==8) return ps8; if(ndir==9) return ps9; if(ndir==10) return ps10; if(ndir==11) return ps11; if(ndir==12) return ps12; if(ndir==13) return ps13; if(ndir==14) return ps14; if(ndir==15) return ps15; if(ndir==16) return ps16; if(ndir==17) return ps17; if(ndir==18) return ps18; if(ndir==19) return ps19; if(ndir==20) return ps20; if(ndir==21) return ps21; if(ndir==22) return ps22; if(ndir==23) return ps23; if(ndir==24) return ps24; if(ndir==25) return ps25; if(ndir==26) return ps26; if(ndir==27) return ps27; if(ndir==28) return ps28; if(ndir==29) return ps29; if(ndir==30) return ps30; if(ndir==31) return ps31; if(ndir==32) return ps32; if(ndir==33) return ps33; if(ndir==34) return ps34; if(ndir==35) return ps35; if(ndir==36) return ps36; if(ndir==37) return ps37; if(ndir==38) return ps38; if(ndir==39) return ps39; if(ndir==40) return ps40; if(ndir==41) return ps41; if(ndir==42) return ps42; if(ndir==43) return ps43; if(ndir==44) return ps44; if(ndir==45) return ps45; if(ndir==46) return ps46; if(ndir==47) return ps47; if(ndir==48) return ps48; if(ndir==49) return ps49; if(ndir==50) return ps50; if(ndir==51) return ps51; if(ndir==52) return ps52; if(ndir==53) return ps53; if(ndir==54) return ps54; if(ndir==55) return ps55; if(ndir==56) return ps56; if(ndir==57) return ps57; if(ndir==58) return ps58; if(ndir==59) return ps59; if(ndir==60) return ps60; if(ndir==61) return ps61; if(ndir==62) return ps62; if(ndir==63) return ps63; if(ndir==64) return ps64; if(ndir==65) return ps65; if(ndir==66) return ps66; if(ndir==67) return ps67; if(ndir==68) return ps68; if(ndir==69) return ps69; if(ndir==70) return ps70; if(ndir==71) return ps71; if(ndir==72) return ps72; if(ndir==73) return ps73; if(ndir==74) return ps74; if(ndir==75) return ps75; if(ndir==76) return ps76; if(ndir==77) return ps77; if(ndir==78) return ps78; if(ndir==79) return ps79; if(ndir==80) return ps80; if(ndir==81) return ps81; if(ndir==82) return ps82; if(ndir==83) return ps83; if(ndir==84) return ps84; if(ndir==85) return ps85; if(ndir==86) return ps86; if(ndir==87) return ps87; if(ndir==88) return ps88; if(ndir==89) return ps89; if(ndir==90) return ps90; if(ndir==91) return ps91; if(ndir==92) return ps92; if(ndir==93) return ps93; if(ndir==94) return ps94; if(ndir==95) return ps95; if(ndir==96) return ps96; if(ndir==97) return ps97; if(ndir==98) return ps98; if(ndir==99) return ps99; if(ndir==100) return ps100; if(ndir==101) return ps101; if(ndir==102) return ps102; if(ndir==103) return ps103; if(ndir==104) return ps104; if(ndir==105) return ps105; if(ndir==106) return ps106; if(ndir==107) return ps107; if(ndir==108) return ps108; if(ndir==109) return ps109; if(ndir==110) return ps110; if(ndir==111) return ps111; if(ndir==112) return ps112; if(ndir==113) return ps113; if(ndir==114) return ps114; if(ndir==115) return ps115; if(ndir==116) return ps116; if(ndir==117) return ps117; if(ndir==118) return ps118; if(ndir==119) return ps119; if(ndir==120) return ps120; if(ndir==121) return ps121; if(ndir==122) return ps122; if(ndir==123) return ps123; if(ndir==124) return ps124; if(ndir==125) return ps125; if(ndir==126) return ps126; if(ndir==127) return ps127; if(ndir==128) return ps128; if(ndir==129) return ps129; if(ndir==130) return ps130; if(ndir==131) return ps131; if(ndir==132) return ps132; if(ndir==133) return ps133; if(ndir==134) return ps134; if(ndir==135) return ps135; if(ndir==136) return ps136; if(ndir==137) return ps137; if(ndir==138) return ps138; if(ndir==139) return ps139; if(ndir==140) return ps140; if(ndir==141) return ps141; if(ndir==142) return ps142; if(ndir==143) return ps143; if(ndir==144) return ps144; if(ndir==145) return ps145; if(ndir==146) return ps146; if(ndir==147) return ps147; if(ndir==148) return ps148; if(ndir==149) return ps149; if(ndir==150) return ps150; // if(ndir==246) return ps246; // if(ndir==256) return ps256; // if(ndir==755) return ps755; return 0; } odin-1.8.5/odinseq/seqloop.cpp0000644000175000017500000003433511455553540013246 00000000000000#include "seqloop.h" #include "seqdelay.h" SeqObjLoop::SeqObjLoop(const STD_string& object_label) : SeqCounter(object_label), SeqObjList(object_label), times(0), numof_acq_cache(0), is_toplevel_reploop(false) { } SeqObjLoop::SeqObjLoop(const SeqObjLoop& sl) : numof_acq_cache(0), is_toplevel_reploop(false) { SeqObjLoop::operator = (sl); } SeqObjLoop& SeqObjLoop::operator = (const SeqObjLoop& sl) { SeqObjList::operator = ((const SeqObjList&)sl); // cast is necessary to avoid calling SeqObjList::operator = (const SeqObjLoop&) SeqCounter::operator = (sl); times=sl.times; return *this; } double SeqObjLoop::get_preduration() const { counterdriver->update_driver(this,this,&vectors); return counterdriver->get_preduration(); } double SeqObjLoop::get_postduration() const { counterdriver->update_driver(this,this,&vectors); return counterdriver->get_postduration(); } float SeqObjLoop::get_single_duration() const { counterdriver->update_driver(this,this,&vectors); // required for correct preduration/postduration_inloop return counterdriver->get_preduration_inloop()+SeqObjList::get_duration()+counterdriver->get_postduration_inloop(); } STD_string SeqObjLoop::get_program(programContext& context) const { Log odinlog(this,"SeqObjLoop::get_program"); STD_string result; if(!get_times()) return result; counterdriver->outdate_cache(); counterdriver->update_driver(this,this,&vectors); if(unroll_program(context)) { ODINLOG(odinlog,normalDebug) << "unrolling loop in program" << STD_endl; // retrieve kernel with counter set to 1st iteration so that can be used later to avoid multiple get_program() calls init_counter(); prep_veciterations(); STD_string loopkernel=SeqObjList::get_program(context); // do we actually have to create a program? if(!counterdriver->create_program(context,loopkernel)) { return result; } result+=counterdriver->get_program_head_unrolled(context, 0); result+=loopkernel; // retrieve remaining loop kernels increment_counter(); for(; get_counter()get_program_head_unrolled(context, get_counter()); result+=SeqObjList::get_program(context); } disable_counter(); prep_veciterations(); // Reset to default iteration if outside loop } else { // unroll_program ODINLOG(odinlog,normalDebug) << "loop command in program" << STD_endl; context.nestlevel++; context.neststatus=true; disable_counter(); // retrieve kernel with counter disabled so that can be used later with loop commands ODINLOG(odinlog,normalDebug) << "retrieving initial loopkernel" << STD_endl; STD_string loopkernel=SeqObjList::get_program(context); // do we actually have to create a program? if(!counterdriver->create_program(context,loopkernel)) { context.nestlevel--; context.neststatus=false; return result; } result+=counterdriver->get_program_head(context,loopkernel,get_times()); result+=loopkernel; context.nestlevel--; result+=counterdriver->get_program_tail(context,loopkernel,get_times()); context.neststatus=false; } return result; } double SeqObjLoop::get_duration() const { Log odinlog(this,"get_duration"); double result=0.0; counterdriver->update_driver(this,this,&vectors); result+=counterdriver->get_preduration(); result+=counterdriver->get_postduration(); double preduration_inloop =counterdriver->get_preduration_inloop(); double postduration_inloop=counterdriver->get_postduration_inloop(); if(!is_repetition_loop(true)) { ODINLOG(odinlog,normalDebug) << "is vector loop" << STD_endl; for(init_counter(); get_counter()set_times(t); } times=t; return *this; } int SeqObjLoop::get_times() const { Log odinlog(this,"get_times"); if(n_vectors()) { return SeqCounter::get_times(); } else { ODINLOG(odinlog,normalDebug) << "times=" << times << STD_endl; return times; } } unsigned int SeqObjLoop::get_numof_acq() const { if(numof_acq_cache) return numof_acq_cache; queryContext context; context.action=count_acqs; unsigned int result=0; if(is_obj_repetition_loop()) { SeqObjList::query(context); result=context.numof_acqs*get_times(); } else { for(init_counter(); get_counter() odinlog(this,"query"); if(context.action==tag_toplevel_reploop) { if(is_repetition_loop() && get_times()>1 && context.repetitions_prot==get_times()) { if(get_numof_acq()) is_toplevel_reploop=true; // do not tag dummy loops } return; // do not query sub-branch } SeqObjList::query(context); // default if(context.action==count_acqs) context.numof_acqs=get_numof_acq(); } bool SeqObjLoop::contains_acq_iter() const { queryContext qc; qc.action=check_acq_iter; SeqObjList::query(qc); return qc.check_acq_iter_result; } RecoValList SeqObjLoop::get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const { Log odinlog(this,"get_recovallist"); RecoValList result(get_label()); if(!contains_acq_iter() && is_acq_repetition_loop()) { unsigned int totaltimes=reptimes*get_times(); ODINLOG(odinlog,normalDebug) << "repetition loop reptimes/get_times()/totaltimes=" << reptimes << "/" << get_times() << "/" << totaltimes << STD_endl; for(constiter it=get_const_begin();it!=get_const_end();++it) { result.add_sublist((*it)->get_recovallist(totaltimes,coords)); } result.multiply_repetitions(get_times()); } else { ODINLOG(odinlog,normalDebug) << "explicit loop reptimes/get_times()=" << reptimes << "/" << get_times() << STD_endl; RecoValList* thisiter; for(init_counter(); get_counter()get_label() << STD_endl; thisiter->add_sublist((*it)->get_recovallist(reptimes,coords)); } result.add_sublist(*thisiter); delete thisiter; } disable_counter(); } return result; } SeqObjLoop& SeqObjLoop::operator () (const SeqObjBase& embeddedBody) { Log odinlog(this,"operator () (const SeqObjBase&)"); ODINLOG(odinlog,normalDebug) << " label=" << get_label() << STD_endl; SeqObjLoop& loop=set_embed_body(embeddedBody); ODINLOG(odinlog,normalDebug) << " loop.label=" << loop.get_label() << STD_endl; return loop; } unsigned int SeqObjLoop::event(eventContext& context) const { Log odinlog(this,"event"); unsigned int result=0; looplevel++; counterdriver->update_driver(this,this,&vectors); double predur=counterdriver->get_preduration(); ODINLOG(odinlog,normalDebug) << "predur=" << predur << STD_endl; if(predur) { SeqDelay sd("predelay",predur); result+=sd.event(context); } int niterations=get_times(); ODINLOG(odinlog,normalDebug) << "niterations=" << niterations << STD_endl; // within fSEQCheck it is sufficient to call the loop kernel for only one iteration: if( context.action==seqRun && context.seqcheck && is_repetition_loop(true) ) { niterations=1; } // to count events, is is sufficient to call the loop kernel for only one iteration: unsigned count_factor=1; if(context.action==countEvents && is_obj_repetition_loop()) { niterations=1; count_factor=get_times(); } unsigned int n_events=0; for(init_counter(); get_counter()get_postduration_inloop(); if(postdur_inloop) { SeqDelay sd("postdelay_inloop",postdur_inloop); n_events+=sd.event(context); } } disable_counter(); prep_veciterations(); // Reset to default iteration if outside loop result+=n_events*count_factor; looplevel--; double postdur=counterdriver->get_postduration(); ODINLOG(odinlog,normalDebug) << "postdur=" << postdur << STD_endl; if(postdur) { SeqDelay sd("postdelay",postdur); result+=sd.event(context); } return result; } SeqValList SeqObjLoop::get_freqvallist(freqlistAction action) const { Log odinlog(this,"get_freqvallist"); SeqValList result(get_label()+STD_string("freqlist")); if(is_repetition_loop()) { for(constiter it=get_const_begin();it!=get_const_end();++it) { result.add_sublist((*it)->get_freqvallist(action)); } result.multiply_repetitions(get_times()); } else { SeqValList* thisiter; for(init_counter(); get_counter()add_sublist((*it)->get_freqvallist(action)); } result.add_sublist(*thisiter); delete thisiter; } disable_counter(); } return result; } SeqValList SeqObjLoop::get_delayvallist() const { Log odinlog(this,"get_delayvallist"); SeqValList result(get_label()+STD_string("delaylist")); if(is_repetition_loop()) { for(constiter it=get_const_begin();it!=get_const_end();++it) { result.add_sublist((*it)->get_delayvallist()); } result.multiply_repetitions(get_times()); } else { SeqValList* thisiter; for(init_counter(); get_counter()add_sublist((*it)->get_delayvallist()); } result.add_sublist(*thisiter); delete thisiter; } disable_counter(); } return result; } double SeqObjLoop::get_rf_energy() const { double result=0.0; if(is_repetition_loop(true)) result=SeqObjList::get_rf_energy()*get_times(); else { for(init_counter(); get_counter()outdate_cache(); return *this; } SeqObjLoop& SeqObjLoop::operator [] (unsigned int t) { set_times(t); counterdriver->outdate_cache(); return *this; } bool SeqObjLoop::is_repetition_loop(bool only_qualvectors) const { Log odinlog(this,"is_repetition_loop"); if(only_qualvectors) { bool result=true; for(veciter=get_vecbegin(); veciter!=get_vecend(); ++veciter) { if((*veciter)->is_qualvector()) { ODINLOG(odinlog,normalDebug) << (*veciter)->get_label() << " alters" << STD_endl; result=false; } else ODINLOG(odinlog,normalDebug) << (*veciter)->get_label() << " NOT alters" << STD_endl; } ODINLOG(odinlog,normalDebug) << result << STD_endl; return result; } else return !(n_vectors()); } bool SeqObjLoop::is_acq_repetition_loop() const { Log odinlog(this,"is_acq_repetition_loop"); if(is_repetition_loop()) { ODINLOG(odinlog,normalDebug) << "is_repetition_loop()==true" << STD_endl; return true; } bool result=true; for(veciter=get_vecbegin(); veciter!=get_vecend(); ++veciter) { if((*veciter)->is_acq_vector()) { ODINLOG(odinlog,normalDebug) << (*veciter)->get_label() << " is acq vector" << STD_endl; result=false; break; } else ODINLOG(odinlog,normalDebug) << (*veciter)->get_label() << " is NOT acq vector" << STD_endl; } ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } bool SeqObjLoop::is_obj_repetition_loop() const { for(veciter=get_vecbegin(); veciter!=get_vecend(); ++veciter) { if((*veciter)->is_obj_vector()) return false; } return true; } bool SeqObjLoop::unroll_program(programContext& context) const { return counterdriver->unroll_program(this,this,&vectors,context); } SeqObjLoop& SeqObjLoop::set_body(const SeqObjBase& so) { clear(); (*this)+=(so); counterdriver->outdate_cache(); return *this; } bool SeqObjLoop::prep() { Log odinlog(this,"prep"); if(!SeqObjList::prep()) return false; if(!SeqCounter::prep()) return false; for(constinstiter it=get_const_inst_begin();it!=get_const_inst_begin();++it) { if((*it)->get_times()==0) { ODINLOG(odinlog,warningLog) << "loop " << (*it)->get_label() << " has 0 iterations" << STD_endl; } } // reset for next prep_acquisition numof_acq_cache=0; is_toplevel_reploop=false; return true; } void SeqObjLoop::clear_container() { SeqObjList::clear_container(); SeqCounter::clear_container(); Embed::clear_instances(); } STD_string SeqObjLoop::get_properties() const { return "Times="+itos(get_times())+", NumOfVectors="+itos(n_vectors())+", "+SeqObjList::get_properties(); } void SeqObjLoop::add_vector(const SeqVector& seqvector) { Log odinlog(this,"add_vector"); for(institer it=get_inst_begin();it!=get_inst_end();++it) { (*it)->add_vector(seqvector); } SeqCounter::add_vector(seqvector); } odin-1.8.5/odinseq/seqparallel.cpp0000644000175000017500000001526411322062345014060 00000000000000#include "seqparallel.h" #include "seqdelay.h" #include "seqgradchan.h" #include "seqgradchanparallel.h" #include SeqParallel::SeqParallel(const STD_string& object_label) : SeqObjBase(object_label), pardriver(object_label) { } SeqParallel::SeqParallel(const SeqParallel& sgp) : pardriver(sgp.get_label()) { SeqParallel::operator = (sgp); } SeqParallel& SeqParallel::operator = (const SeqParallel& sgp) { SeqObjBase::operator = (sgp); pardriver=sgp.pardriver; pulsptr=sgp.pulsptr; gradptr=sgp.gradptr; return *this; } SeqParallel& SeqParallel::operator /= (SeqGradChan& sgc) { SeqGradChanParallel* sgcp=new SeqGradChanParallel(sgc.get_label()); sgcp->set_temporary(); (*sgcp)+=sgc; set_gradptr((SeqGradObjInterface*)sgcp); return *this; } SeqParallel& SeqParallel::operator /= (SeqGradChanList& sgcl) { SeqGradChanParallel* sgcp=new SeqGradChanParallel(sgcl.get_label()); sgcp->set_temporary(); (*sgcp)+=sgcl; set_gradptr((SeqGradObjInterface*)sgcp); return *this; } SeqParallel& SeqParallel::operator /= (SeqGradChanParallel& sgcp) { set_gradptr((SeqGradObjInterface*)&sgcp); return *this; } SeqParallel& SeqParallel::operator /= (SeqGradObjInterface& sgoa) { set_gradptr((SeqGradObjInterface*)&sgoa); return *this; } SeqParallel& SeqParallel::operator /= (const SeqObjBase& soa) { SeqObjList* sol=new SeqObjList(soa.get_label()); sol->set_temporary(); (*sol)+=soa; set_pulsptr(sol); return *this; } double SeqParallel::get_duration() const { Log odinlog(this,"SeqParallel::get_duration()"); const SeqObjBase* soa=get_pulsptr(); const SeqGradObjInterface* sgoa=get_const_gradptr(); double result=0.0; if(soa) result=soa->get_duration(); double graddur=0.0; if(sgoa) graddur=sgoa->get_gradduration(); if(graddur>result) result=graddur; double dur_driver=pardriver->get_duration(soa,sgoa); if(dur_driver>result) result=dur_driver; return result; } double SeqParallel::get_gradduration() const { Log odinlog(this,"SeqParallel::get_gradduration()"); double result=0.0; const SeqGradObjInterface* sgoa=get_const_gradptr(); if(sgoa) { result=sgoa->get_gradduration(); ODINLOG(odinlog,normalDebug) << "gradduration=" << result << STD_endl; } else ODINLOG(odinlog,normalDebug) << "no gradobject defined" << STD_endl; return result; } double SeqParallel::get_pulprogduration() const { return pardriver->get_predelay(get_pulsptr(),get_const_gradptr()); } SeqGradInterface& SeqParallel::set_strength(float gradstrength) { SeqGradObjInterface* sgoa=get_gradptr(); if(sgoa) sgoa->set_strength(gradstrength); return *this; } SeqGradInterface& SeqParallel::invert_strength() { SeqGradObjInterface* sgoa=get_gradptr(); if(sgoa) sgoa->invert_strength(); return *this; } float SeqParallel::get_strength() const { float result=0.0; const SeqGradObjInterface* sgoa=get_const_gradptr(); if(sgoa) result=sgoa->get_strength(); return result; } SeqGradInterface& SeqParallel::set_gradrotmatrix(const RotMatrix& matrix) { SeqGradObjInterface* sgoa=get_gradptr(); if(sgoa) sgoa->set_gradrotmatrix(matrix); return *this; } fvector SeqParallel::get_gradintegral() const { fvector result(3); const SeqGradObjInterface* sgoa=get_const_gradptr(); if(sgoa) result=sgoa->get_gradintegral(); return result; } void SeqParallel::query(queryContext& context) const { SeqTreeObj::query(context); // default context.parentnode=this; const SeqObjBase* soa=get_pulsptr(); context.treelevel++; if(soa) soa->query(context); if(context.action!=count_acqs) { context.parentnode=this; // reset to this because it might changed by last query const SeqGradObjInterface* sgoa=get_const_gradptr(); if(sgoa) sgoa->query(context); } context.treelevel--; } RecoValList SeqParallel::get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const { RecoValList result(get_label()); const SeqObjBase* soa=get_pulsptr(); if(soa) result=soa->get_recovallist(reptimes,coords); return result; } STD_string SeqParallel::get_properties() const { STD_string result; if(get_pulsptr()) result+="RF"; else result+="-"; result+="/"; if(get_const_gradptr()) result+="Grad"; else result+="-"; return result; } unsigned int SeqParallel::event(eventContext& context) const { Log odinlog(this,"event"); unsigned int result=0; double startelapsed=context.elapsed; ODINLOG(odinlog,normalDebug) << "startelapsed=" << startelapsed << STD_endl; const SeqObjBase* soa=get_pulsptr(); const SeqGradObjInterface* sgoa=get_const_gradptr(); double starteleapsed_pre=startelapsed+pardriver->get_predelay(soa,sgoa); bool flush_cache=context.noflush; context.noflush=true; context.elapsed=starteleapsed_pre; if(sgoa) result+=sgoa->event(context); context.elapsed=starteleapsed_pre; if(soa) result+=soa->event(context); context.noflush=flush_cache; context.elapsed=startelapsed+get_duration(); return result; } SeqValList SeqParallel::get_freqvallist(freqlistAction action) const { const SeqObjBase* soa=get_pulsptr(); if(soa) return soa->get_freqvallist(action); else return SeqValList(); } SeqValList SeqParallel::get_delayvallist() const { const SeqObjBase* soa=get_pulsptr(); if(soa) return soa->get_delayvallist(); else return SeqValList(); } double SeqParallel::get_rf_energy() const { double result=0.0; const SeqObjBase* soa=get_pulsptr(); if(soa) result=soa->get_rf_energy(); return result; } void SeqParallel::clear() { pulsptr.clear_handledobj(); gradptr.clear_handledobj(); const_gradptr.clear_handledobj(); } SeqParallel& SeqParallel::set_pulsptr(const SeqObjBase* pptr) { pulsptr.set_handled(pptr); return *this; } const SeqObjBase* SeqParallel::get_pulsptr() const {return pulsptr.get_handled();} SeqParallel& SeqParallel::set_gradptr(SeqGradObjInterface* gptr) { gradptr.set_handled(gptr); return *this; } SeqParallel& SeqParallel::set_gradptr(const SeqGradObjInterface* gptr) { const_gradptr.set_handled(gptr); return *this; } SeqParallel& SeqParallel::clear_gradptr() { gradptr.clear_handledobj(); const_gradptr.clear_handledobj(); return *this; } SeqGradObjInterface* SeqParallel::get_gradptr() const {return gradptr.get_handled();} const SeqGradObjInterface* SeqParallel::get_const_gradptr() const { if(gradptr.get_handled()) return gradptr.get_handled(); else return const_gradptr.get_handled(); } // Template instantiations template class Handled; template class Handler; template class Handled; template class Handler; template class Handled; template class Handler; odin-1.8.5/odinseq/seqclass.cpp0000644000175000017500000001275311455553540013402 00000000000000#include "seqclass.h" #include "seqplatform.h" #include "seqvec.h" #include #include const char* Seq::get_compName() {return "Seq";} LOGGROUNDWORK(Seq) /////////////////////////////////////////////////////////////////////////// SeqClass::SeqClass() : systemInfo(*systemInfo_ptr) { Log odinlog("SeqClass","SeqClass"); set_label("unnamedSeqClass"); // Do NOT use the MessageHandlers in here if(allseqobjs) allseqobjs->push_back(this); } SeqClass::~SeqClass() { Log odinlog(this,"~SeqClass"); if(allseqobjs) allseqobjs->remove(this); if(tmpseqobjs) tmpseqobjs->remove(this); if(seqobjs2prep) seqobjs2prep->remove(this); if(seqobjs2clear) seqobjs2clear->remove(this); } SeqClass& SeqClass::operator = (const SeqClass& sc) { Labeled::operator = (sc); return *this; } void SeqClass::marshall_error() const { Log odinlog(this, "marshall_error"); ODINLOG(odinlog,errorLog) << "Marshalling error: No sub-object available" << STD_endl; } bool SeqClass::prep_all() { Log odinlog("SeqClass","prep_all"); bool result=true; STD_list< SeqClass* >::iterator it; // two stage iteration through the list because prep() may modify the 'allseqobjs' list seqobjs2prep->clear(); for(it=allseqobjs->begin(); it!=allseqobjs->end(); ++it) { (*it)->prepped=false; seqobjs2prep->push_back(*it); } while(seqobjs2prep->begin()!=seqobjs2prep->end()) { ODINLOG(odinlog,normalDebug) << "seqobjs2prep->size()=" << seqobjs2prep->size() << STD_endl; SeqClass* scs=*(seqobjs2prep->begin()); bool do_prep=true; if(scs->prepped) do_prep=false; if(do_prep) { ODINLOG(odinlog,normalDebug) << "prepping " << scs->get_label() << STD_endl; if(!(scs->prep())) { result=false; ODINLOG(odinlog,errorLog) << scs->get_label() << "->prep() failed" << STD_endl; } scs->prepped=true; } seqobjs2prep->remove(scs); } return result; } void SeqClass::init_static() { Log odinlog("SeqClass","init_static"); allseqobjs.init("allseqobjs"); tmpseqobjs.init("tmpseqobjs"); seqobjs2prep.init("seqobjs2prep"); seqobjs2clear.init("seqobjs2clear"); ODINLOG(odinlog,normalDebug) << "seqobjs done" << STD_endl; geometryInfo.init("geometryInfo"); ODINLOG(odinlog,normalDebug) << "geometryInfo done" << STD_endl; studyInfo.init("studyInfo"); ODINLOG(odinlog,normalDebug) << "studyInfo done" << STD_endl; recoInfo.init("recoInfo"); ODINLOG(odinlog,normalDebug) << "recoInfo done" << STD_endl; systemInfo_ptr=new SystemInterface(); // create systemInfo_platform ODINLOG(odinlog,normalDebug) << "systemInfo_ptr done" << STD_endl; SeqPlatformProxy(); // create platform instances } void SeqClass::destroy_static() { Log odinlog("SeqClass","destroy_static"); delete systemInfo_ptr; recoInfo.destroy(); geometryInfo.destroy(); studyInfo.destroy(); seqobjs2clear.destroy(); seqobjs2prep.destroy(); tmpseqobjs.destroy(); allseqobjs.destroy(); } SeqClass& SeqClass::set_temporary() { if(tmpseqobjs) tmpseqobjs->push_back(this); return *this; } void SeqClass::clear_temporary() { Log odinlog("SeqClass","clear_temporary"); if(!tmpseqobjs) return; STD_list garbage; STD_list::iterator it; for(it=tmpseqobjs->begin(); it!=tmpseqobjs->end(); ++it) { ODINLOG(odinlog,normalDebug) << "tmpobj >" << (*it)->get_label() << "<" << STD_endl; garbage.push_back(*it); } tmpseqobjs->erase(tmpseqobjs->begin(),tmpseqobjs->end()); for(it=garbage.begin(); it!=garbage.end(); ++it) { ODINLOG(odinlog,normalDebug) << "deleting >" << (*it)->get_label() << "<(" << (void*)(*it) << ")" << STD_endl; allseqobjs->remove(*it); delete (*it); } } void SeqClass::clear_containers() { Log odinlog("SeqClass","clear_containers"); STD_list< SeqClass*>::iterator it; // two stage iteration through the list because clear_container() may modify the 'allseqobjs' list seqobjs2clear->clear(); for(it=allseqobjs->begin(); it!=allseqobjs->end(); ++it) seqobjs2clear->push_back(*it); while(seqobjs2clear->begin()!=seqobjs2clear->end()) { SeqClass* scs=*(seqobjs2clear->begin()); ODINLOG(odinlog,normalDebug) << "clearing >" << scs->get_label() << "<" << STD_endl; scs->clear_container(); ODINLOG(odinlog,normalDebug) << "removing >" << scs->get_label() << "<" << STD_endl; seqobjs2clear->remove(scs); } } void SeqClass::clear_objlists() { if(allseqobjs) allseqobjs->clear(); if(tmpseqobjs) tmpseqobjs->clear(); if(seqobjs2prep) seqobjs2prep->clear(); if(seqobjs2clear) seqobjs2clear->clear(); } SystemInterface* SeqClass::systemInfo_ptr; template class SingletonHandler; SingletonHandler SeqClass::geometryInfo; template class SingletonHandler; SingletonHandler SeqClass::studyInfo; template class SingletonHandler; SingletonHandler SeqClass::recoInfo; template class SingletonHandler; SingletonHandler SeqClass::allseqobjs; SingletonHandler SeqClass::tmpseqobjs; SingletonHandler SeqClass::seqobjs2prep; SingletonHandler SeqClass::seqobjs2clear; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; SeqVector& SeqClass::get_dummyvec() { if(!dummyvec) dummyvec=new SeqVector("dummyvec"); return *dummyvec; } SeqVector* SeqClass::dummyvec=0; odin-1.8.5/odinseq/seqgradphase.h0000644000175000017500000001576511455553540013706 00000000000000/*************************************************************************** seqgradphase.h - description ------------------- begin : Tue Mar 21 2006 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADPHASE_H #define SEQGRADPHASE_H #include #include #define DEFAULT_ACL_BANDS 4 /** * @addtogroup odinseq * @{ */ /** * \brief Phase Encoding * * A phase encoding gradient * */ class SeqGradPhaseEnc : public SeqGradVectorPulse { public: /** * Constructs a phase encoding gradient labeled 'object_label' with the following properties: * - nsteps: The number of phase encoding steps * - fov: The Field of View * - gradchannel: The channel this object should be played out * - gradstrength: The maximum gradient strength * - scheme: The phase encoding scheme * - reorder: The reordering scheme * - nsegments: The number of segments for segmented reordering * - reduction: Reduction factor for parallel imaging (sparsely sampled k-space) * - acl_bands: Number of autocalibration bands (bunch of adjacent lines between actual k-space lines) for GRAPPA * - partial_fourier: The amount of partial Fourier undersampling (0=no undersampling, 1=half fourier) * - nucleus: The nucleus this object should be calculated for */ SeqGradPhaseEnc(const STD_string& object_label, unsigned int nsteps, float fov, direction gradchannel, float gradstrength, encodingScheme scheme=linearEncoding, reorderScheme reorder=noReorder, unsigned int nsegments=1, unsigned int reduction=1, unsigned int acl_bands=DEFAULT_ACL_BANDS, float partial_fourier=0.0, const STD_string& nucleus=""); /** * Constructs a phase encoding gradient labeled 'object_label' with the following properties: * - nsteps: The number of phase encoding steps * - fov: The Field of View * - gradduration: The duration of the gradient * - gradchannel: The channel this object should be played out * - scheme: The phase encoding scheme * - reorder: The reordering scheme * - nsegments: The number of segments for segmented reordering * - reduction: Reduction factor for parallel imaging (sparsely sampled k-space) * - acl_bands: Number of autocalibration bands (bunch of adjacent lines between actual k-space lines) for GRAPPA * - partial_fourier: The amount of partial Fourier undersampling (0=no undersampling, 1=half fourier) * - nucleus: The nucleus this object should be calculated for */ SeqGradPhaseEnc(const STD_string& object_label, unsigned int nsteps, float fov, float gradduration, direction gradchannel, encodingScheme scheme=linearEncoding, reorderScheme reorder=noReorder, unsigned int nsegments=1, unsigned int reduction=1, unsigned int acl_bands=DEFAULT_ACL_BANDS, float partial_fourier=0.0, const STD_string& nucleus=""); /** * Constructs an empty phase encoding gradient labeled 'object_label' */ SeqGradPhaseEnc(const STD_string& object_label="unnamedSeqGradPhaseEnc") : SeqGradVectorPulse(object_label) {} /** * Constructs a copy of 'sgpe' */ SeqGradPhaseEnc(const SeqGradPhaseEnc& sgpe) {SeqGradPhaseEnc::operator = (sgpe);} /** * Assignment operator that makes this object become a copy of 'sgpe' */ SeqGradPhaseEnc& operator = (const SeqGradPhaseEnc& sgpe) {SeqGradVectorPulse::operator = (sgpe); return *this;} private: void init_encoding(unsigned int nsteps,encodingScheme scheme, reorderScheme reorder, unsigned int nsegments, unsigned int reduction, unsigned int acl_bands, float partial_fourier); }; /////////////////////////////////////////////////////////////////////////////////////////////////// /** * \brief Flow-Compensated Phase Encoding * * A phase encoding gradient with 1st order flow compensation * */ class SeqGradPhaseEncFlowComp : public SeqGradChanList { public: /** * Constructs a flow-compensated phase encoding gradient labeled 'object_label' with the following properties: * - t0: The starting time of the gradient after excitation * - nsteps: The number of phase encoding steps * - fov: The Field of View * - gradchannel: The channel this object should be played out * - gradstrength: The maximum gradient strength * - scheme: The phase encoding scheme * - reorder: The reordering scheme * - nsegments: The number of segments for segmented reordering * - reduction: Reduction factor for parallel imaging (sparsely sampled k-space) * - acl_bands: Number of autocalibration bands (bunch of adjacent lines between actual k-space lines) for GRAPPA * - partial_fourier: The amount of partial Fourier undersampling (0=no undersampling, 1=half fourier) * - nucleus: The nucleus this object should be calculated for */ SeqGradPhaseEncFlowComp(const STD_string& object_label, double t0, unsigned int nsteps, float fov, direction gradchannel, float gradstrength, encodingScheme scheme=linearEncoding, reorderScheme reorder=noReorder, unsigned int nsegments=1, unsigned int reduction=1, unsigned int acl_bands=DEFAULT_ACL_BANDS, float partial_fourier=0.0, const STD_string& nucleus=""); /** * Constructs an empty flow-compensated phase encoding gradient labeled 'object_label' */ SeqGradPhaseEncFlowComp(const STD_string& object_label="unnamedSeqGradPhaseEncFlowComp") : SeqGradChanList(object_label) {} /** * Constructs a copy of 'sgpefc' */ SeqGradPhaseEncFlowComp(const SeqGradPhaseEncFlowComp& sgpefc) {SeqGradPhaseEncFlowComp::operator = (sgpefc);} /** * Assignment operator that makes this object become a copy of 'sgpefc' */ SeqGradPhaseEncFlowComp& operator = (const SeqGradPhaseEncFlowComp& sgpefc); /** * conversion operator for loop insertion */ operator const SeqVector& () const {return simvec;} private: void build_seq(); static void calc_flowcomp_pe(float& negfact, float& tc, float Gpos, float M0, float t0, float slewrate); SeqGradVectorPulse pos; SeqGradVectorPulse neg; SeqSimultanVector simvec; }; /** @} */ #endif odin-1.8.5/odinseq/seqpulsar.cpp0000644000175000017500000003741111322062345013570 00000000000000#include "seqpulsar.h" #include "seqsim.h" #include "seqgradramp.h" #include SeqPulsar::SeqPulsar(const STD_string& object_label, bool rephased, bool interactive) : SeqPulsNdim(object_label), OdinPulse(object_label) { Log odinlog(this,"SeqPulsar(object_label)"); register_pulse(this); for(int i=0;i odinlog(this,"~SeqPulsar"); unregister_pulse(this); for(int i=0;i odinlog(this,"set_flipangle"); OdinPulse::set_flipangle(flipangle); // refresh(); return *this; } SeqPulsInterface& SeqPulsar::set_pulsduration(float pulsduration) { Log odinlog(this,"set_pulsduration"); OdinPulse::set_Tp(pulsduration); // refresh(); return *this; } SeqPulsInterface& SeqPulsar::set_power(float pulspower) { SeqPulsNdim::set_power(pulspower); attenuation_set=true; return *this; } SeqPulsInterface& SeqPulsar::set_pulse_type(pulseType type) { SeqPulsNdim::set_pulse_type(type); OdinPulse::set_pulse_type(type); return *this; } SeqPulsar& SeqPulsar::set_rephased(bool rephased, float strength) { Log odinlog(this,"set_refocused"); rephased_pulse=rephased; rephaser_strength=strength; SeqPulsar::update(); return *this; } fvector SeqPulsar::get_reph_gradintegral() const { fvector result(n_directions); result=0.0; for(int i=0;iget_gradintegral(); } return result; } SeqPulsar& SeqPulsar::operator = (const SeqPulsar& sp) { Log odinlog(this,"operator="); always_refresh=sp.always_refresh; // assign before OdinPulse::operator = to avoid call of SeqPulsar::update() OdinPulse::operator = (sp); SeqPulsNdim::operator = (sp); attenuation_set=sp.attenuation_set; rephased_pulse=sp.rephased_pulse; rephaser_strength=sp.rephaser_strength; SeqPulsar::update(); // do NOT call virtual function in constructor return *this; } OdinPulse& SeqPulsar::update() { Log odinlog(this,"update"); if(always_refresh) refresh(); return *this; } SeqPulsar& SeqPulsar::set_interactive(bool flag) { always_refresh=flag; return *this; } STD_string SeqPulsar::get_properties() const { return "Shape="+get_shape()+", Trajectory="+get_trajectory()+", Filter="+get_filter(); } SeqPulsar& SeqPulsar::refresh() { Log odinlog(this,"refresh"); int i,j,index; SeqPulsNdim::set_nucleus(OdinPulse::get_nucleus()); OdinPulse::recalc_pulse(); int npts=OdinPulse::get_size(); float Tp=OdinPulse::get_Tp(); float dt=secureDivision(Tp,float(npts)); float G0=OdinPulse::get_G0(); ODINLOG(odinlog,normalDebug) << "npts/Tp/dt/G0=" << npts << "/" << Tp << "/" << dt << "/" << G0 << STD_endl; fvector pulsegrad[n_directions]; for(i=0;iGinitMax) { GinitMax=fabs(Ginit); GinitMaxChannel=direction(i); } } ODINLOG(odinlog,normalDebug) << "GinitMax/GinitMaxChannel=" << GinitMax << "/" << GinitMaxChannel << STD_endl; // find maximum final gradient strength float GfinalMax=0.0; direction GfinalMaxChannel=readDirection; for(i=0;iGfinalMax) { GfinalMax=fabs(Gfinal); GfinalMaxChannel=direction(i); } } ODINLOG(odinlog,normalDebug) << "GfinalMax=" << GfinalMax << STD_endl; ODINLOG(odinlog,normalDebug) << "GfinalMaxChannel=" << GfinalMaxChannel << STD_endl; // use gradient ramp objects to generate the pulse ramps // these are pointers because of the delete[]-does-not-call-destructor-of-base-class bug in GCC SeqGradRamp* onramp[n_directions]; SeqGradRamp* offramp[n_directions]; for(i=0;iget_duration(); ODINLOG(odinlog,normalDebug) << "maxinit/dur[" << i << "]=" << initStrength*G0 << "/" << onrampdur << STD_endl; } if(i==GfinalMaxChannel && finalStrength!=0.0) { offramp[i]=new SeqGradRamp("offramp",direction(i),finalStrength*G0,0.0,dt); offrampdur=(offramp[i])->get_duration(); ODINLOG(odinlog,normalDebug) << "maxfinal/dur[" << i << "]=" << finalStrength*G0 << "/" << offrampdur << STD_endl; } } // generate the other ramps for(i=0;iget_npts(); int rampOff_npts=0; if(offramp[GfinalMaxChannel]) rampOff_npts=offramp[GfinalMaxChannel]->get_npts(); int total_pts=rampOn_npts+npts+rampOff_npts; ODINLOG(odinlog,normalDebug) << "dt=" << dt << STD_endl; ODINLOG(odinlog,normalDebug) << "rampOn_npts=" << rampOn_npts << STD_endl; ODINLOG(odinlog,normalDebug) << "rampOff_npts=" << rampOff_npts << STD_endl; // the arrays that will be assigned to the SeqPulsNdim base class cvector wv(total_pts); fvector Gpulse[n_directions]; for(i=0;iget_strength()/G0; else Gpulse[i][j]=0.0; } } /////////////////////////////////// // Gradient part No 2 cvector b1pulse=OdinPulse::get_B1(); for(j=0;jget_strength()/G0; else Gpulse[i][index]=0.0; } } /////////////////////////////////// // Deal with rephasing gradient lobe bool add_refoc_lobe=false; if(rephased_pulse && get_rel_center()!=1.0) add_refoc_lobe=true; ODINLOG(odinlog,normalDebug) << "add_refoc_lobe=" << add_refoc_lobe << STD_endl; // calculate the gradient integral that will be rephased float rephase_integral[n_directions]; for(i=0;i0.0) { reph_grad[i]=new SeqGradTrapez(get_label()+"_reph_grad", -rephase_integral[i], rephaser_strength, direction(i)); } else { reph_grad[i]=new SeqGradTrapez(get_label()+"_reph_grad", -rephase_integral[i], direction(i), rephdur); } } } /////////////////////////////////// // copying generated pulse into the base class SeqPulsNdim update_B10andPower(); float rel_magnetic_center=( (float)rampOn_npts + get_rel_center() * float(npts) ) / float(total_pts); set_rel_magnetic_center(rel_magnetic_center); SeqPulsNdim::set_rfwave(wv); SeqPulsNdim::set_pulsduration(total_pts*dt); ODINLOG(odinlog,normalDebug) << "total_pts=" << total_pts << STD_endl; ODINLOG(odinlog,normalDebug) << "dt=" << dt << STD_endl; ODINLOG(odinlog,normalDebug) << "pulsduration=" << total_pts*dt << STD_endl; for(i=0;i odinlog(this,"SeqPulsar::update_B10andPower"); OdinPulse::update_B10andPower(); float pow,argument; if(is_adiabatic()) { argument=secureInv(get_Tp_1pulse()); } else { argument=secureInv(get_Tp_1pulse())*get_flipangle()/90.0; } if (argument==0.0) pow=_MAX_PULSE_ATTENUATION_; else pow=-20.*log10(argument)+get_pulse_gain()+systemInfo->get_reference_gain(); if(!attenuation_set) SeqPulsNdim::set_power(pow); float sysflip=get_flipangle()*get_flipangle_corr_factor(); float b10=OdinPulse::get_B10(); ODINLOG(odinlog,normalDebug) << "pow/sysflip/b10=" << pow << "/" << sysflip << "/" << b10 << STD_endl; SeqPulsNdim::set_system_flipangle(sysflip); SeqPulsNdim::set_B1max(b10); } SeqFreqChanInterface& SeqPulsar::set_nucleus(const STD_string& nucleus) { OdinPulse::set_nucleus(nucleus); SeqPulsNdim::set_nucleus(nucleus); SeqPulsar::update(); return *this; } int SeqPulsar::get_dims() const { int result=0; funcMode dimmode=get_dim_mode(); if(dimmode == zeroDeeMode) result=0; if(dimmode == oneDeeMode) result=1; if(dimmode == twoDeeMode) result=2; return result; } void SeqPulsar::register_pulse(SeqPulsar* pls) { Log odinlog("SeqPulsar","register_pulse"); ODINLOG(odinlog,normalDebug) << " " << pls->get_label() << STD_endl; active_pulsar_pulses->push_back(pls); } void SeqPulsar::unregister_pulse(SeqPulsar* pls) { Log odinlog("SeqPulsar","unregister_pulse"); ODINLOG(odinlog,normalDebug) << " " << pls->get_label() << STD_endl; active_pulsar_pulses->remove(pls); } void SeqPulsar::init_static() { active_pulsar_pulses.init("active_pulsar_pulses"); } void SeqPulsar::destroy_static() { active_pulsar_pulses.destroy(); } template class SingletonHandler; SingletonHandler SeqPulsar::active_pulsar_pulses; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; ///////////////////////////////////////////////////////////////////////////// SeqPulsarReph::SeqPulsarReph(const STD_string& object_label,const SeqPulsar& puls) : SeqGradChanParallel(object_label) { dim=puls.get_dims(); if(puls.reph_grad[readDirection]) gxpulse=*(puls.reph_grad[readDirection]); if(puls.reph_grad[phaseDirection]) gypulse=*(puls.reph_grad[phaseDirection]); if(puls.reph_grad[sliceDirection]) gzpulse=*(puls.reph_grad[sliceDirection]); build_seq(); } SeqPulsarReph::SeqPulsarReph(const SeqPulsarReph& spr): SeqGradChanParallel(spr) { dim=0; SeqPulsarReph::operator = (spr); } SeqPulsarReph::SeqPulsarReph(const STD_string& object_label) : SeqGradChanParallel(object_label) { dim=0; } SeqPulsarReph& SeqPulsarReph::operator = (const SeqPulsarReph& spr) { SeqGradChanParallel::operator = (spr); dim=spr.dim; gxpulse=spr.gxpulse; gypulse=spr.gypulse; gzpulse=spr.gzpulse; build_seq(); return *this; } SeqPulsarReph::~SeqPulsarReph() { } float SeqPulsarReph::get_onramp_duration() const {return gzpulse.get_onramp_duration();} float SeqPulsarReph::get_constgrad_duration() const {return gzpulse.get_constgrad_duration();} float SeqPulsarReph::get_offramp_duration() const {return gzpulse.get_offramp_duration();} void SeqPulsarReph::build_seq() { clear(); if(dim==3) (*this) += gxpulse / gypulse / gzpulse; if(dim==2) (*this) += gxpulse / gypulse; if(dim==1) (*this) += gzpulse; } ///////////////////////////////////////////////////////////////////////////// SeqPulsarSinc::SeqPulsarSinc(const STD_string& object_label, float slicethicknes, bool rephased, float duration, float flipangle, float resolution, unsigned int npoints) : SeqPulsar(object_label,rephased,false) { set_dim_mode(oneDeeMode); set_Tp(duration); resize(npoints); SeqPulsar::set_flipangle(flipangle); // do NOT call virtual function in constructor set_shape("Sinc("+ftos(slicethicknes)+")"); set_trajectory("Const(0.0,1.0)"); set_filter("Triangle"); set_spat_resolution(resolution); SeqPulsar::set_encoding_scheme(maxDistEncoding); // do NOT call virtual function in constructor refresh(); set_interactive(true); } SeqPulsarSinc::SeqPulsarSinc(const SeqPulsarSinc& sps) { SeqPulsarSinc::operator = (sps); } SeqPulsarSinc& SeqPulsarSinc::operator = (const SeqPulsarSinc& sps) { SeqPulsar::operator = (sps); refresh(); return *this; } ///////////////////////////////////////////////////////////////////////////// SeqPulsarGauss::SeqPulsarGauss(const STD_string& object_label, float slicethicknes, bool rephased, float duration, float flipangle, unsigned int npoints) : SeqPulsar(object_label, rephased, false) { set_dim_mode(oneDeeMode); set_Tp(duration); resize(npoints); SeqPulsar::set_flipangle(flipangle); // do NOT call virtual function in constructor set_shape("Const"); set_trajectory("Const(0.0,1.0)"); set_filter("Gauss"); set_spat_resolution(0.5*slicethicknes); SeqPulsar::set_encoding_scheme(maxDistEncoding); // do NOT call virtual function in constructor refresh(); set_interactive(true); } SeqPulsarGauss::SeqPulsarGauss(const SeqPulsarGauss& spg) { SeqPulsarGauss::operator = (spg); } SeqPulsarGauss& SeqPulsarGauss::operator = (const SeqPulsarGauss& spg) { SeqPulsar::operator = (spg); refresh(); return *this; } ///////////////////////////////////////////////////////////////////////////// SeqPulsarBP::SeqPulsarBP(const STD_string& object_label, float duration, float flipangle, const STD_string& nucleus) : SeqPulsar(object_label, false, false) { set_dim_mode(zeroDeeMode); SeqPulsar::set_nucleus(nucleus); // do NOT call virtual function in constructor set_Tp(duration); unsigned int npoints=32; resize(npoints); SeqPulsar::set_flipangle(flipangle); // do NOT call virtual function in constructor set_shape("Const"); set_trajectory("Const(0.0,1.0)"); set_filter("NoFilter"); refresh(); set_interactive(true); } SeqPulsarBP::SeqPulsarBP(const SeqPulsarBP& spb) { SeqPulsarBP::operator = (spb); } SeqPulsarBP& SeqPulsarBP::operator = (const SeqPulsarBP& spb) { SeqPulsar::operator = (spb); refresh(); return *this; } odin-1.8.5/odinseq/seqgradtrapez.h0000644000175000017500000003275511455553540014111 00000000000000/*************************************************************************** seqgradtrapez.h - description ------------------- begin : Tue Apr 27 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADTRAPEZ_H #define SEQGRADTRAPEZ_H #include #include #include #include //////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The base class for platform specific drivers of trapezoidal gradient pulses */ class SeqGradTrapezDriver : public SeqDriverBase { public: SeqGradTrapezDriver() {} virtual ~SeqGradTrapezDriver() {} /** * Update the driver with the following properties: * - channel: The channel (direction) of the trapez * - onrampdur: Duration of the on-ramp * - constdur: Duration of the flat top * - offrampdur: Duration of the off-ramp * - strength: Max gradient strength * - timestep: Dwell time (gradient raster) of the ramps * - type: The shape for the ramps * - exclude_offramp_from_timing: Exclude the off-ramp from timing calculations */ virtual bool update_driver(direction channel, double onrampdur, double constdur, double offrampdur, float strength, double timestep, rampType type, bool exclude_offramp_from_timing) = 0; virtual float get_onramp_integral (double tmin, double tmax) const = 0; virtual float get_offramp_integral(double tmin, double tmax) const = 0; virtual const fvector& get_onramp() const = 0; virtual const fvector& get_offramp() const = 0; virtual SeqGradChanList get_driverchanlist() = 0; virtual bool check_ramptype(rampType type) const = 0; virtual SeqGradTrapezDriver* clone_driver() const = 0; }; //////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The Default driver for trapezoidal gradient pulses */ class SeqGradTrapezDefault : public SeqGradTrapezDriver, public SeqGradChan { public: SeqGradTrapezDefault(); SeqGradTrapezDefault(const SeqGradTrapezDefault& sgtd); ~SeqGradTrapezDefault() {} // overloading virtual functions from SeqGradTrapezDriver bool update_driver(direction channel, double onrampdur, double constdur, double offrampdur, float strength, double timestep, rampType type, bool exclude_offramp_from_timing); float get_onramp_integral (double tmin, double tmax) const {return onramp_cache. get_integral(tmin,tmax);} float get_offramp_integral(double tmin, double tmax) const {return offramp_cache.get_integral(tmin,tmax);} const fvector& get_onramp() const {return onramp_cache.get_wave();} const fvector& get_offramp() const {return offramp_cache.get_wave();} SeqGradChanList get_driverchanlist(); bool check_ramptype(rampType type) const {return true;} SeqGradTrapezDriver* clone_driver() const {return new SeqGradTrapezDefault(*this);} // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} private: // overwriting virtual functions from SeqClass bool prep(); // overloading virtual function from SeqTreeObj STD_string get_properties() const; // overloading virtual functions from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); SeqGradInterface& invert_strength(); float get_strength() const {return onramp_cache.get_strength();} double get_gradduration() const; SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); // overloading virtual functions from SeqGradChan STD_string get_grdpart(float matrixfactor) const {return graddriver->get_trapez_program(get_strength(),matrixfactor);} SeqGradChan& get_subchan(double starttime, double endtime) const; direction get_channel() const {return onramp_cache.get_channel();} float get_integral() const; SeqGradRamp onramp_cache; SeqGradRamp offramp_cache; double const_dur; bool exclude_offramp; }; //////////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * \brief Trapezoidal gradient * * This class represents a gradient pulse with a trapezoidal shape, i.e. * a piecewise constant gradient with ramps */ class SeqGradTrapez : public SeqGradChanList { public: /** * Constructs a gradient pulse labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - gradstrength: The maximum gradient strength for this object * - constgradduration: The duration of the constant part of the gradient pulse * - timestep: The time resolution for the ramps * - type: The shape for the ramps * - minrampduration: The minimum duration for the ramps * - steepness: This parameter in the range of ]0,1] determines the relative rising * speed of the gradient strength, i.e. with 1 the gradients are switched * as fast as possible */ SeqGradTrapez(const STD_string& object_label,direction gradchannel, float gradstrength, double constgradduration, double timestep=0.01, rampType type = linear, double minrampduration=0.0, float steepness=1.0); /** * Constructs a gradient pulse labeled 'object_label' with the following properties: * - gradintegral: The overall integral for the gradient pulse * - gradchannel: The channel this object should be played out * - constgradduration: The duration of the constant part of the gradient pulse * - timestep: The time resolution for the ramps * - rampType: The shape for the ramps * - minrampduration: The minimum duration for the ramps * - steepness: This parameter in the range of ]0,1] determines the relative rising * speed of the gradient strength, i.e. with 1 the gradients are switched * as fast as possible */ SeqGradTrapez(const STD_string& object_label,float gradintegral, direction gradchannel, double constgradduration, double timestep=0.01, rampType type = linear, double minrampduration=0.0, float steepness=1.0); /** * Constructs a gradient pulse labeled 'object_label' with the following properties: * - gradintegral: The overall integral for the gradient pulse * - gradstrength: The strength of the constant part of the gradient pulse * - gradchannel: The channel this object should be played out * - timestep: The time resolution for the ramps * - rampType: The shape for the ramps * - minrampduration: The minimum duration for the ramps * - steepness: This parameter in the range of ]0,1] determines the relative rising * speed of the gradient strength, i.e. with 1 the gradients are switched * as fast as possible */ SeqGradTrapez(const STD_string& object_label,float gradintegral, float gradstrength, direction gradchannel, double timestep=0.01, rampType type = linear, double minrampduration=0.0, float steepness=1.0); /** * Constructs a copy of 'sgt' */ SeqGradTrapez(const SeqGradTrapez& sgt); /** * Construct an empty gradient pulse with the given label */ SeqGradTrapez(const STD_string& object_label = "unnamedSeqGradTrapez"); /** * Assignment operator that makes this gradient pulse become a copy of 'sgt' */ SeqGradTrapez& operator = (const SeqGradTrapez& sgt); /** * Sets the duration of the constant part of the gradient pulse */ SeqGradTrapez& set_constgrad_duration(double duration); /** * Returns the duration of the ramp that switches the gradient pulse on */ double get_onramp_duration() const {return onrampdur;} /** * Returns the duration of the constant part of the gradient pulse */ double get_constgrad_duration() const {return constdur;} /** * Returns the duration of the ramp that switches the gradient pulse off */ double get_offramp_duration() const {return offrampdur;} /** * Returns the integral of the ramp that switches the gradient pulse on from tmin to tmax */ float get_onramp_integral(double tmin, double tmax) const {return trapezdriver->get_onramp_integral(tmin,tmax);} /** * Returns the integral of the ramp that switches the gradient pulse on */ float get_onramp_integral() const {return get_onramp_integral(0.0,get_onramp_duration());} /** * Returns the integral of the constant part */ float get_constgrad_integral() const {return constdur*trapezstrength;} /** * Returns the integral of the ramp that switches the gradient pulse off from tmin to tmax */ float get_offramp_integral(double tmin, double tmax) const {return trapezdriver->get_offramp_integral(tmin,tmax);} /** * Returns the integral of the ramp that switches the gradient pulse off */ float get_offramp_integral() const {return get_offramp_integral(0.0,get_offramp_duration());} /** * Sets the overall integral of the gradient pulse */ SeqGradTrapez& set_integral(float gradintegral); /** * Returns the overall integral of the gradient pulse */ float get_integral() const; /** * Returns the number of digitised points of the ramp that switches the gradient pulse on */ unsigned int get_onramp_npts() const; /** * Returns the number of digitised points during the constant part */ unsigned int get_const_npts() const; /** * Returns the number of digitised points of the ramp that switches the gradient pulse off */ unsigned int get_offramp_npts() const; /** * Returns the total number of digitised points */ unsigned int get_npts() const; /** * Returns the waveform of the ramp that switches the gradient pulse on */ fvector get_onramp() const {return trapezdriver->get_onramp();} /** * Returns the waveform of the ramp that switches the gradient pulse on */ fvector get_offramp() const {return trapezdriver->get_offramp();} /** * Returns a waveform which is a digitised version of the whole trapezoid */ fvector get_trapezshape() const; /** * Returns the time resolution for the ramps */ double get_timestep() const {return dt;} /** * Returns the shape type of the ramps */ rampType get_ramptype() const {return rampMode;} /** * Spefifies whether to exclude the off-ramp from timing calculations */ SeqGradTrapez& exclude_offramp_from_timing(bool flag); // overloading virtual function from SeqGradInterface float get_strength() const {return trapezstrength;} double get_gradduration() const {return get_onramp_duration()+get_constgrad_duration()+get_offramp_duration();} // override result of SeqGradChanList which may differ due to concatenating other SeqGradChans private: void common_init(); void check_platform(); void update_driver(); void build_seq(); static void get_ramps(const STD_string& label, float& rampintegral, double& rampondur, double& rampoffdur, float strength, double dwelltime, rampType ramptype, float steepness, double mindur); mutable SeqDriverInterface trapezdriver; rampType rampMode; double dt; float steepnessfactor; bool exclude_offramp_timing; direction trapezchannel; double onrampdur; double constdur; double offrampdur; float trapezstrength; }; //////////////////////////////////////////////////////////////////// /** * \brief 3 simultaneous trapezoids * * A class to place 3 synchronous gradient pulses with * trapezoidal shape on all 3 axes simultaneously. */ class SeqGradTrapezParallel : public SeqGradChanParallel { public: /** * Constructs a gradient pulse labeled 'object_label' with the following properties: * - gradintegral_read: The desired gradient integral on the read channel * - gradintegral_phase: The desired gradient integral on the phase channel * - gradintegral_slice: The desired gradient integral on the slice channel * - maxgradstrength: The maximum gradient strength * - timestep: The time resolution for the ramps * - rampType: The shape for the ramps * - minrampduration: The minimum duration for the ramps */ SeqGradTrapezParallel(const STD_string& object_label, float gradintegral_read, float gradintegral_phase, float gradintegral_slice, float maxgradstrength, double timestep=0.01, rampType type = linear, double minrampduration=0.0); /** * Constructs a copy of 'sgtp' */ SeqGradTrapezParallel(const SeqGradTrapezParallel& sgtp); /** * Construct an empty gradient pulse with the given label */ SeqGradTrapezParallel(const STD_string& object_label = "unnamedSeqGradTrapezParallel"); /** * Assignment operator that makes this gradient pulse become a copy of 'sgtp' */ SeqGradTrapezParallel& operator = (const SeqGradTrapezParallel& sgtp); private: void build_seq(); SeqGradTrapez readgrad; SeqGradTrapez phasegrad; SeqGradTrapez slicegrad; }; /** @} */ #endif odin-1.8.5/odinseq/seqacqspiral.h0000644000175000017500000001017211322062345013701 00000000000000/*************************************************************************** seqacqspiral.h - description ------------------- begin : Tue Nov 11 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQACQSPIRAL_H #define SEQACQSPIRAL_H #include #include #include #include #include #include #include /** * @addtogroup odinseq * @{ */ /** * \brief Acquisition + spiral gradient * * This class contains a gradient with a spiral k-space trajectory together with an acquisition window */ class SeqAcqSpiral : public virtual SeqAcqInterface, public SeqObjList { // virtual functions of SeqFreqChanInterface are marhshalled to acq public: /** * Constructs an acquisition window with a simultaneous spiral gradient labeled 'object_label' and the * following properties: * - sweepwidth: The sampling frequency * - fov: The Field of View in radial direction * - sizeRadial: The number of image points in radial direction * - numofSegments : The number of spiral interleaves * - traj: The spiral trajectory (will be modified, if neccessary) * - inout: Spiral-in spiral-out trajectory * - optimize: Optimize trajectory for minimum readout length if trajectory has a free tunable parameter * - nucleus: See class 'SeqAcq' for explanation * - phaselist: See class 'SeqAcq' for explanation */ SeqAcqSpiral(const STD_string& object_label,double sweepwidth, float fov, unsigned int sizeRadial, unsigned int numofSegments, JDXtrajectory& traj, bool inout=false, bool optimize=false, const STD_string& nucleus="",const dvector& phaselist=0); /** * Constructs an acquisition window with spiral gradient which is a copy of 'sas' */ SeqAcqSpiral(const SeqAcqSpiral& sas); /** * Constructs an empty acquisition window with spiral gradient with the given label. */ SeqAcqSpiral(const STD_string& object_label="unnamedSeqAcqSpiral"); /** * This assignment operator will make this object become an exact copy of 'sar'. */ SeqAcqSpiral& operator = (const SeqAcqSpiral& sas); /** * Returns the vector of the spiral interleaves (for loop insertion) */ const SeqVector& get_segment_vector() const {return rotvec;} /** * Returns the k-space trajectory for the interleave 'iseg' */ fvector get_ktraj(unsigned int iseg, direction channel) const; /** * Returns the Jacobian determinante, i.e. the correction function * for non-uniform weighting of k-space */ fvector get_denscomp() const; // marshalling virtual functions of SeqAcqInterface to acq, except: double get_acquisition_center() const {return preacq.get_duration()+acq.get_acquisition_center();} double get_acquisition_start() const {return preacq.get_duration()+acq.get_acquisition_start();} SeqAcqInterface& set_sweepwidth(double sw, float os_factor); // produce warning private: // overwriting virtual functions from SeqClass bool prep(); void common_init(); void build_seq(); SeqParallel par; SeqGradSpiral spirgrad_in; SeqGradSpiral spirgrad_out; SeqDelay preacq; SeqAcq acq; SeqGradTrapezParallel gbalance; SeqRotMatrixVector rotvec; bool inout_traj; }; /** @} */ #endif odin-1.8.5/odinseq/seqphase.cpp0000644000175000017500000000404111322062345013353 00000000000000#include "seqphase.h" #include "seqfreq.h" /////////////////////////////////////////////////////////////////// SeqPhaseListVector::SeqPhaseListVector(const STD_string& object_label, const dvector& phase_list) : phasedriver(object_label) { set_label(object_label); set_phaselist(phase_list); } SeqPhaseListVector::SeqPhaseListVector(const SeqPhaseListVector& spl) : phasedriver(spl.get_label()) { SeqPhaseListVector::operator = (spl); } SeqPhaseListVector& SeqPhaseListVector::operator = (const SeqPhaseListVector& spl) { // do NOT copy user because it is set by SeqFreqChan and remains the same over the whole lifetime phasedriver=spl.phasedriver; phaselist=spl.phaselist; return *this; }; bool SeqPhaseListVector::prep() { if(!SeqClass::prep()) return false; phasedriver->prep_driver(phaselist); return true; } bool SeqPhaseListVector::prep_iteration() const { Log odinlog(this,"prep_iteration"); ODINLOG(odinlog,normalDebug) << "user=" << user->get_label() << STD_endl; return user->prep_iteration(); } SeqPhaseListVector& SeqPhaseListVector::set_phaselist(const dvector& pl) { Log odinlog(this,"set_phaselist"); phaselist=pl; // Limit to range 0-360, just as a precaution for flaky drivers for(unsigned int i=0; i #include #include #include #include #include #include #include #include #include #include #include #include /** * @addtogroup odinseq_internals * @{ */ /////////////////////////////////////////////////////////////////////////// // For debugging the Seq component class Seq { public: static const char* get_compName(); }; /////////////////////////////////////////////////////////////////////////// class SeqVector; //forward declaration /** * This is the base class for all Seq* classes. It provides * functions that are common to all classes of the sequence library, * e.g. functions for error/debug message handling and acces to * proxies, i.e. geometryInfo, studyInfo and systemInfo. */ class SeqClass : public virtual Labeled, public StaticHandler { public: /** * Mark object as temporary so that it will be deleted automatically */ SeqClass& set_temporary(); System& get_systemInfo() {return *systemInfo;} // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); protected: // prevent direct construction/assignment/destruction of this class SeqClass(); virtual ~SeqClass(); SeqClass& operator = (const SeqClass& sc); /** * Writes a marshalling error, i.e. mashalling without appropriate sub-object, to the log */ void marshall_error() const; /** * Delete all temporary objects */ static void clear_temporary(); /** * Overload this function in case the class is a container object, i.e. * it contains other sequence objects. The function should clear all * references to other sequence objects, i.e. to thos it contains. */ virtual void clear_container() {} /** * Clear the contents of all container objects */ static void clear_containers(); /** * Overload this function to prepare objects before the measurement. This function * will then be called automatically after editing the sequence parameters and * before the measurement is started. This function should not alter the physical * properties of the sequence object, e.g. its duration. */ virtual bool prep() {prepped=true; return true;} // call prep() of all objects static bool prep_all(); // points to systemInfo of the currently active platform SystemInterface& systemInfo; // points to the geometry parameters static SingletonHandler geometryInfo; // points to the geometry parameters static SingletonHandler studyInfo; // points to the reco parameters static SingletonHandler recoInfo; static SeqVector& get_dummyvec(); private: friend class SeqOperator; friend class SeqMethod; friend class SeqMethodProxy; friend class SystemInterface; friend class SeqPlatformProxy; // remove all references to other sequence objects static void clear_objlists(); bool prepped; // List to hold references to SeqClass objects struct SeqClassList : public STD_list, public Labeled {}; static SingletonHandler allseqobjs; static SingletonHandler tmpseqobjs; static SingletonHandler seqobjs2prep; static SingletonHandler seqobjs2clear; static SystemInterface* systemInfo_ptr; static SeqVector* dummyvec; }; /** @} */ #endif odin-1.8.5/odinseq/seqobjvec.cpp0000644000175000017500000000650311322062345013530 00000000000000#include "seqobjvec.h" #include "seqgrad.h" #include "seqparallel.h" #include "seqgradchanlist.h" SeqObjVector::SeqObjVector(const STD_string& object_label) : SeqVector(object_label), SeqObjBase(object_label) { set_label(object_label); } SeqObjVector::SeqObjVector(const SeqObjVector& sov) { SeqObjVector::operator = (sov); } SeqObjVector& SeqObjVector::operator = (const SeqObjVector& sov) { SeqObjBase::operator = (sov); SeqVector::operator = (sov); clear(); for(constiter it=sov.get_const_begin();it!=sov.get_const_end();++it) { append(**it); } return *this; } SeqObjVector& SeqObjVector::operator += (const SeqObjBase& soa) { append(soa); return *this; } SeqObjVector& SeqObjVector::operator += (SeqGradObjInterface& sgoa) { SeqParallel* par=new SeqParallel(sgoa.get_label()); par->set_temporary(); par->set_gradptr(&sgoa); (*this)+=(*par); return *this; } SeqObjVector& SeqObjVector::operator += (SeqGradChanList& sgcl) { SeqParallel* par=new SeqParallel(sgcl.get_label()); par->set_temporary(); (*par) /= sgcl; (*this)+=(*par); return *this; } STD_string SeqObjVector::get_program(programContext& context) const { STD_string result; constiter it=get_current(); if(it!=get_const_end()) result=(*it)->get_program(context); return result; } double SeqObjVector::get_duration() const { double result=0.0; constiter it=get_current(); if(it!=get_const_end()) result=(*it)->get_duration(); return result; } unsigned int SeqObjVector::event(eventContext& context) const { unsigned int result=0; constiter it=get_current(); if(it!=get_const_end()) result+=(*it)->event(context); return result; } SeqValList SeqObjVector::get_freqvallist(freqlistAction action) const { SeqValList result; constiter it=get_current(); if(it!=get_const_end()) result=(*it)->get_freqvallist(action); return result; } SeqValList SeqObjVector::get_delayvallist() const { SeqValList result; constiter it=get_current(); if(it!=get_const_end()) result=(*it)->get_delayvallist(); return result; } double SeqObjVector::get_rf_energy() const { double result=0.0; constiter it=get_current(); if(it!=get_const_end()) result=(*it)->get_rf_energy(); return result; } void SeqObjVector::clear_container() { List::clear(); } void SeqObjVector::query(queryContext& context) const { SeqTreeObj::query(context); // defaults if(context.action==count_acqs) { constiter it=get_current(); if(it!=get_const_end()) (*it)->query(context); return; } for(constiter it=get_const_begin();it!=get_const_end();++it) { context.parentnode=this; // reset to this because it might changed by last query (*it)->query(context); } } RecoValList SeqObjVector::get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const { RecoValList result(get_label()); constiter it=get_current(); if(it!=get_const_end()) result=(*it)->get_recovallist(reptimes,coords); return result; } List::constiter SeqObjVector::get_current() const { unsigned int i=0; unsigned int index=get_current_index(); constiter result=get_const_end(); for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if(i==index) { result=it; return result; } i++; } return result; } odin-1.8.5/odinseq/seqdriver_idea.cpp0000644000175000017500000000174311322062345014536 00000000000000#ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif #ifdef IDEA_PLUGIN #include "../platforms/IDEA_n4/odinseq_idea/seqidea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqacq_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqacqepi_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqcounter_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqdec_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqdelay_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqfreq_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqgradchan_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqgradtrapez_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqlist_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqparallel_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqphase_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqpuls_idea.cpp" #include "../platforms/IDEA_n4/odinseq_idea/seqtrigg_idea.cpp" #endif odin-1.8.5/odinseq/seqblsiegprep.h0000755000175000017500000000506711625224370014074 00000000000000/* Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ #ifndef SEQBLSIEGPREP_H #define SEQBLSIEGPREP_H #include /** * @addtogroup odinseq * @{ */ /** * \brief Bloch-Siegert preparation module for B1-mapping * * Preparation module for B1 mapping according to * Sacolick et al. MRM(65)2010: 1315-1322): * Fermi-shaped pulse which is applied off-resonance to produce a * B0-shift depending on the Fermi-shaped pulse's B1 distribution */ class SeqBlSiegPrep : public SeqPulsar { public: /** * Constructs a Fermi-shaped pulse with the following properties: * - duration [ms] * - angle [degree] * - offset [Hz] * - width: fractional distance of the turning points of the fermipulse * - slope: steepnes of the ramp of the fermipulse */ SeqBlSiegPrep ( const STD_string& object_label = "unnamedSeqBlSiegPrep", float duration = 8, float angle = 1000, float offset = 4000, float width = 0.8, float slope = 130 ); /** * constructs a copy of "sbsp" */ SeqBlSiegPrep ( const SeqBlSiegPrep& sbsp ); /** * copies "sbsp" */ SeqBlSiegPrep& operator = ( const SeqBlSiegPrep& sbsp ); /** * destructor */ ~SeqBlSiegPrep() {} /** * prepares the Fermi-shaped rf-pulse -> ready for use */ bool prep(); JcampDxBlock pars; JcampDxBlock info; JDXdouble duration; JDXdouble angle; JDXdouble offset; JDXdouble width; JDXdouble slope; JDXdouble weighting; JDXdouble amplitude; private: }; /** @} */ #endif // SEQBLSIEGPREP_H odin-1.8.5/odinseq/seqacqepi.cpp0000644000175000017500000007336611625224370013541 00000000000000#include "seqacqepi.h" #include "seqgradchanparallel.h" #include "seqgradvec.h" #include "seqveciter.h" SeqEpiDriverDefault::SeqEpiDriverDefault() { SeqAcqInterface::set_marshall(&adc); SeqFreqChanInterface::set_marshall(&adc); templtype=no_template; } SeqEpiDriverDefault::SeqEpiDriverDefault(const SeqEpiDriverDefault& sedi) : SeqEpiDriver(sedi) { SeqAcqInterface::set_marshall(&adc); SeqFreqChanInterface::set_marshall(&adc); adc=sedi.adc; acqdelay_begin=sedi.acqdelay_begin; acqdelay_middle=sedi.acqdelay_middle; acqdelay_end=sedi.acqdelay_end; posread=sedi.posread; negread=sedi.negread; phaseblip1st=sedi.phaseblip1st; phaseblip2nd=sedi.phaseblip2nd; phasezero1st=sedi.phasezero1st; phasezero2nd=sedi.phasezero2nd; phasezero_lastblip=sedi.phasezero_lastblip; gradkernel=sedi.gradkernel; lastgradkernel=sedi.lastgradkernel; oneadckernel=sedi.oneadckernel; adckernel=sedi.adckernel; lastadckernel=sedi.lastadckernel; kernel=sedi.kernel; lastkernel=sedi.lastkernel; loop=sedi.loop; gradint2center_read=sedi.gradint2center_read; gradint2center_phase=sedi.gradint2center_phase; centerindex_phase=sedi.centerindex_phase; readshape=sedi.readshape; templtype=sedi.templtype; echopairs=sedi.echopairs; lastecho=sedi.lastecho; build_seq(); } void SeqEpiDriverDefault::init_driver(const STD_string& object_label,double sweepwidth, float kread_min, float kread_max, unsigned readntps, float kphase_min, float kphase_max, unsigned phasentps,int startindex_phase, bool ramp_sampling,rampType rampmode, float ramp_steepness, const STD_string& nucleus, const dvector& phaselist, const dvector& freqlist, unsigned int echo_pairs) { set_label(object_label); Log odinlog(this,"init_driver"); echopairs=echo_pairs; double read_integral=kread_max-kread_min; double readgraddur=secureDivision(double(readntps),sweepwidth); float readstrength=secureDivision(read_integral,readgraddur); // double rastertime=systemInfo->get_rastertime(gradObj); // if(rastertime>0.0) { // int nraster=(int)secureDivision(readgraddur,rastertime); // if(rastertime*nraster!=readgraddur) nraster++; // always increase length of constant part // readgraddur=nraster*rastertime; // } ODINLOG(odinlog,normalDebug) << "readntps/sweepwidth=" << readntps << "/" << sweepwidth << STD_endl; ODINLOG(odinlog,normalDebug) << "kread_max/kread_min=" << kread_max << "/" << kread_min << STD_endl; ODINLOG(odinlog,normalDebug) << "readgraddur/readstrength=" << readgraddur << "/" << readstrength << STD_endl; adc.set_sweepwidth(sweepwidth,1.0); // To obtain correct pre/post delays double adcpredelay=get_acquisition_start(); double adcpostdelay=adc.get_duration()-adc.get_acquisition_duration()-adcpredelay; double minadcdelay=STD_max(adcpredelay,adcpostdelay); // The min delay at either sides of the ADC kernel, i.e. prior to posread ADC and after negread ODINLOG(odinlog,normalDebug) << "adcpredelay/adcpostdelay/minadcdelay=" << adcpredelay << "/" << adcpostdelay << "/" << minadcdelay << STD_endl; double rastime=systemInfo->get_rastertime(gradObj); // Sampling rate for ramps posread=SeqGradTrapez(object_label+"_posread",readDirection, readstrength,readgraddur,rastime,rampmode,minadcdelay,ramp_steepness); negread=SeqGradTrapez(object_label+"_negread",readDirection,-readstrength,readgraddur,rastime,rampmode,minadcdelay,ramp_steepness); ODINLOG(odinlog,normalDebug) << "posread/negread.get_duration()=" << posread.get_duration() << "/" << negread.get_duration() << STD_endl; double rampondur= posread.get_onramp_duration(); double rampoffdur=posread.get_offramp_duration(); double rampdur=0.5*(rampondur+rampoffdur); ODINLOG(odinlog,normalDebug) << "rampondur/rampoffdur/rampdur=" << rampondur << "/" << rampoffdur << "/" << rampdur << STD_endl; // defaults for non-ramp-sampling double adc2adc_duration=2.0*rampdur; // Duration from the end of acquisition of one ADC to the acquisition start of the next unsigned int nAcqPoints=readntps; float addint4deph=posread.get_onramp_integral(); // Extra dephaser for ramps unsigned int ramp_npoints=0; float rel_gradstartval=1.0; ODINLOG(odinlog,normalDebug) << "ramp_sampling=" << ramp_sampling << STD_endl; if(ramp_sampling) { // Shorten constant part of read gradient according to available ramp integral double onrampintegral_acq=posread.get_onramp_integral(minadcdelay,rampondur); double offrampintegral_acq=posread.get_offramp_integral(0.0,rampoffdur-minadcdelay); double rampintegral_acq=onrampintegral_acq+offrampintegral_acq; ODINLOG(odinlog,normalDebug) << "onrampintegral_acq/offrampintegral_acq/rampintegral_acq=" << onrampintegral_acq << "/" << offrampintegral_acq << "/" << rampintegral_acq << STD_endl; // calculate the shortening of the readout gradient as multiples of the dwell time double subtract_duration=secureDivision(rampintegral_acq, readstrength); unsigned int subtract_npoints=(unsigned int)(subtract_duration*sweepwidth+0.5); double subtract_duration_grid=secureDivision(subtract_npoints,sweepwidth); ODINLOG(odinlog,normalDebug) << "subtract_duration/subtract_npoints/subtract_duration_grid=" << subtract_duration << "/" << subtract_npoints << "/" << subtract_duration_grid << STD_endl; double newconstdur=posread.get_constgrad_duration()-subtract_duration_grid; ODINLOG(odinlog,normalDebug) << "newconstdur=" << newconstdur << STD_endl; posread.set_constgrad_duration(newconstdur); negread.set_constgrad_duration(newconstdur); ODINLOG(odinlog,normalDebug) << "posread/negread.get_duration()=" << posread.get_duration() << "/" << negread.get_duration() << STD_endl; // Number of extra points we can stuff into the ramps double effective_rampdur=rampdur-minadcdelay; ramp_npoints=(unsigned int)(effective_rampdur*sweepwidth); // round down so that the duration of the ADC kernel will not exceed the duration of the gradient kernel ODINLOG(odinlog,normalDebug) << "effective_rampdur/ramp_npoints=" << effective_rampdur << "/" << ramp_npoints << STD_endl; // New number of samples in ADC nAcqPoints=nAcqPoints-subtract_npoints+2*ramp_npoints; // Shortest possible delay between ADCs adc2adc_duration=2.0*minadcdelay; ODINLOG(odinlog,normalDebug) << "adc2adc_duration(rampsampling)=" << adc2adc_duration << STD_endl; // The relative gradient strength the ramp starts with rel_gradstartval=secureDivision(minadcdelay,rampdur); ODINLOG(odinlog,normalDebug) << "rel_gradstartval=" << rel_gradstartval << STD_endl; // Additional dephasing integral to account for the part of the ramp without sampling addint4deph=0.5*minadcdelay*readstrength*rel_gradstartval; } adc=SeqAcq(object_label+"_adc",nAcqPoints,sweepwidth,1.0,nucleus,phaselist,freqlist); ODINLOG(odinlog,normalDebug) << "adc.get_duration()=" << adc.get_duration() << STD_endl; // Construct readout shape for reco readshape.resize(nAcqPoints); readshape=1.0; unsigned int i; for(i=0; iget_grad_shift_delay(); if(fabs(sysgradshift)>max_possible_shift) { ODINLOG(odinlog,warningLog) << "sysgradshift=" << sysgradshift << " exceeds max_possible_shift=" << max_possible_shift << STD_endl; if(sysgradshift<0.0) sysgradshift=-max_possible_shift; else sysgradshift= max_possible_shift; } double acqdelay_shifted_begin=begin_delaydur+sysgradshift; double acqdelay_shifted_end =end_delaydur -sysgradshift; acqdelay_begin=SeqDelay(object_label+"_acqdelay_begin",acqdelay_shifted_begin); acqdelay_end=SeqDelay(object_label+"_acqdelay_end",acqdelay_shifted_end); acqdelay_middle=SeqDelay(object_label+"_acqdelay_middle",middle_acqdelay); float blipint=secureDivision(kphase_max-kphase_min,float(phasentps)); if(phasentps<=1) blipint=0.0; // We do not need blips in this case ODINLOG(odinlog,normalDebug) << "blipint=" << blipint << STD_endl; centerindex_phase=int(secureDivision(-kphase_min,kphase_max-kphase_min)*float(phasentps)); if(echopairs>0) centerindex_phase*=(2*echopairs); // The actual phase encoding blips phaseblip1st=SeqGradTrapez(object_label+"_phaseblip1st",blipint,phaseDirection,0.0,rastime,rampmode,rampdur); phaseblip2nd=SeqGradTrapez(object_label+"_phaseblip2nd",blipint,phaseDirection,0.0,rastime,rampmode,rampdur); if(phaseblip1st.get_gradduration()!=2.0*rampdur) { ODINLOG(odinlog,warningLog) << "Timing mismatch: phaseblip1st(" << phaseblip1st.get_gradduration() << ") != 2.0*rampdur(" << 2.0*rampdur << ")" << STD_endl; } phaseblip2nd.exclude_offramp_from_timing(true); if(phaseblip2nd.get_gradduration()!=2.0*rampdur) { ODINLOG(odinlog,warningLog) << "Timing mismatch: phaseblip2nd(" << phaseblip2nd.get_gradduration() << ") != 2.0*rampdur(" << 2.0*rampdur << ")" << STD_endl; } // The padding delays double phasezerodur1=posread.get_constgrad_duration()+phaseblip2nd.get_offramp_duration(); double phasezerodur2=posread.get_constgrad_duration(); double phasezerodur_lastblip=posread.get_gradduration()+negread.get_onramp_duration()+negread.get_constgrad_duration(); phasezero1st=SeqGradDelay(object_label+"_phasezero1st",phaseDirection,phasezerodur1); phasezero2nd=SeqGradDelay(object_label+"_phasezero2nd",phaseDirection,phasezerodur2); phasezero_lastblip=SeqGradDelay(object_label+"_phasezero_lastblip",phaseDirection,phasezerodur_lastblip); lastecho=bool(phasentps%2); int n_kernels=phasentps/2; ODINLOG(odinlog,normalDebug) << "n_kernels/startindex_phase/phasentps/lastecho=" << n_kernels << "/" << startindex_phase << "/" << phasentps << "/" << lastecho << STD_endl; gradkernel.set_label(object_label+"_gradkernel"); lastgradkernel.set_label(object_label+"_lastgradkernel"); oneadckernel.set_label(object_label+"_oneadckernel"); adckernel.set_label(object_label+"_adckernel"); lastadckernel.set_label(object_label+"_lastadckernel"); kernel.set_label(object_label+"_kernel"); lastkernel.set_label(object_label+"_lastkernel"); loop.set_label(object_label+"_loop"); loop.set_times(n_kernels); build_seq(); } unsigned int SeqEpiDriverDefault::get_numof_gradechoes() const { Log odinlog(this,"get_numof_gradechoes"); unsigned int looptimes=loop.get_times(); unsigned int result=2*looptimes+int(lastecho); if(echopairs>0) result*=2*echopairs; ODINLOG(odinlog,normalDebug) << "looptimes/lastecho/echopairs/result=" << looptimes << "/" << lastecho << "/" << echopairs << "/" << result << STD_endl; return result; } SeqAcqInterface& SeqEpiDriverDefault::set_template_type(templateType type) { templtype=type; adc.set_template_type(type); if(type==phasecorr_template) { phaseblip1st.set_strength(0.0); phaseblip2nd.set_strength(0.0); gradint2center_phase=0.0; } build_seq(); return *this; } fvector SeqEpiDriverDefault::get_gradintegral() const { fvector result(3); result=0; result += loop.get_times()*kernel.get_gradintegral(); if(lastecho) result += lastkernel.get_gradintegral(); return result; } double SeqEpiDriverDefault::get_acquisition_center() const { return (double(centerindex_phase)+0.5)*posread.get_gradduration(); } double SeqEpiDriverDefault::get_acquisition_start() const { return adc.get_acquisition_start(); } void SeqEpiDriverDefault::build_seq() { Log odinlog(this,"build_seq"); gradkernel.clear(); lastgradkernel.clear(); oneadckernel.clear(); adckernel.clear(); lastadckernel.clear(); lastkernel.clear(); oneadckernel = acqdelay_begin + adc + acqdelay_middle + adc + acqdelay_end; ODINLOG(odinlog,normalDebug) << "echopairs=" << echopairs << STD_endl; if(echopairs>0) { int nkernels=2*echopairs; for(int i=0; iphase_size) segments_cache=1; reduction_cache=reduction; if(!reduction_cache || reduction_cache>phase_size) reduction_cache=1; unsigned int phase_increment=segments_cache*reduction_cache; phasesize_cache=(unsigned int)(phase_size/phase_increment)*phase_increment; // phase_size must be multiple of (segments * reduction factor) echo_pairs_cache=echo_pairs; float gamma=systemInfo->get_gamma(nucleus); float resread=secureDivision( FOVread , read_size ); float resphase=secureDivision( FOVphase , phasesize_cache ); float k_indep_read=secureDivision( 2.0*PII , gamma * resread ); float k_indep_phase=secureDivision( 2.0*PII , gamma * resphase ); float k_indep_read_min=-0.5*k_indep_read; float k_indep_read_max=0.5*k_indep_read; float kspace_part=1.0-fourier_factor; if(kspace_part<0.0) kspace_part=0.0; if(kspace_part>1.0) kspace_part=1.0; float k_indep_phase_min; float k_indep_phase_max; if (invert_partial_fourier) { k_indep_phase_min=-0.5*k_indep_phase; k_indep_phase_max=0.5*kspace_part*k_indep_phase; } else { k_indep_phase_min=-0.5*kspace_part*k_indep_phase; k_indep_phase_max=0.5*k_indep_phase; } int phasenpts=(unsigned int)(float(phasesize_cache)*(0.5*kspace_part+0.5)); int startindex_phase=phasesize_cache-phasenpts; // Achieve segmentation/GRAPPA while keeping FOV unsigned int driver_phasenpts=int(secureDivision(phasenpts,phase_increment)+0.5); unsigned int driver_startindex=int(secureDivision(startindex_phase,phase_increment)+0.5); blipint_cache=secureDivision(k_indep_phase_max-k_indep_phase_min, driver_phasenpts); // remember blip integral for dephasing segmented EPI ODINLOG(odinlog,normalDebug) << "phase_increment/driver_phasenpts/driver_startindex=" << phase_increment << "/" << driver_phasenpts << "/" << driver_startindex << STD_endl; for(int itry=0; itry<10; itry++) { // several attempts possible to get a valid setup, but avois infinite loop // Use ADC of driver to adjust sweepwidth and use it in init_driver() // do this here so we do not have to do it separately in each driver // Thereby, add overampling at this point driver->set_sweepwidth(os_factor*sweepwidth,1.0); ODINLOG(odinlog,normalDebug) << "sweepwidth/os_factor/driver->get_sweepwidth()=" << sweepwidth << "/" << os_factor << "/" << driver->get_sweepwidth() << STD_endl; // Initialize driver for only one segment (and/or GRAPPA interleave), different segments will be encoded by dephasing gradient driver->init_driver(object_label,driver->get_sweepwidth(), k_indep_read_min, k_indep_read_max,readsize_os_cache, k_indep_phase_min, k_indep_phase_max, driver_phasenpts, driver_startindex, ramp_sampling,rampmode,ramp_steepness, nucleus,phaselist,freqlist,echo_pairs); double gradfreq=secureInv(2.0*driver->get_echoduration()); double low,upp; if(systemInfo->allowed_grad_freq(gradfreq, low, upp)) { break; } else { double downscale=STD_max(0.5,1.0-secureDivision(2.0*fabs(upp-low),gradfreq)); sweepwidth*=downscale; ODINLOG(odinlog,warningLog) << "Gradient switching frequency (" << gradfreq << ODIN_FREQ_UNIT << ") not allowed, scaling sweepwidth down (factor=" << downscale << ") to " << sweepwidth << ODIN_FREQ_UNIT << STD_endl; } } // Initialize dephasers/rephasers so that consecutive calls to get_dephgrad do not have to alter them create_deph_and_reph(); } void SeqAcqEPI::create_deph_and_reph() { Log odinlog(this,"create_deph_and_reph"); float centint_read= driver->get_gradintegral2center_read(); float centint_phase=driver->get_gradintegral2center_phase(); fvector gradint_driver=driver->get_gradintegral(); ODINLOG(odinlog,normalDebug) << "centint_read/centint_phase/gradint_driver=" << centint_read << "/" << centint_phase << "/" << gradint_driver.printbody() << STD_endl; float integral_deph_read =-centint_read; float integral_deph_phase =-centint_phase; float integral_reph_read= -(gradint_driver[readDirection]- centint_read); float integral_reph_phase=-(gradint_driver[phaseDirection]-centint_phase); float maxintegral=STD_max( STD_max(fabs(integral_deph_read),fabs(integral_deph_phase)), STD_max(fabs(integral_reph_read),fabs(integral_reph_phase)) ); float dephdur=secureDivision(maxintegral,fabs(driver->get_strength())); ODINLOG(odinlog,normalDebug) << "integral_deph_read/integral_deph_phase/maxintegral/dephdur=" << integral_deph_read << "/" << integral_deph_phase << "/" << maxintegral << "/" << dephdur << STD_endl; float rampdt=driver->get_ramp_rastertime(); STD_string object_label(get_label()); // Initialize objects with the same integral to obtain synchronous switch points dephobjs->readdephgrad= SeqGradTrapez(object_label+"_readdephgrad", maxintegral,readDirection, dephdur,rampdt,ramptype_cache); dephobjs->readrephgrad= SeqGradTrapez(object_label+"_readrephgrad", maxintegral,readDirection, dephdur,rampdt,ramptype_cache); dephobjs->phasedephgrad=SeqGradTrapez(object_label+"_phasedephgrad",maxintegral,phaseDirection,dephdur,rampdt,ramptype_cache); dephobjs->phaserephgrad=SeqGradTrapez(object_label+"_phaserephgrad",maxintegral,phaseDirection,dephdur,rampdt,ramptype_cache); // Adjust amplitude dephobjs->readdephgrad.set_integral(integral_deph_read); dephobjs->readrephgrad.set_integral(integral_reph_read); dephobjs->phasedephgrad.set_integral(integral_deph_phase); dephobjs->phaserephgrad.set_integral(integral_reph_phase); unsigned int phase_increment=segments_cache*reduction_cache; if(phase_increment>1) { // Create vector even if there is no phase encoding because it used in loop // use duration of on-ramp and constant part of read gradient as duration of constant part of the gradient vector double phasevecdur=dephobjs->readdephgrad.get_constgrad_duration()+dephobjs->readdephgrad.get_onramp_duration(); fvector deph_strengthvec(phase_increment); fvector reph_strengthvec(phase_increment); for(unsigned int i=0; iphasesegdephgrad=SeqGradVector(object_label+"_phasesegdephgrad", phaseDirection, deph_maxstrength, deph_strengthvec, phasevecdur); dephobjs->phasesegrephgrad=SeqGradVector(object_label+"_phasesegrephgrad", phaseDirection, reph_maxstrength, reph_strengthvec, phasevecdur); ODINLOG(odinlog,normalDebug) << "phasesegdephgrad.get_numof_iterations()=" << dephobjs->phasesegdephgrad.get_numof_iterations() << STD_endl; // achieve GRAPPA encoding by interleavedSegmented reordering if(reduction_cache>1) { dephobjs->phasesegdephgrad.set_reorder_scheme(interleavedSegmented, reduction_cache); dephobjs->phasesegrephgrad.set_reorder_scheme(interleavedSegmented, reduction_cache); ODINLOG(odinlog,normalDebug) << "reduction_cache=" << reduction_cache << STD_endl; ODINLOG(odinlog,normalDebug) << "phasesegdephgrad.get_numof_iterations()/reorder.get_numof_iterations()=" << dephobjs->phasesegdephgrad.get_numof_iterations() << "/" << dephobjs->phasesegdephgrad.get_reorder_vector().get_numof_iterations() << STD_endl; } } } const SeqVector* SeqAcqEPI::get_dephgrad(SeqGradChanParallel& dephobj, bool rephase) const { Log odinlog(this,"get_dephgrad"); const SeqVector* result=0; if(dephobjs->phasedephgrad.get_strength()!=0.0) { if(segments_cache>1 || reduction_cache>1) { if(rephase) { dephobj += ((dephobjs->readrephgrad)/(dephobjs->phasesegrephgrad)); result=&(dephobjs->phasesegrephgrad); } else { dephobj += ((dephobjs->readdephgrad)/(dephobjs->phasesegdephgrad)); result=&(dephobjs->phasesegdephgrad); } } else { if(rephase) dephobj += ((dephobjs->readrephgrad)/(dephobjs->phaserephgrad)); else dephobj += ((dephobjs->readdephgrad)/(dephobjs->phasedephgrad)); } } else { if(rephase) dephobj += dephobjs->readrephgrad; else dephobj += dephobjs->readdephgrad; } ODINLOG(odinlog,normalDebug) << "result/dephobj.get_gradintegral()=" << (void*)result << "/" << dephobj.get_gradintegral().printbody() << STD_endl; return result; } SeqAcqInterface& SeqAcqEPI::set_template_type(templateType type) { templtype_cache=type; driver->set_template_type(type); create_deph_and_reph(); return *this; } SeqAcqEPI::SeqAcqEPI(const SeqAcqEPI& sae) : driver(sae.get_label()) { common_init(); SeqAcqEPI::operator = (sae); } SeqAcqEPI::SeqAcqEPI(const STD_string& object_label) : SeqObjBase(object_label), driver(object_label) { common_init(); } RecoValList SeqAcqEPI::get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const { Log odinlog(this,"get_recovallist"); int nTEs=2*echo_pairs_cache; if(nTEs<=0) nTEs=1; int nechoes=driver->get_numof_gradechoes(); int startindex_phase=int(phasesize_cache)-nechoes/nTEs*segments_cache*reduction_cache; // recalculate with actual number of grad echoes ODINLOG(odinlog,normalDebug) << "nechoes/phasesize/startindex_phase=" << nechoes << "/" << phasesize_cache << "/" << startindex_phase << STD_endl; unsigned int padded_zeroes=0; kSpaceCoord kcoord_base(driver->get_kcoord_template(padded_zeroes)); kcoord_base.oversampling=os_factor_cache; RecoValList result; int isegment=dephobjs->phasesegdephgrad.get_current_index(); if(templtype_cache==no_template) ODINLOG(odinlog,normalDebug) << "isegment=" << isegment << STD_endl; for(int iecho=0; iecho0) { kcoord.index[te]=iecho%nTEs; } coords.append_coord(kcoord); RecoValList rvl; rvl.set_value(kcoord.number); result.add_sublist(rvl); } return result; } SeqAcqInterface& SeqAcqEPI::set_sweepwidth(double sw, float os_factor) { Log odinlog(this,"set_sweepwidth"); ODINLOG(odinlog,warningLog) << "Ignoring request to change sweepwidth after construction" << STD_endl; return *this; } bool SeqAcqEPI::prep() { Log odinlog(this,"prep"); double gradfreq=secureInv(2.0*driver->get_echoduration()); double low,upp; if(!systemInfo->allowed_grad_freq(gradfreq, low, upp)) { ODINLOG(odinlog,normalDebug) << "gradient frequency " << gradfreq << ODIN_FREQ_UNIT << " not allowed" << STD_endl; return false; } fvector gread=driver->get_readout_shape(); unsigned int greadsize=gread.size(); if( greadsize != readsize_os_cache ) { // assume ramp sampling driver->set_readout_shape(gread,readsize_os_cache); } if(echo_pairs_cache>0) { // Only store TEs in a multi-TE EPI scan int nTEs=2*echo_pairs_cache; dvector TEs(nTEs); double echodur=driver->get_echoduration(); TEs.fill_linear(0.5*echodur, (0.5+double(nTEs-1))*echodur); recoInfo->set_DimValues(te,TEs); } ODINLOG(odinlog,normalDebug) << "templtype_cache=" << templtype_cache << STD_endl; if(templtype_cache==no_template) { // Only store echo time stamps for non-template EPI as they are the basis for field-map based distortion corrections unsigned int nechoes=get_numof_gradechoes(); double echodur=driver->get_echoduration(); ODINLOG(odinlog,normalDebug) << "nechoes/echodur=" << nechoes << "/" << echodur << STD_endl; if(nechoes && echodur>0.0) { // discard empty EPIs dvector echotimestamps(nechoes); echotimestamps.fill_linear(0.0, double(nechoes-1)*echodur); ODINLOG(odinlog,normalDebug) << "echotimestamps=" << echotimestamps.printbody() << STD_endl; recoInfo->set_DimValues(echo,echotimestamps); } } return true; } SeqAcqEPI& SeqAcqEPI::operator = (const SeqAcqEPI& sae) { SeqObjBase::operator = (sae); readsize_os_cache=sae.readsize_os_cache; os_factor_cache=sae.os_factor_cache; phasesize_cache=sae.phasesize_cache; segments_cache=sae.segments_cache; reduction_cache=sae.reduction_cache; echo_pairs_cache=sae.echo_pairs_cache; blipint_cache=sae.blipint_cache; templtype_cache=sae.templtype_cache; ramptype_cache=sae.ramptype_cache; driver=sae.driver; create_deph_and_reph(); // initialize dephobjs return *this; } odin-1.8.5/odinseq/seqdec.cpp0000644000175000017500000000664611322062345013023 00000000000000#include "seqdec.h" #include SeqDecoupling::SeqDecoupling(const STD_string& object_label,const STD_string& nucleus,float decpower,const dvector& freqlist, const STD_string decprog,float decpulsduration) : SeqObjList(object_label), SeqFreqChan(object_label,nucleus,freqlist), decdriver(object_label) { set_decpower(decpower); set_program(decprog); set_pulsduration(decpulsduration); } SeqDecoupling::SeqDecoupling(const SeqDecoupling& sd) { SeqDecoupling::operator = (sd); } SeqDecoupling::SeqDecoupling(const STD_string& object_label) : SeqObjList(object_label), SeqFreqChan(object_label), decdriver(object_label) { set_decpower(120.0); set_program(""); set_pulsduration(0.0); } bool SeqDecoupling::prep() { if(!SeqFreqChan::prep()) return false; return decdriver->prep_driver(SeqObjList::get_duration(),get_channel(),get_decpower(),get_program(),get_pulsduration()); } const SeqVector& SeqDecoupling::get_freqlist_vector() const { SeqSimultanVector* result=new SeqSimultanVector(STD_string(get_label())+"_instancevec"); result->set_temporary(); for(constinstiter it=get_const_inst_begin(); it!=get_const_inst_end(); ++it) (*result)+=(**it); return *result; } STD_string SeqDecoupling::get_program(programContext& context) const { STD_string result; result+=decdriver->get_preprogram(context,get_iteratorcommand(freqObj)); result+=SeqObjList::get_program(context); result+=decdriver->get_postprogram(context); return result; } SeqValList SeqDecoupling::get_freqvallist(freqlistAction action) const { Log odinlog(this,"get_freqvallist"); SeqValList result(get_label()); double newfreq=SeqFreqChan::get_frequency(); if(action==calcDecList) { result.set_value(newfreq); ODINLOG(odinlog,normalDebug) << "freq=" << newfreq << STD_endl; } return result; } void SeqDecoupling::clear_container() { SeqObjList::clear_container(); clear_instances(); } double SeqDecoupling::get_duration() const { double result=0.0; result+=decdriver->get_preduration(); result+=SeqObjList::get_duration(); result+=decdriver->get_postduration(); return result; } unsigned int SeqDecoupling::event(eventContext& context) const { Log odinlog(this,"event"); unsigned int result=0; double start=context.elapsed+decdriver->get_preduration(); if(context.action==seqRun) { SeqFreqChan::pre_event(context,start); decdriver->event(context,start); result+=SeqObjList::event(context); SeqFreqChan::post_event(context,start+SeqObjList::get_duration()); } if(context.event_progmeter) context.event_progmeter->increase_counter(); result++; return result; } SeqDecoupling& SeqDecoupling::operator () (const SeqObjBase& so) { SeqDecoupling& dec=set_embed_body(so); return dec; } STD_string SeqDecoupling::get_program() const {return decprogram;} void SeqDecoupling::set_program(const STD_string& p) { decprogram=p; } double SeqDecoupling::get_pulsduration() const {return pulsduration;} void SeqDecoupling::set_pulsduration(float d) { pulsduration=d; } SeqDecoupling& SeqDecoupling::operator = (const SeqDecoupling& sd) { SeqObjList::operator = (sd); SeqFreqChan::operator = (sd); decdriver=sd.decdriver; set_program(sd.get_program()); set_decpower(sd.get_decpower()); set_pulsduration(sd.get_pulsduration()); return *this; } int SeqDecoupling::set_body(const SeqObjBase& so) { clear(); (*this)+=(so); return 0; } odin-1.8.5/odinseq/seqtemplate.h0000644000175000017500000000513511322062345013540 00000000000000/*************************************************************************** seqtemplate.h - description ------------------- begin : Mon Tue 23 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQTEMPLATE_H #define SEQTEMPLATE_H #include /** * @addtogroup odinseq * @{ */ struct SeqFieldMapPars; // forward declaration struct SeqFieldMapObjects; // forward declaration /** * \brief Multi-echo module for field-map pre-scan * * In order to acquire a field-map together with the actual scan, this * sequence module employs an EPI-like readout where each shot acquires * an even number of alternating echoes (each with a different TE) * separately for each line in k-space. * */ class SeqFieldMap : public SeqObjList { // Disable copying SeqFieldMap(const SeqFieldMap& sfm) {} SeqFieldMap& operator = (const SeqFieldMap& sfm) {return *this;} void alloc_data(); SeqFieldMapPars* pars; SeqFieldMapObjects* objs; public: /** * Constructs a field-map scan */ SeqFieldMap() : pars(0), objs(0) {} ~SeqFieldMap(); /** * Initialize field-map scan with default values, sequence objects are prefixed by 'objlabel'. * This function is usually called in the sequence initialization step. */ void init(const STD_string& objlabel); /** * Builds the field-map scan using bandwidth 'sweepwidth' with oversampling factor 'os_factor', an extra preparation 'prep' prior to each excitation and minimum relaxation delay 'min_relaxdelay'. * This function is usually called in the sequence building step. */ void build_seq(double sweepwidth, float os_factor=1.0, const SeqObjList& prep=SeqObjList(), double min_relaxdelay=0.0); /** * Returns block of local parameters */ JcampDxBlock& get_parblock(); }; /** @} */ #endif odin-1.8.5/odinseq/seqgradspiral.cpp0000644000175000017500000002072711735132611014416 00000000000000#include "seqgradspiral.h" #include "seqgradramp.h" #include "odinpulse.h" // for _TRAJ_OPTIMIZE_PARLABEL_ #define TEST_NPTS 1000 float SeqGradSpiral::readout_npts() const { Log odinlog(this,"readout_npts"); if(!traj_cache) return -1.0; // make a test run to approximate the tangential step size, maximum gradient strengt and slew rate float deltaKtangential=0.0; float last_kx=0.0; float last_ky=0.0; float last_Gx=0.0; float last_Gy=0.0; float max_grad_magn=0.0; float max_grad_diff=0.0; for(unsigned int i=0; icalculate(s); if(i) { deltaKtangential=STD_max(double(deltaKtangential),norm(tds.kx-last_kx,tds.ky-last_ky)); max_grad_diff=STD_max(double(max_grad_diff),fabs(tds.Gx-last_Gx)); max_grad_diff=STD_max(double(max_grad_diff),fabs(tds.Gy-last_Gy)); } max_grad_magn=STD_max(double(max_grad_magn),fabs(tds.Gx)); max_grad_magn=STD_max(double(max_grad_magn),fabs(tds.Gy)); last_kx=tds.kx; last_ky=tds.ky; last_Gx=tds.Gx; last_Gy=tds.Gy; } ODINLOG(odinlog,normalDebug) << "deltaKtangential/max_grad_magn/max_grad_diff = " << deltaKtangential << "/" << max_grad_magn << "/" << max_grad_diff << STD_endl; if(deltaKtangential==0.0) { ODINLOG(odinlog,errorLog) << "Zero trajectory" << STD_endl; return 0; } // the desired (relative) k-space step size float deltaKdesired=secureInv(sizeRadial_cache); // calculate the total number of points to get a sufficient coverage of k-space float npts=float(TEST_NPTS)*secureDivision(deltaKtangential,deltaKdesired); float k0=secureDivision(PII,resolution_cache); float gradfactor=secureDivision(k0, gamma_cache*npts*dt_cache); // Estimate maximum gradient strength and slew rate according to the test trajectory float dt_test=dt_cache*secureDivision(npts,TEST_NPTS); float maxgrad_test = max_grad_magn * gradfactor; float maxslew_test = secureDivision(max_grad_diff * gradfactor, dt_test); ODINLOG(odinlog,normalDebug) << "dt_test/maxgrad_test/maxslew_test = " << dt_test << " / " << maxgrad_test << " / " << maxslew_test << STD_endl; // Correct npts if max grad strength or slew is exceeded float prolongfactor=1.0; if(maxgrad_test>systemInfo->get_max_grad()) { prolongfactor=STD_max(double(prolongfactor),secureDivision(maxgrad_test,systemInfo->get_max_grad())); } if(maxslew_test>systemInfo->get_max_slew_rate()) { prolongfactor=STD_max(double(prolongfactor),secureDivision(maxslew_test,systemInfo->get_max_slew_rate())); } ODINLOG(odinlog,normalDebug) << "prolongfactor = " << prolongfactor << STD_endl; if(prolongfactor>1.0) npts*=prolongfactor; return npts; } float SeqGradSpiral::evaluate(const fvector& spirpar) const { Log odinlog(this,"evaluate"); if(!traj_cache) return -1.0; ODINLOG(odinlog,normalDebug) << "spirpar=" << spirpar[0] << STD_endl; if(!traj_cache->set_parameter(_TRAJ_OPTIMIZE_PARLABEL_,ftos(spirpar[0]))) { ODINLOG(odinlog,normalDebug) << _TRAJ_OPTIMIZE_PARLABEL_ << " not available" << STD_endl; return -1.0; } float result=readout_npts(); ODINLOG(odinlog,normalDebug) << "result(" << spirpar[0] << ")=" << result << STD_endl; return result; } SeqGradSpiral::SeqGradSpiral(const STD_string& object_label, JDXtrajectory& traj, double dt, float resolution, unsigned int sizeRadial, unsigned int numofSegments, bool inwards, bool optimize, const STD_string& nucleus) : SeqGradChanParallel(object_label), predelay(0.0), dt_cache(dt), resolution_cache(resolution), sizeRadial_cache(sizeRadial), gamma_cache(systemInfo->get_gamma(nucleus)) { Log odinlog(this,"SeqGradSpiral(...)"); common_init(); unsigned int i; if(traj.get_function_mode()!=twoDeeMode) { ODINLOG(odinlog,errorLog) << "traj has wrong funcMode" << STD_endl; return; } if(!numofSegments) numofSegments=1; // set the number of cycles according to the step size in radial direction traj.set_parameter("NumCycles",itos(int(secureDivision(sizeRadial,(2*numofSegments))))); traj_cache=&traj; if(optimize && traj.set_parameter(_TRAJ_OPTIMIZE_PARLABEL_,ftos(0.0))) { // perform optimization only if appropriate parameter is available float minpar=bruteforce_minimize1d(*this, 0.0, 1.0)[0]; ODINLOG(odinlog,normalDebug) << "minpar=" << minpar << STD_endl; traj.set_parameter(_TRAJ_OPTIMIZE_PARLABEL_,ftos(minpar)); } float fnpts=readout_npts(); if(fnpts<=0.0) { ODINLOG(odinlog,errorLog) << "Cannot calculate readout length" << STD_endl; return; } unsigned int npts=(unsigned int)(fnpts+0.5); float k0=secureDivision(PII,resolution); float gradfactor=secureDivision(k0, gamma_cache*npts*dt); spiral_dur=npts*dt; ODINLOG(odinlog,normalDebug) << "npts / k0 / spiral_dur = " << npts << " / " << k0 << " / " << spiral_dur << STD_endl; if(spiral_dur==0.0) { ODINLOG(odinlog,errorLog) << "Zero duration spiral" << STD_endl; return; } fvector Gx(npts); fvector Gy(npts); denscomp.resize(npts); kx.resize(npts); ky.resize(npts); float sign=1.0; if(!inwards) sign=-1.0; // trajectory is traversed backwards // calculate the gradient arrays for (i=0; i odinlog(this,"get_ktraj"); fvector result(spiral_size()); result=0.0; if(channel==readDirection) result=kx; if(channel==phaseDirection) result=ky; return result; } void SeqGradSpiral::build_seq() { clear(); gxdelay.set_duration(predelay); gydelay.set_duration(predelay); if(predelay>0.0) { (*this) += (gxdelay+gx) / (gydelay+gy); } else { (*this) += gx / gy; } } odin-1.8.5/odinseq/seqdelay.h0000644000175000017500000000613711322062345013026 00000000000000/*************************************************************************** seqdelay.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDELAY_H #define SEQDELAY_H #include #include #include /** * @ingroup odinseq_internals * The base class for platform specific drivers of delays */ class SeqDelayDriver : public SeqDriverBase { public: SeqDelayDriver() {} virtual ~SeqDelayDriver() {} virtual STD_string get_program(programContext& context, double duration, const STD_string& cmd, const STD_string& durcmd) const = 0; virtual SeqDelayDriver* clone_driver() const = 0; }; /////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * \brief Timing delay * * This class represents a delay with an optional command. */ class SeqDelay : public SeqObjBase, public SeqDur { public: /** * Constructs a delay labeled 'object_label' with the following properties: * - delayduration: The duration of the delay. * - command: An optional command that will be issued during the delay in * the pulse program. * - durationVariable: If the the command that specifies the delay duration in * the pulse program should differ from the default, it can be * overwritten by this string. */ SeqDelay(const STD_string& object_label = "unnamedSeqDelay",float delayduration=0.0, const STD_string& command="",const STD_string& durationVariable="" ); /** * Constructs a delay which is a copy of 'sd' */ SeqDelay(const SeqDelay& sd); /** * This assignment operator will make this object become an exact copy of 'sd'. */ SeqDelay& operator = (const SeqDelay& sd); /** * This assignment operator can be used to specify the duration of the delay */ SeqDelay& operator = (float dur); /** * Specifies the extra command for the delay */ SeqDelay& set_command(const STD_string& command); // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; private: mutable SeqDriverInterface delaydriver; STD_string cmd; STD_string durcmd; }; /** @} */ #endif odin-1.8.5/odinseq/seqdriver_paravision.cpp0000644000175000017500000000257611322062345016014 00000000000000#ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif // include Qt stuff first to avoid ambiguities with 'debug' /* #ifdef GUISUPPORT #include #endif */ #ifdef PARAVISION_PLUGIN #include "../platforms/Paravision/odinseq_paravision/seqparavision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqacq_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqacqepi_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqcounter_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqdec_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqdelay_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqfreq_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqgradchan_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqgradtrapez_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqlist_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqparallel_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqphase_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqpilot_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqpuls_paravision.cpp" #include "../platforms/Paravision/odinseq_paravision/seqtrigg_paravision.cpp" #endif odin-1.8.5/odinseq/seqtree.cpp0000644000175000017500000000352411322062345013217 00000000000000#ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif #ifdef HAVE_TYPEINFO #include #endif #include "seqtree.h" SeqTreeObj::SeqTreeObj() : SeqClass() { Log odinlog("SeqTreeObj","SeqTreeObj()"); set_label("unnamedSeqTreeObj"); // this is neccessary because SeqClass is a virtual base class } void SeqTreeObj::display_event(eventContext& context) const { if(!context.event_display) return; svector columntext; columntext.resize(2); columntext[0]=ftos(context.elapsed); columntext[1]=get_label(); context.event_display->display_node(this,0,looplevel,columntext); } void SeqTreeObj::query(queryContext& context) const { if(context.action==count_acqs) context.numof_acqs=0; if(context.action==checkoccur) context.checkoccur_result=context.checkoccur_result || (context.checkoccur_sto==this); if(context.action==display_tree) { svector columntext; columntext.resize(4); const char* type="unknown"; #ifdef HAVE_TYPEINFO type=typeid(*this).name(); while( (*type) >='0' && (*type) <='9' ) type++; #endif STD_string typestr(type); // replace SeqMethod_... by SeqMethod for seqtree dump of seqtest if(typestr.find("SeqMethod_")==0) typestr="SeqMethod"; columntext[0]=get_label(); columntext[1]=typestr; columntext[2]=ftos(get_duration()); columntext[3]=get_properties(); context.tree_display->display_node(this,context.parentnode,context.treelevel,columntext); } } bool SeqTreeObj::contains(const SeqTreeObj* sto) const { queryContext qc; qc.action=checkoccur; qc.checkoccur_sto=sto; this->query(qc); return qc.checkoccur_result; } void SeqTreeObj::tree(SeqTreeCallbackAbstract* display) const { queryContext qc; qc.action=display_tree; qc.tree_display=display; qc.parentnode=this; this->query(qc); } int SeqTreeObj::looplevel=0; odin-1.8.5/odinseq/seqlist.cpp0000644000175000017500000001405511322062345013234 00000000000000#include "seqlist.h" #include "seqloop.h" #include "seqdec.h" #include "seqparallel.h" #include "seqgradobj.h" #include "seqgradchanparallel.h" #include #include SeqObjList::SeqObjList(const STD_string& object_label) : SeqObjBase(object_label), listdriver(object_label) { Log odinlog(this,"SeqObjList()"); } SeqObjList::SeqObjList(const SeqObjList& so) { SeqObjList::operator = (so); } SeqObjList::~SeqObjList() { Log odinlog(this,"~SeqObjList()"); } SeqObjList& SeqObjList::operator = (const SeqObjList& so) { SeqObjBase::operator = (so); List::operator = (so); listdriver=so.listdriver; return *this; } SeqObjList& SeqObjList::operator = (const SeqObjLoop& sl) { clear(); (*this)+=sl; return *this; } SeqObjList& SeqObjList::operator = (const SeqDecoupling& sd) { clear(); (*this)+=sd; return *this; } SeqObjList& SeqObjList::operator = (const SeqObjBase& soa) { clear(); (*this)+=soa; return *this; } SeqObjList& SeqObjList::operator += (const SeqObjBase& soa) { Log odinlog(this,"+="); if((&soa)->contains(this)) { ODINLOG(odinlog,errorLog) << "Refusing to append >" << soa.get_label() << "< to >" << get_label() << "< which would then contain itself" << STD_endl; } else append(soa); return *this; } SeqObjList& SeqObjList::operator += (SeqGradObjInterface& sgoa) { SeqParallel* par=new SeqParallel(STD_string("[")+sgoa.get_label()+"]"); par->set_temporary(); par->set_gradptr(&sgoa); (*this)+=(*par); return *this; } SeqObjList& SeqObjList::operator += (SeqGradChan& sgc) { SeqGradChanList* sgcl=new SeqGradChanList(STD_string("(")+sgc.get_label()+")"); sgcl->set_temporary(); (*sgcl)+=sgc; (*this)+=(*sgcl); return *this; } SeqObjList& SeqObjList::operator += (SeqGradChanList& sgcl) { SeqGradChanParallel* par=new SeqGradChanParallel(STD_string("{")+sgcl.get_label()+"}"); par->set_temporary(); (*par)+=sgcl; (*this)+=(*par); return *this; } unsigned int SeqObjList::event(eventContext& context) const { Log odinlog(this,"event"); unsigned int result=0; const RotMatrix* rotmatrix=0; if(gradrotmatrixvec.get_handled()) { current_gradrotmatrixvec.set_handled(gradrotmatrixvec.get_handled()); rotmatrix=&(current_gradrotmatrixvec.get_handled()->get_current_matrix()); } listdriver->pre_event(context,rotmatrix); for(constiter it=get_const_begin();it!=get_const_end();++it) { listdriver->pre_itemevent(*it,context); ODINLOG(odinlog,normalDebug) << (*it)->get_label() << "->event" << STD_endl; result+=(*it)->event(context); listdriver->post_itemevent(*it,context); } listdriver->post_event(context,rotmatrix); current_gradrotmatrixvec.clear_handledobj(); return result; } double SeqObjList::get_duration() const { Log odinlog(this,"get_duration"); double result=0.0; if(gradrotmatrixvec.get_handled()) current_gradrotmatrixvec.set_handled(gradrotmatrixvec.get_handled()); for(constiter it=get_const_begin();it!=get_const_end();++it) { result+=(*it)->get_duration(); ODINLOG(odinlog,normalDebug) << "duration(" << (*it)->get_label() << ")=" << (*it)->get_duration() << STD_endl; } current_gradrotmatrixvec.clear_handledobj(); return result; } STD_string SeqObjList::get_properties() const { return "NumOfObjects="+itos(size()); } STD_string SeqObjList::get_program(programContext& context) const { STD_string result; if(gradrotmatrixvec.get_handled()) current_gradrotmatrixvec.set_handled(gradrotmatrixvec.get_handled()); result+=listdriver->pre_program(context, gradrotmatrixvec.get_handled()); for(constiter it=get_const_begin();it!=get_const_end();++it) { result+=listdriver->get_itemprogram(*it,context); } result+=listdriver->post_program(context, gradrotmatrixvec.get_handled()); current_gradrotmatrixvec.clear_handledobj(); return result; } void SeqObjList::query(queryContext& context) const { Log odinlog(this,"query"); SeqTreeObj::query(context); // defaults context.treelevel++; unsigned int acqresult=0; for(constiter it=get_const_begin();it!=get_const_end();++it) { context.parentnode=this; // reset to this because it might changed by last query (*it)->query(context); acqresult+=context.numof_acqs; } context.treelevel--; if(context.action==count_acqs) context.numof_acqs=acqresult; } RecoValList SeqObjList::get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const { Log odinlog(this,"get_recovallist"); RecoValList result(get_label()); for(constiter it=get_const_begin();it!=get_const_end();++it) { ODINLOG(odinlog,normalDebug) << reptimes << "x from " << (*it)->get_label() << STD_endl; RecoValList oneiter=(*it)->get_recovallist(reptimes,coords); result.add_sublist(oneiter); } ODINLOG(odinlog,normalDebug) << "returning" << STD_endl; return result; } SeqValList SeqObjList::get_freqvallist(freqlistAction action) const { Log odinlog(this,"get_freqvallist"); SeqValList result(get_label()); for(constiter it=get_const_begin();it!=get_const_end();++it) { SeqValList oneiter=(*it)->get_freqvallist(action); result.add_sublist(oneiter); } return result; } SeqValList SeqObjList::get_delayvallist() const { Log odinlog(this,"get_delayvallist"); SeqValList result(get_label()); for(constiter it=get_const_begin();it!=get_const_end();++it) { SeqValList oneiter=(*it)->get_delayvallist(); result.add_sublist(oneiter); } return result; } double SeqObjList::get_rf_energy() const { double result=0.0; for(constiter it=get_const_begin();it!=get_const_end();++it) { result+=(*it)->get_rf_energy(); } return result; } bool SeqObjList::prep() { if(!SeqObjBase::prep()) return false; return listdriver->prep_driver(); } Handler SeqObjList::current_gradrotmatrixvec; // Template instantiations template class ListItem; template class List; template class Handler; odin-1.8.5/odinseq/seqmakefile.h0000644000175000017500000000507611322062345013506 00000000000000/*************************************************************************** seqmakefile.h - description ------------------- begin : Wed Apr 14 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQMAKEFILE_H #define SEQMAKEFILE_H #include #ifndef NO_CMDLINE /** * @ingroup odinseq_internals * Helper class to generate Makefiles for different platforms */ class SeqMakefile : public SeqClass { public: SeqMakefile(const STD_string& methlabel, const STD_string& odin_install_prefix="", const STD_string& compiler="", const STD_string& compiler_flags=CXXFLAGS, const STD_string& linker="", const STD_string& extra_includes="", const STD_string& extra_libs=""); STD_string get_Makefile(const STD_string& methroot) const; svector get_method_compile_chain(bool executable, bool shared_object) const; STD_string get_method_clean() const; STD_string get_method_install(const STD_string& methdir) const; svector get_odin4idea_method_compile_chain(const STD_string& in_dir, const STD_string& odindir, const STD_string& vxworks_path, const STD_string& vxworks_cxx, const STD_string& vxworks_flags, const STD_string& win_cxx, const STD_string& hostd_flags, const STD_string& host_flags) const; static STD_string get_exe_postfix(); static STD_string get_so_postfix(); static STD_string get_obj_postfix(); private: STD_string get_methlabel() const {return get_label();} STD_string get_methdefines(const STD_string& main, const STD_string& classlabel) const; JDXfileName inst_prefix; STD_string cxx; STD_string cxxflags; STD_string ld; STD_string add_includes; STD_string add_libs; }; #endif #endif odin-1.8.5/odinseq/seqgradchanparallel.h0000644000175000017500000001033311322062345015205 00000000000000/*************************************************************************** seqgradchanparallel.h - description ------------------- begin : Thu Apr 22 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADCHANPARALLEL_H #define SEQGRADCHANPARALLEL_H #include #include #include //////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The base class for platform specific drivers of lists of simultaneous gradient objects */ class SeqGradChanParallelDriver : public SeqDriverBase { public: SeqGradChanParallelDriver() {} virtual ~SeqGradChanParallelDriver() {} virtual bool prep_driver(SeqGradChanList* chanlists[3]) const = 0; virtual STD_string get_program(programContext& context) const = 0; virtual SeqGradChanParallelDriver* clone_driver() const = 0; }; //////////////////////////////////////////////////////////////////// /** * @addtogroup odinseq_internals * @{ */ /** * This class is a container for three SeqGradChanList's */ class SeqGradChanParallel : public SeqGradObjInterface { public: /** * Construct an empty gradient channel list with the given label */ SeqGradChanParallel(const STD_string& object_label = "unnamedSeqGradChanParallel" ); /** * Constructs a copy of 'sgcp' */ SeqGradChanParallel(const SeqGradChanParallel& sgcp); /** * Destructor */ ~SeqGradChanParallel(); /** * Assignment operator that makes this gradient sequence object become a copy of 'sgcp' */ SeqGradChanParallel& operator = (const SeqGradChanParallel& sgcp); /** * Uses 'sgc' for the corresponding channel */ SeqGradChanParallel& operator /= (SeqGradChan& sgc); /** * Uses 'sgcl' for the corresponding channel */ SeqGradChanParallel& operator /= (SeqGradChanList& sgcl); // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; STD_string get_properties() const; unsigned int event(eventContext& context) const; void query(queryContext& context) const; // overloading virtual function from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); SeqGradInterface& invert_strength(); float get_strength() const; fvector get_gradintegral() const; double get_gradduration() const; SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); /** * Appends 'sgc' to this */ SeqGradChanParallel& operator += (SeqGradChan& sgc); /** * Appends 'sgcl' to this */ SeqGradChanParallel& operator += (SeqGradChanList& sgcl); /** * Appends 'sgcp' to this */ SeqGradChanParallel& operator += (SeqGradChanParallel& sgcp); /** * Clear all sublists */ void clear(); private: friend class SeqOperator; friend class SeqGradChan; friend class SeqGradChanList; friend class SeqGradEPI; friend class SeqEpiKernel; // overwriting virtual functions from SeqClass bool prep(); void clear_container(); // overwriting virtual functions from SeqGradObjInterface bool need_gp_terminator() const {return true;} void padd_channel_with_delay(direction chanNo, double maxdur); SeqGradChanList* get_gradchan(direction channel) const; SeqGradChanParallel& set_gradchan(direction channel, SeqGradChanList* sgcl); mutable SeqDriverInterface paralleldriver; Handler gradchan[3]; }; /** @} */ #endif odin-1.8.5/odinseq/seqmeth.cpp0000644000175000017500000005406211322062345013220 00000000000000#include "seqmeth.h" #include "seqacq.h" #include "seqdelayvec.h" #include "seqfreq.h" #include "seqpulsar.h" #include "seqcmdline.h" // for gradient intro #include "seqgradpulse.h" #include "seqdelay.h" #include #include ////////////////////////////////////////////////////////////////////// #if defined(HAVE_DL) && defined(HAVE_SIGNAL_H) && defined(HAVE_SETJMP_H) #define CATCH_SEGFAULT_ON_UNIX #endif #ifdef CATCH_SEGFAULT_ON_UNIX #include #include #include // forward declaration function which will be registered as signal handler void segfaultHandler( int ); // Class to catch segmentation faults in functions of the method plug-in. // Otherwise the whole ODIN UI would crash... class CatchSegFaultContext : public StaticHandler { public: CatchSegFaultContext(const char* contextlabel) { Log odinlog(contextlabel,"CatchSegFaultContext"); (*lastmsg)=""; (*label)=contextlabel; sa.sa_handler=segfaultHandler; // sa.sa_sigaction=0; sa.sa_flags=0; sigprocmask(SIG_SETMASK,&sa.sa_mask,0); /* #ifndef sgi sa.sa_restorer=0; #endif */ if(sigaction(SIGSEGV,&sa,0)) ODINLOG(odinlog,errorLog) << "unable to register segfaultHandler for " << (*label) << STD_endl; } ~CatchSegFaultContext() { Log odinlog(label->c_str(),"~CatchSegFaultContext"); sa.sa_handler=SIG_DFL; sigaction(SIGSEGV,&sa,0); segfault_occured=false; } bool segfault() volatile { Log odinlog(label->c_str(),"segfault"); bool result=segfault_occured; segfault_occured=false; return result; } static void catch_segfault() { Log odinlog("","catch_segfault"); if(lastmsg) { (*lastmsg)="Segmentation fault in " + (*label); ODINLOG(odinlog,errorLog) << (*lastmsg) << STD_endl; } segfault_occured=true; longjmp(CatchSegFaultContext::segfault_cont_pos, 0); } static void report_exception(const char* funcname) { Log odinlog("","report_exception"); if(lastmsg) { (*lastmsg)=STD_string("Exception in ") + funcname; ODINLOG(odinlog,errorLog) << (*lastmsg) << STD_endl; } } static const char* get_lastmsg() { if(lastmsg) return lastmsg->c_str(); return 0; } // functions to initialize/delete static members by the StaticHandler template class static void init_static() { label=new STD_string; lastmsg=new STD_string; } static void destroy_static() { if(label) delete label; label=0; if(lastmsg) delete lastmsg; lastmsg=0; } private: friend class SeqMethod; friend class SeqMethodProxy; static STD_string* label; struct sigaction sa; static bool segfault_occured; static jmp_buf segfault_cont_pos; static STD_string* lastmsg; }; STD_string* CatchSegFaultContext::label=0; bool CatchSegFaultContext::segfault_occured = false; jmp_buf CatchSegFaultContext::segfault_cont_pos; STD_string* CatchSegFaultContext::lastmsg=0; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; // function which will be registered as signal handler void segfaultHandler( int ) {CatchSegFaultContext::catch_segfault();} // macro to call functions whose segfaults will be catched #define CATCHSEGFAULT(func,func_name)\ try {\ volatile CatchSegFaultContext csfc(func_name);\ setjmp(CatchSegFaultContext::segfault_cont_pos);\ if(!csfc.segfault()) func;\ else return false;\ } catch(...) {\ CatchSegFaultContext::report_exception(func_name);\ return false;\ } #else // simply call the function if we do not have CatchSegFaultContext #define CATCHSEGFAULT(func,func_name) func; #endif ////////////////////////////////////////////////////////////////////// #ifdef USING_WIN32 #ifndef ODIN4IDEA #define METHOD_IN_DLL #endif #endif #ifdef METHOD_IN_DLL // function signature typedef void (*set_global_stuff_fptr) (SingletonMap* sol_map); #if __cplusplus extern "C" { #endif // the DLL exported function which will be called after loading the DLL __declspec(dllexport) void set_global_stuff(SingletonMap* sol_map) { // NOTE: Debug uses SingletonHandler -> do not use Debug in here SingletonBase::set_singleton_map_external(sol_map); } #if __cplusplus } // extern "C" #endif #endif ////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Fallback method */ class SeqEmpty : public SeqMethod { public: SeqEmpty() : SeqMethod("SeqEmpty") {} void method_pars_init() {} void method_seq_init() {} void method_rels() {} void method_pars_set() {} }; ////////////////////////////////////////////////////////////////////// void SeqMethodProxy::set_current_method(unsigned int index) { if(!registered_methods) return; unsigned int i=0; for(STD_list::iterator it=registered_methods->begin(); it!=registered_methods->end(); ++it) { (*it)->clear(); if(i==index) current_method->ptr=(*it); i++; } } SeqMethod* SeqMethodProxy::get_current_method() { if(get_numof_methods()) return current_method->ptr; else return empty_method; } unsigned int SeqMethodProxy::get_numof_methods() { if(!registered_methods) return 0; return registered_methods->size(); } unsigned int SeqMethodProxy::delete_methods() { Log odinlog("SeqMethodProxy","delete_methods"); unsigned int result=get_numof_methods(); ODINLOG(odinlog,normalDebug) << "deleting " << result << " method(s) ..." << STD_endl; if(result) { for(STD_list::iterator it=registered_methods->begin(); it!=registered_methods->end(); ++it) { // tmp copy of handle void* handle=(*it)->dl_handle; ODINLOG(odinlog,normalDebug) << "clearing " << (*it)->get_label() << STD_endl; (*it)->clear(); ODINLOG(odinlog,normalDebug) << "deleting " << (*it)->get_label() << STD_endl; CATCHSEGFAULT(delete (*it),("~"+STD_string((*it)->get_label())).c_str()) if(handle!=NULL) { if(dlclose(handle)) { ODINLOG(odinlog,errorLog) << "dlclose: " << dlerror() << STD_endl; } } } } registered_methods->erase(registered_methods->begin(),registered_methods->end()); // clear residual pointers to pulses which do not longer exist if(SeqPulsar::active_pulsar_pulses) SeqPulsar::active_pulsar_pulses->clear(); // clear references which might be left over SeqClass::clear_objlists(); return result; } void SeqMethodProxy::register_method(SeqMethod* meth) { Log odinlog("SeqMethodProxy","register_method"); if(!get_numof_methods()) current_method->ptr=meth; registered_methods->push_back(meth); registered_methods->sort(); registered_methods->unique(); ODINLOG(odinlog,normalDebug) << "registered " << meth->get_label() << STD_endl; } const char* SeqMethodProxy::get_method_label() {return current_method->ptr->get_label().c_str();} const char* SeqMethodProxy::get_status_string() { Log odinlog("SeqMethodProxy","get_status_string"); const char* result=0; #ifdef CATCH_SEGFAULT_ON_UNIX ODINLOG(odinlog,normalDebug) << "obtaining from CatchSegFaultContext" << STD_endl; result=CatchSegFaultContext::get_lastmsg(); #endif if(!result || (result && STD_string(result)=="")) { ODINLOG(odinlog,normalDebug) << "obtaining from current method" << STD_endl; result= get_current_method()->get_current_state_label().c_str(); } if(result) ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; else ODINLOG(odinlog,normalDebug) << "result=0" << STD_endl; return result; } SeqMethod& SeqMethodProxy::operator [] (unsigned int index) { if(!registered_methods) return *empty_method; unsigned int i=0; for(STD_list::iterator it=registered_methods->begin(); it!=registered_methods->end(); ++it) { if(i==index) return *(*it); i++; } return *empty_method; } bool SeqMethodProxy::load_method_so(const STD_string& so_filename) { Log odinlog("SeqMethodProxy","load_method_so"); int flag=0; #ifdef HAVE_DL flag=RTLD_LAZY; #endif void *handle = dlopen (so_filename.c_str(), flag); if(handle==NULL) { ODINLOG(odinlog,errorLog) << dlerror() << STD_endl; return false; } // remove methods which are still linked delete_methods(); #ifdef METHOD_IN_DLL // set global map of singleton objects in DLL before calling odinmain Profiler profdummy("dummy"); ODINLOG(odinlog,normalDebug) << "profdummy done" << STD_endl; SeqPulsar plsdummy; // create list of registered Pulsar pulses ODINLOG(odinlog,normalDebug) << "plsdummy done" << STD_endl; SeqAcq acqdummy; // create acq singletons ODINLOG(odinlog,normalDebug) << "acqdummy done" << STD_endl; // LogBase::set_log_output_function(dll_tracefunction); // Route debug output through own cerr to get output on shell set_global_stuff_fptr set_global_stuff_f=(void (*)(SingletonMap*))dlsym(handle, "set_global_stuff"); ODINLOG(odinlog,normalDebug) << "set_global_stuff_f=" << (void*)set_global_stuff_f << STD_endl; set_global_stuff_f(SingletonBase::get_singleton_map()); ODINLOG(odinlog,normalDebug) << "set_global_stuff_f called" << STD_endl; #endif // call main of the linked method to initialize it int (*odinmain)(int, char**)=(int (*)(int, char**))dlsym(handle, "main"); ODINLOG(odinlog,normalDebug) << "handle/odinmain=" << (void*)handle << "/" << (void*)odinmain << STD_endl; CATCHSEGFAULT(odinmain(0,0),(so_filename+"::odinmain").c_str()) // store handle current_method->ptr->dl_handle=handle; return true; } void SeqMethodProxy::init_static() { Log odinlog("SeqMethodProxy","init_static"); registered_methods.init("registered_methods"); ODINLOG(odinlog,normalDebug) << "registered_methods allocated" << STD_endl; empty_method=new SeqEmpty; ODINLOG(odinlog,normalDebug) << "empty_method allocated" << STD_endl; current_method.init("current_method"); current_method->ptr=empty_method; } void SeqMethodProxy::destroy_static() { Log odinlog("SeqMethodProxy","destroy_static"); current_method.destroy(); registered_methods.destroy(); // totalDuration.destroy(); delete empty_method; } ////////////////////////////////////////////////////////////////////// template class SingletonHandler; SingletonHandler SeqMethodProxy::registered_methods; template class SingletonHandler; SingletonHandler SeqMethodProxy::current_method; SeqMethod* SeqMethodProxy::empty_method=0; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; ////////////////////////////////////////////////////////////////////// SeqMethod::SeqMethod(const STD_string& method_label) : SeqObjList(method_label), StateMachine(&empty), commonPars(0),methodPars(0), dl_handle(0), protcache(0), empty (this,"Empty", 0, &SeqMethod::reset), initialised(this,"Initialised",&empty, &SeqMethod::empty2initialised), built (this,"Built", &initialised,&SeqMethod::initialised2built), prepared (this,"Prepared", &built, &SeqMethod::built2prepared) { Log odinlog(this,"SeqMethod()"); set_current_testcase(0); } SeqMethod::~SeqMethod() { Log odinlog(this,"~SeqMethod()"); clear(); if(methodPars) delete methodPars; if(commonPars) delete commonPars; if(protcache) delete protcache; } SeqMethod& SeqMethod::append_parameter(JcampDxClass& ldr,const STD_string& label,parameterMode parmode) { ldr.set_label(label); JcampDxBlock* blockdum=ldr.cast(blockdum); if(!blockdum) ldr.set_parmode(parmode); // Do not change parmode of a whole block if(methodPars) methodPars->append(ldr); return *this; } SeqMethod& SeqMethod::set_sequence(const SeqObjBase& s) { SeqObjList::clear(); if(commonPars->get_GradientIntro()) { SeqDelay* tokdelay=new SeqDelay("tokdelay",500.0); tokdelay->set_temporary(); float maxgrad=systemInfo->get_max_grad(); SeqGradConstPulse* tok1=new SeqGradConstPulse("tok1",readDirection,0.2*maxgrad,1.0); tok1->set_temporary(); SeqGradConstPulse* tok2=new SeqGradConstPulse("tok2",readDirection,0.4*maxgrad,1.0); tok2->set_temporary(); SeqGradConstPulse* tok3=new SeqGradConstPulse("tok3",readDirection,0.6*maxgrad,1.0); tok3->set_temporary(); (*this)+=(*tokdelay); (*this)+=(*tok1); (*this)+=(*tokdelay); (*this)+=(*tok2); (*this)+=(*tokdelay); (*this)+=(*tok3); (*this)+=(*tokdelay); } (*this)+=s; return *this; } int SeqMethod::process(int argc, char *argv[]) { // Debug already initialized by ODINMETHOD_ENTRY_POINT register_method(this); if(!argc) return 0; // process function is only used to register the method return SeqCmdLine::process(argc,argv); } void SeqMethod::create_protcache() const { Log odinlog(this,"create_protcache"); if(!protcache) protcache=new Protocol; (*protcache)=Protocol(PROTOCOL_BLOCK_LABEL); // start with a fresh protocol in order to avoid adding method pars multiple times, use same label as in recoInfo protcache->system=(*systemInfo); geometryInfo.copy(protcache->geometry); studyInfo.copy(protcache->study); if(commonPars) protcache->seqpars=(*commonPars); if(methodPars) protcache->methpars.create_copy(*methodPars); protcache->append_all_members(); // re-merge all parameters } int SeqMethod::load_protocol(const STD_string& filename) { Log odinlog(this,"load_protocol"); int npars=0; int result=0; int retval; retval=geometryInfo->load(filename); if(retval<0) result=retval; else npars+=retval; retval=studyInfo->load(filename); if(retval<0) result=retval; else npars+=retval; retval=SeqPlatformProxy::load_systemInfo(filename); if(retval<0) result=retval; else npars+=retval; retval=SeqMethodProxy()->load_sequencePars(filename); if(retval<0) result=retval; else npars+=retval; if(result>=0) result=npars; return result; } SeqMethod& SeqMethod::init_systemInfo(double basicfreq,double maxgrad,double slewrate) { systemInfo->set_B0_from_freq(basicfreq); systemInfo->max_grad=maxgrad; systemInfo->max_slew_rate=slewrate; return *this; } int SeqMethod::write_recoInfo(const STD_string& filename) const { create_protcache(); recoInfo->prot.clear(); // Clear and merge instead of assignment to work around bug in assignment of JDX on MinGW recoInfo->prot.merge(*protcache); return recoInfo->write(filename); } int SeqMethod::write_meas_contex(const STD_string& prefix) const { Log odinlog(this,"write_meas_contex"); Profiler prof("write_meas_contex"); int result=0; #ifndef NO_FILEHANDLING // result+=write_protocol(prefix+"protocol"); // result+=write_systemInfo(prefix+"systemInfo"); // result+=write_geometry(prefix+"geometryInfo"); // result+=write_sequencePars(prefix+"sequencePars"); result+=write_recoInfo(prefix+"recoInfo"); #endif return result; } double SeqMethod::get_totalDuration() const { if(commonPars) return commonPars->get_ExpDuration(); return 0.0; } int SeqMethod::load_sequencePars(const STD_string& filename) { Log odinlog(this,"load_sequencePars"); if(commonPars) { commonPars->load(filename); commonPars->set_Sequence(get_label()); // restore sequence label } ODINLOG(odinlog,normalDebug) << "commonPars->load(" << filename << ") done" << STD_endl; if(methodPars) methodPars->load(filename); ODINLOG(odinlog,normalDebug) << "methodPars->load(" << filename << ") done" << STD_endl; set_parblock_labels(); // Overwrite block labels of file return 0; } int SeqMethod::write_sequencePars(const STD_string& filename) const { JcampDxBlock block( (STD_string(get_label())+"_sequencePars") ); if(commonPars) block.merge(*commonPars); if(methodPars) block.merge(*methodPars); return block.write(filename); } bool SeqMethod::set_sequenceParameter(const STD_string& parameter_label, const STD_string& value) { Log odinlog(this,"set_sequenceParameter"); bool result=false; // first send it to common pars without prefix STD_string parlabel=parameter_label; if(commonPars) if(commonPars->JcampDxBlock::parseval(parlabel,value)) result=true; // then send it to method pars with prefix STD_string prefixstr=STD_string(get_label())+"_"; if(parameter_label.find(prefixstr)!=0) parlabel=prefixstr+parameter_label; if(methodPars) if(methodPars->JcampDxBlock::parseval(parlabel,value)) result=true; return result; } SeqMethod& SeqMethod::set_commonPars(const SeqPars& pars) { (*commonPars)=pars; commonPars->set_Sequence(get_label()); // restore sequence label return *this; } int SeqMethod::load_systemInfo(const STD_string& filename) { return SeqPlatformProxy::load_systemInfo(filename); } unsigned int SeqMethod::event(eventContext& context) const { Log odinlog(this,"event"); if(context.action==seqRun) { ODINLOG(odinlog,normalDebug) << "calling pre_event of " << platform->get_label() << STD_endl; platform->pre_event(context); } ODINLOG(odinlog,normalDebug) << "------------------- action=" << context.action << "-------------------" << STD_endl; unsigned int result=SeqObjList::event(context); if(context.action==seqRun) { ODINLOG(odinlog,normalDebug) << "calling post_event of " << platform->get_label() << STD_endl; platform->post_event(context); } return result; } void SeqMethod::parameter_relations(JDXeditWidget* editwidget) { #ifdef GUISUPPORT clear(); build(); editwidget->updateWidget(); #endif } STD_list SeqMethod::get_active_pulsar_pulses() const { Log odinlog(this,"get_active_pulsar_pulses"); SeqPulsar::PulsarList result; if(SeqPulsar::active_pulsar_pulses) SeqPulsar::active_pulsar_pulses.copy(result); return result;; } unsigned int SeqMethod::get_numof_acquisitions() const { Log odinlog(this,"get_numof_acquisitions"); queryContext qc; qc.action=count_acqs; SeqObjList::query(qc); return qc.numof_acqs; } bool SeqMethod::prep_acquisition() const { Log odinlog(this,"prep_acquisition",significantDebug); Profiler prof("prep_acquisition"); double totaldur=get_totalDuration(); unsigned int nacqs_total=get_numof_acquisitions(); ODINLOG(odinlog,infoLog) << "duration=" << totaldur << " min" << STD_endl; ODINLOG(odinlog,infoLog) << "numof_acquisitions=" << nacqs_total << STD_endl; if(platform->create_recoInfo()) { // do this only if really necessary, i.e. NOT on VxWorks (recoInfo->DataFormat) =platform->get_rawdatatype(); (recoInfo->RawFile) =platform->get_rawfile(); (recoInfo->RawHeaderSize) =platform->get_rawheader_size(); (recoInfo->ImageProc) =platform->get_image_proc(); for(int idir=readDirection; idir<=sliceDirection; idir++) { (recoInfo->RelativeOffset)[idir]=secureDivision(geometryInfo->get_offset(direction(idir)),geometryInfo->get_FOV(direction(idir))); } recoInfo->ChannelScaling=platform->get_acq_channel_scale_factors(); ODINLOG(odinlog,normalDebug) << "getting k-space ordering from sequence" << STD_endl; recoInfo->kSpaceCoords.clear(); recoInfo->kSpaceOrdering=SeqObjList::get_recovallist(1,recoInfo->kSpaceCoords); unsigned int nacqs_recoInfo=recoInfo->get_NumOfAdcChunks(); if(nacqs_recoInfo!=nacqs_total) { ODINLOG(odinlog,errorLog) << "Inconsistent number of acqs: " << nacqs_recoInfo << "!=" << nacqs_total << STD_endl; return false; } } // tag repetition loop queryContext qc; qc.action=tag_toplevel_reploop; qc.repetitions_prot=commonPars->get_NumOfRepetitions(); SeqObjList::query(qc); // execute platform-specific initialization platform->prepare_measurement(nacqs_total); // set current date/time studyInfo->set_timestamp(); return true; } bool SeqMethod::reset() { Log odinlog(this,"reset", significantDebug); // SeqClass::clear_messages(); clear_containers(); clear_temporary(); recoInfo->reset(); return true; } bool SeqMethod::empty2initialised() { Log odinlog(this,"empty2initialised", significantDebug); Profiler prof("empty2initialised"); STD_string method_label(get_label()); int maxmethname=platform->get_max_methodname_length(); if(maxmethname>=0 && int(method_label.length())>maxmethname) { ODINLOG(odinlog,warningLog) << "Method identifier >" << method_label << "< too long (max=" << maxmethname << " chars), will be cut" << STD_endl; STD_string cut=get_label().substr(0,maxmethname); set_label(cut); } if(!commonPars) { commonPars=new SeqPars(); commonPars->set_Sequence(get_label()); // init sequence label ODINLOG(odinlog,normalDebug) << "commonPars allocated" << STD_endl; } if(!methodPars) { methodPars=new JcampDxBlock(); CATCHSEGFAULT(method_pars_init(),"method_pars_init") methodPars->set_prefix(get_label()); ODINLOG(odinlog,normalDebug) << "methodPars allocated" << STD_endl; } set_parblock_labels(); platform->init(); return true; } bool SeqMethod::initialised2built() { Log odinlog(this,"initialised2built", significantDebug); Profiler prof("initialised2built"); ODINLOG(odinlog,significantDebug) << "calling method_seq_init()" << STD_endl; CATCHSEGFAULT(method_seq_init(),"method_seq_init") return calc_timings(); } void SeqMethod::set_parblock_labels() { commonPars->set_label("Common Sequence Parameters"); methodPars->set_label(STD_string(get_label())+" Sequence Parameters"); } bool SeqMethod::calc_timings() { Log odinlog(this,"calc_timings", significantDebug); ODINLOG(odinlog,significantDebug) << "calling method_rels()" << STD_endl; CATCHSEGFAULT(method_rels(),"method_rels") double totalDuration_sec=SeqObjList::get_duration()/1000.0; ODINLOG(odinlog,normalDebug) << "totalDuration_sec=" << totalDuration_sec << STD_endl; if(commonPars) commonPars->set_ExpDuration(totalDuration_sec/60.0); return true; } bool SeqMethod::update_timings() { Log odinlog(this,"update_timings", significantDebug); if(!build()) return false; if(!calc_timings()) return false; return true; } bool SeqMethod::built2prepared() { Log odinlog(this,"built2prepared", significantDebug); ODINLOG(odinlog,significantDebug) << "calling method_pars_set()" << STD_endl; CATCHSEGFAULT(method_pars_set(),"method_pars_set") SeqTreeObj::looplevel=0; platform->reset_before_prep(); return prep_all(); } odin-1.8.5/odinseq/seqgradphase.cpp0000644000175000017500000002002511455553540014222 00000000000000#include "seqgradphase.h" void SeqGradPhaseEnc::init_encoding(unsigned int nsteps, encodingScheme scheme, reorderScheme reorder, unsigned int nsegments, unsigned int reduction, unsigned int acl_bands, float partial_fourier) { Log odinlog(this,"init_encoding"); if(partial_fourier<0.0) partial_fourier=0.0; if(partial_fourier>1.0) partial_fourier=1.0; unsigned int startindex=(unsigned int)(partial_fourier*0.5*nsteps+0.5); // some plausibility checks if(reduction>nsteps) reduction=nsteps; // / order is important if(reduction<1) reduction=1; // \ here because nsteps might be 0 unsigned int ngaps=nsteps/reduction; if(acl_bands>ngaps) acl_bands=ngaps; // The indices covering the central part with auto-calibration lines unsigned int acl_start= (ngaps-acl_bands)/2 * reduction; unsigned int acl_end=acl_start+acl_bands*reduction; ODINLOG(odinlog,normalDebug) << "acl_start/acl_end=" << acl_start << "/" << acl_end << STD_endl; // decrease startindex so that we cover all of the ACL area if(reduction>1 && startindex>acl_start) startindex=acl_start; unsigned int ncovered=nsteps-startindex; // the number of encoding steps actually covered by partial Fourier unsigned int n_scanned=ncovered/reduction; if(ncovered%reduction) n_scanned++; // we can stuff in one more unsigned int vecsize=n_scanned+acl_bands*(reduction-1); // the number of lines actually scanned ODINLOG(odinlog,normalDebug) << "nsteps/startindex/reduction/ngaps/acl_bands/vecsize=" << nsteps << "/" << startindex << "/" << reduction << "/" << ngaps << "/" << acl_bands << "/" << vecsize << STD_endl; fvector petrims(vecsize); ivector recoindexivec(vecsize); float stepsize=secureDivision(2.0,nsteps); unsigned int ivec=0; for(unsigned int istep=0; istep=acl_start && istepget_gamma(nucleus); float resolution=secureDivision(fov,nsteps); float integral=secureDivision( PII , ( gamma * resolution ) ); float sr=systemInfo->get_max_slew_rate(); float Gmax_sr=sqrt(integral * sr); if(fabs(gradstrength)>Gmax_sr) { gradstrength=secureDivision(gradstrength,fabs(gradstrength)); //preserve sign gradstrength*=Gmax_sr; SeqGradVectorPulse::set_strength(gradstrength); ODINLOG(odinlog,warningLog) << "Reducing strength of SeqGradPhaseEnc in order satisfy integral" << STD_endl; } double dur=secureDivision( integral , gradstrength ); set_constduration(dur); } SeqGradPhaseEnc::SeqGradPhaseEnc(const STD_string& object_label, unsigned int nsteps, float fov, float gradduration, direction gradchannel, encodingScheme scheme, reorderScheme reorder, unsigned int nsegments, unsigned int reduction, unsigned int acl_bands, float partial_fourier, const STD_string& nucleus) : SeqGradVectorPulse(object_label,gradchannel,0.0,fvector(nsteps),gradduration) { Log odinlog(this,"SeqGradPhaseEnc(fov)"); init_encoding(nsteps, scheme, reorder, nsegments, reduction, acl_bands, partial_fourier); float gamma=systemInfo->get_gamma(nucleus); float resolution=secureDivision(fov,nsteps); float integral=secureDivision( PII , ( gamma * resolution ) ); float gradstrength=secureDivision( integral , gradduration ); SeqGradVectorPulse::set_strength(gradstrength); } ///////////////////////////////////////////////////////////////////////////////////////////////////////// void SeqGradPhaseEncFlowComp::calc_flowcomp_pe(float& negfact, float& tc, float Gpos, float M0, float t0, float slewrate) { Log odinlog("SeqGradPhaseEncFlowComp","calc_flowcomp_pe"); ODINLOG(odinlog,normalDebug) << "Gpos/M0/t0/slewrate=" << Gpos << "/" << M0 << "/" << t0 << "/" << slewrate << STD_endl; // ramp time float tr=secureDivision(Gpos,slewrate); ODINLOG(odinlog,normalDebug) << "tr=" << tr << STD_endl; // constant part of trapez ending at tc with ramp time tr and starting at t0 was // calculated with maxima: // solve ( Gp* ( integrate(t*(t-t0 )/tr ,t, t0, t0+tr) + integrate(t, t, t0+tr, t0+tc ) + integrate(t*(t0+tr+tc -t)/tr, t, t0+tc, t0+tr+tc ) ) - (Gp-M0/tc)*( integrate(t*(t-t0-tr-tc)/tr ,t, t0+tr+tc, t0+tc+2*tr) + integrate(t, t, t0+tc+2*tr, t0+tr+2*tc) + integrate(t*(t0+2*(tr+tc)-t)/tr, t, t0+tr+2*tc, t0+2*(tr+tc)) ), tc ); float arg= 9.0*M0*M0 + (12.0*Gpos*tr + 16.0*Gpos*t0)*M0 + 4.0*Gpos*Gpos*tr*tr; ODINLOG(odinlog,normalDebug) << "arg=" << arg << STD_endl; float tc1=0.0; float tc2=0.0; if(arg>=0) { tc1=secureDivision(-sqrt(arg) - 3.0*M0 + 2.0*Gpos*tr, 4.0*Gpos); tc2=secureDivision(+sqrt(arg) + 3.0*M0 - 2.0*Gpos*tr, 4.0*Gpos); ODINLOG(odinlog,normalDebug) << "tc1/tc2=" << tc1 << "/" << tc2 << STD_endl; } else { ODINLOG(odinlog,errorLog) << "Cannot solve equation for flow compensation" << STD_endl; } tc=STD_max(tc1,tc2); negfact=secureDivision(Gpos-secureDivision(M0,tc), Gpos); ODINLOG(odinlog,normalDebug) << "negfact=" << negfact << STD_endl; } SeqGradPhaseEncFlowComp::SeqGradPhaseEncFlowComp(const STD_string& object_label, double t0, unsigned int nsteps, float fov, direction gradchannel, float gradstrength, encodingScheme scheme, reorderScheme reorder, unsigned int nsegments, unsigned int reduction, unsigned int acl_bands, float partial_fourier, const STD_string& nucleus) : SeqGradChanList(object_label), simvec(object_label+"_simvec") { // Template for gradient trims SeqGradPhaseEnc petmp(object_label, nsteps, fov, gradchannel, gradstrength, scheme, reorder, nsegments, reduction, acl_bands, partial_fourier, nucleus); // Calculate flow-compensated bipolar gradients float negfact, tc; calc_flowcomp_pe(negfact, tc, petmp.get_strength(), petmp.get_strength()*petmp.get_constduration(), t0, systemInfo->get_max_slew_rate()); pos=SeqGradVectorPulse(object_label+"pos", gradchannel, petmp.get_strength(), petmp.get_trims(), tc); neg=SeqGradVectorPulse(object_label+"neg", gradchannel, petmp.get_strength(), -negfact*petmp.get_trims(), tc); simvec.set_indexvec(((const SeqVector&)petmp).get_indexvec()); // Preserve k-space indices build_seq(); } SeqGradPhaseEncFlowComp& SeqGradPhaseEncFlowComp::operator = (const SeqGradPhaseEncFlowComp& sgpefc) { SeqGradChanList::operator = (sgpefc); pos=sgpefc.pos; neg=sgpefc.neg; simvec=sgpefc.simvec; build_seq(); return *this; } void SeqGradPhaseEncFlowComp::build_seq() { SeqGradChanList::clear(); simvec.clear(); simvec+=pos; simvec+=neg; (*this)+=pos; (*this)+=neg; } odin-1.8.5/odinseq/seqpulsndim.h0000644000175000017500000000656611322062345013571 00000000000000/*************************************************************************** seqpulsndim.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPULSNDIM_H #define SEQPULSNDIM_H #include #include struct SeqPulsNdimObjects; // forward declaration /** * @addtogroup odinseq * @{ */ /** * * \brief RF Pulse + gradients * * This class represents a shaped n-dimesional RF-pulse, i.e. it * consists of a complex waveform and in addition three gradient * waveforms in the three spatial directions that are played out simultaneously */ class SeqPulsNdim : public SeqParallel, public virtual SeqPulsInterface, public Handled { // virtual functions of SeqPulsInterface are marshalled to sp // virtual functions of SeqFreqChanInterface are marshalled to sp public: /** * Default constructor */ SeqPulsNdim(const STD_string& object_label = "unnamedSeqPulsNdim" ); /** * Copy constructor */ SeqPulsNdim(const SeqPulsNdim& spnd); /** * Destructor */ ~SeqPulsNdim(); /** * Sets the RF waveform of the pulse */ SeqPulsNdim& set_rfwave(const cvector& waveform); /** * Sets the waveform for the gradient pulse in direction 'dir' */ SeqPulsNdim& set_gradwave(direction dir, const fvector& waveform); /** * Sets the B1 scaling for simulation */ SeqPulsNdim& set_B1max(float b1max); /** * Returns the complex RF waveform */ cvector get_rfwave() const; /** * Returns the waveform of the gradient pulse in direction 'dir' */ fvector get_gradwave(direction dir) const; /** * Specifies an extra shift between RF and the gradient channels */ SeqPulsNdim& set_grad_shift_offset(float grad_shift_offset); /** * Dimensionality of the pulse */ virtual int get_dims() const; // virtual functions of SeqPulsInterface are (mostly) marshalled to sp, except: SeqPulsInterface& set_pulsduration(float pulsduration); float get_magnetic_center() const; // forwarding virtual functions of SeqVector to sp SeqVector& set_indexvec(const ivector& iv); /** * This assignment operator will make this object become an exact copy of 'spnd'. */ SeqPulsNdim& operator = (const SeqPulsNdim& spnd); /** * Appends the gradient list sgcl to the gradient part of the pulse */ SeqPulsNdim& operator += (SeqGradChanList& sgcl); protected: SeqPulsNdim& set_system_flipangle(float angle); SeqPulsNdim& build_seq(); private: int dims; double gradshift; SeqPulsNdimObjects* objs; }; /** @} */ #endif odin-1.8.5/odinseq/seqgradpulse.h0000644000175000017500000001311411322062345013707 00000000000000/*************************************************************************** seqgradpulse.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADPULSE_H #define SEQGRADPULSE_H #include #include #include #include /** * @addtogroup odinseq * @{ */ ///////////////////////////////////////////////////////////////////////////////// /** * \brief Constant gradient pulse * * This class represents a gradient pulse with a constant gradient field */ class SeqGradConstPulse : public SeqGradChanList { public: /** * Constructs a constant gradient pulse labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - gradstrength: The gradient strength for this object * - gradduration: The duration of this gradient object */ SeqGradConstPulse(const STD_string& object_label,direction gradchannel, float gradstrength, float gradduration); /** * Constructs a copy of 'sgcp' */ SeqGradConstPulse(const SeqGradConstPulse& sgcp); /** * Construct an empty constant gradient pulse with the given label */ SeqGradConstPulse(const STD_string& object_label = "unnamedSeqGradConstPulse"); /** * Assignment operator that makes this constant gradient pulse object become a copy of 'sgcp' */ SeqGradConstPulse& operator = (const SeqGradConstPulse& sgcp); /** * setting duration of the constant part */ SeqGradConstPulse& set_constduration(float duration) {constgrad.set_duration(duration);return *this;}; /** * getting duration of the constant part */ double get_constduration() const {return constgrad.get_gradduration();} // overloading virtual function from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); private: SeqGradConst constgrad; SeqGradDelay offgrad; }; ///////////////////////////////////////////////////////////////////////////////// /** * \brief Vector of gradient pulses * * This class represents a gradient pulse with a constant gradient * shape with the the strength taken from a vector. This object * can be attached to a SeqLoop to iterate over the values in the * vector. */ class SeqGradVectorPulse : public SeqGradChanList { public: /** * Constructs a gradient vector pulse labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - maxgradstrength: The maximum gradient strength for this object * - trimarray: The vector of gradient strength values * - gradduration: The duration of this gradient object */ SeqGradVectorPulse(const STD_string& object_label,direction gradchannel, float maxgradstrength, const fvector& trimarray, float gradduration); /** * Constructs a copy of 'sgvp' */ SeqGradVectorPulse(const SeqGradVectorPulse& sgvp); /** * Construct an empty gradient pulse with the given label */ SeqGradVectorPulse(const STD_string& object_label = "unnamedSeqGradVectorPulse"); /** * Assignment operator that makes this constant gradient pulse object become a copy of 'sgvp' */ SeqGradVectorPulse& operator = (const SeqGradVectorPulse& sgvp); /** * Specifies the trim values that will be used */ SeqGradVectorPulse& set_trims(const fvector& trims) { vectorgrad.set_trims(trims); return *this;} /** * Returns the trim values that will be used */ fvector get_trims() const {return vectorgrad.get_trims();} /** * Sets the reordering scheme and the number of segments */ SeqGradVectorPulse& set_reorder_scheme(reorderScheme scheme,unsigned int nsegments=1) {vectorgrad.set_reorder_scheme(scheme,nsegments); return *this;} /** * Sets the phase encoding scheme and the number of phase encoding steps */ SeqGradVectorPulse& set_encoding_scheme(encodingScheme scheme) {vectorgrad.set_encoding_scheme(scheme); return *this;} /** * Returns the reordering vector (for loop insertion) */ const SeqVector& get_reorder_vector() const {return vectorgrad.get_reorder_vector();} /** * setting duration of the gradient vector part */ SeqGradVectorPulse& set_constduration(float duration){vectorgrad.set_duration(duration);return *this;}; /** * getting duration of the gradient vector part */ double get_constduration() const {return vectorgrad.get_gradduration();} /** * conversion operator for loop insertion */ operator const SeqVector& () const {return vectorgrad;} // overloading virtual function from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); private: friend class SeqGradPhaseEnc; friend class SeqGradEcho; SeqGradVector vectorgrad; SeqGradDelay offgrad; }; /** @} */ #endif odin-1.8.5/odinseq/seqcounter.cpp0000644000175000017500000000511311322062345013733 00000000000000#include "seqcounter.h" SeqCounter::SeqCounter(const STD_string& object_label) : counterdriver(object_label) { disable_counter(); set_label(object_label); } SeqCounter::SeqCounter(const SeqCounter& sc) { disable_counter(); SeqCounter::operator = (sc); } SeqCounter& SeqCounter::operator = (const SeqCounter& sc) { SeqTreeObj::operator = (sc); counterdriver=sc.counterdriver; counterdriver->outdate_cache(); clear_vectorlist(); for(veciter=sc.get_vecbegin(); veciter!=sc.get_vecend(); ++veciter) { add_vector(**veciter); } return *this; } void SeqCounter::set_vechandler_for_all() const { Log odinlog(this,"set_vechandler_for_all"); for(veciter=get_vecbegin(); veciter!=get_vecend(); ++veciter) { ODINLOG(odinlog,normalDebug) << "veciter=" << (*veciter)->get_label() << STD_endl; (*veciter)->set_vechandler(this); } return; } bool SeqCounter::prep_veciterations() const { Log odinlog(this,"prep_veciterations"); for(veciter=get_vecbegin(); veciter!=get_vecend(); ++veciter) { ODINLOG(odinlog,normalDebug) << "calling prep_iteration of vector " << (*veciter)->get_label() << STD_endl; if(!(*veciter)->prep_iteration()) return false; ODINLOG(odinlog,normalDebug) << "prep done" << STD_endl; } return true; } void SeqCounter::init_counter(unsigned int start) const { set_vechandler_for_all(); int niter=get_times(); if(start && niter>0) counter=start%niter; else counter=0; } void SeqCounter::add_vector(const SeqVector& seqvector) { Log odinlog(this,"add_vector"); if( get_times() && (int(seqvector.get_numof_iterations())!=get_times()) ) { ODINLOG(odinlog,errorLog) << "size mismatch: this=" << get_times() << ", " << seqvector.get_label() << "=" << seqvector.get_numof_iterations() << STD_endl; } else { vectors.append(seqvector); seqvector.set_vechandler(this); seqvector.nr_cache_up2date=false; ODINLOG(odinlog,normalDebug) << "added vector >" << seqvector.get_label() << "<" << STD_endl; } counterdriver->outdate_cache(); } int SeqCounter::get_times() const { Log odinlog(this,"get_times"); if(n_vectors()) { ODINLOG(odinlog,normalDebug) << "vectorsize(" << (*(get_vecbegin()))->get_label() << ")=" << (*(get_vecbegin()))->get_numof_iterations() << STD_endl; return (*(get_vecbegin()))->get_numof_iterations(); } return 0; } bool SeqCounter::prep() { if(!SeqTreeObj::prep()) return false; if(!counterdriver->prep_driver()) return false; return true; } void SeqCounter::clear_container() { clear_vectorlist(); counterdriver->outdate_cache(); } odin-1.8.5/odinseq/seqgradchanlist.h0000644000175000017500000000603411322062345014367 00000000000000/*************************************************************************** seqgradchanlist.h - description ------------------- begin : Thu Apr 22 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADCHANLIST_H #define SEQGRADCHANLIST_H #include /** * @addtogroup odinseq_internals * @{ */ /** * This class represents a list of gradient channel objects (i.e. those derived from SeqGradChan) * It is suitable to hold a gradient train for ONE gradient channel */ class SeqGradChanList : public List, public Handled, public virtual SeqGradInterface, public virtual SeqTreeObj { public: /** * Construct an empty gradient channel list with the given label */ SeqGradChanList(const STD_string& object_label = "unnamedSeqGradChanList" ); /** * Constructs a copy of 'sgcl' */ SeqGradChanList(const SeqGradChanList& sgcl); /** * Destructor */ ~SeqGradChanList(); /** * Assignment operator that makes this gradient sequence object become a copy of 'sgcl' */ SeqGradChanList& operator = (const SeqGradChanList& sgcl); // overloading virtual function from SeqTreeObj double get_duration() const; STD_string get_properties() const; unsigned int event(eventContext& context) const; void query(queryContext& context) const; // overloading virtual function from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); SeqGradInterface& invert_strength(); float get_strength() const; fvector get_gradintegral() const; double get_gradduration() const; SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); /** * Returns the occupied channel */ direction get_channel() const; /** * Appends the elements of 'sgcl' to this */ SeqGradChanList& operator += (SeqGradChanList& sgcl); /** * Appends 'sgc' to this */ SeqGradChanList& operator += (SeqGradChan& sgc); fvector get_switchpoints() const; SeqGradChanList& get_chanlist4gp(const fvector& switchpoints); private: friend class SeqGradChanParallel; // overloading virtual function from SeqClass void clear_container(); SeqGradChan* get_chan(double& chanstart, double midtime); }; /** @} */ #endif odin-1.8.5/odinseq/seqgradconst.h0000644000175000017500000000737511322062345013721 00000000000000/*************************************************************************** seqgradconst.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADCONST_H #define SEQGRADCONST_H #include /** * @addtogroup odinseq * @{ */ /** * \brief Constant gradient * * This class represents a gradient object with a constant gradient field */ class SeqGradConst : public SeqGradChan { public: /** * Constructs a constant gradient field labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - gradstrength: The gradient strength for this object * - gradduration: The duration of this gradient object */ SeqGradConst(const STD_string& object_label,direction gradchannel, float gradstrength, double gradduration); /** * Constructs a copy of 'sgc' */ SeqGradConst(const SeqGradConst& sgc); /** * Construct an empty gradient object with the given label */ SeqGradConst(const STD_string& object_label = "unnamedSeqGradConst" ); /** * Assignment operator that makes this gradient channel object become a copy of 'sgc' */ SeqGradConst& operator = (const SeqGradConst& sgc); private: friend class SeqGradVector; // overwriting virtual functions from SeqClass bool prep(); // overwriting virtual functions from SeqGradChan SeqGradChan& get_subchan(double starttime, double endtime) const; STD_string get_grdpart(float matrixfactor) const; float get_integral() const {return get_strength() * get_duration();} }; ////////////////////////////////////////////////////////////////////////////////// /** * \brief Gradient delay * * This class represents a gradient delay which can be inserted into a list of gradient objects */ class SeqGradDelay : public SeqGradChan { public: /** * Constructs a constant gradient field labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - gradduration: The duration of this gradient object */ SeqGradDelay(const STD_string& object_label, direction gradchannel, double gradduration); /** * Constructs a copy of 'sgd' */ SeqGradDelay(const SeqGradDelay& sgd); /** * Construct an empty gradient object with the given label */ SeqGradDelay(const STD_string& object_label = "unnamedSeqGradDelay" ); /** * Assignment operator that makes this gradient channel object become a copy of 'sgd' */ SeqGradDelay& operator = (const SeqGradDelay& sgd); // overwriting virtual functions from SeqGradInterface float get_strength() const {return 0.0;} // always return zero strength private: // overwriting virtual functions from SeqGradChan SeqGradChan& get_subchan(double starttime, double endtime) const; STD_string get_grdpart(float matrixfactor) const; float get_integral() const {return 0.0;} }; /** @} */ #endif odin-1.8.5/odinseq/seqgrad.cpp0000644000175000017500000000027511322062345013175 00000000000000#include "seqgrad.h" float SeqGradInterface::get_gradintegral_norm() const { fvector intgegralvec=get_gradintegral(); return norm3(intgegralvec[0],intgegralvec[1],intgegralvec[2]); } odin-1.8.5/odinseq/seqgradspiral.h0000644000175000017500000001016411735132611014055 00000000000000/*************************************************************************** seqgradspiral.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADSPIRAL_H #define SEQGRADSPIRAL_H #include #include #include #include #include #include /** * @addtogroup odinseq_internals * @{ */ /** * Spiral Gradients */ class SeqGradSpiral: public SeqGradChanParallel, public MinimizationFunction { public: /** * Constructs a spiral gradient labeled 'object_label' and the * following properties: * - traj: The spiral trajectory (will be modified, if neccessary) * - dt: The dwell time * - resolution: Spatial resolution * - sizeRadial: The number of image points in radial direction * - numofSegments : The number of spiral interleaves * - inwards: Reverse trajectory so that the spiral ends in the center of k-space, in addition, rotates trajectory by 180 deg * - optimize: Optimize trajectory for minimum readout length if trajectory has a free tunable parameter * - nucleus: The imaging nucleus */ SeqGradSpiral(const STD_string& object_label, JDXtrajectory& traj, double dt, float resolution, unsigned int sizeRadial, unsigned int numofSegments, bool inwards=false, bool optimize=false, const STD_string& nucleus=""); /** * Constructs an empty spiral gradient with the given label. */ SeqGradSpiral(const STD_string& object_label = "unnamedSeqGradSpiral" ); /** * Constructs a spiral gradient which is a copy of 'sgs' */ SeqGradSpiral(const SeqGradSpiral& sgs); /** * This assignment operator will make this object become an exact copy of 'sgs'. */ SeqGradSpiral& operator = (const SeqGradSpiral& sgs); /** * Returns the size of the spiral without ramps */ unsigned int spiral_size() const {return denscomp.size();} /** * Returns the duration of the ramp that switches the gradients off */ double get_ramp_duration() const {return (get_gradduration()-spiral_dur);} /** * Sets the delay of the gradient delays preceding the spiral gradients */ SeqGradSpiral& set_predelay_duration(double dur); /** * Returns the Jacobian determinante, i.e. the correction function * for non-uniform weighting of k-space */ const fvector& get_denscomp() const {return denscomp;} /** * Returns the k-space trajectory for the interleave 'iseg' and the given channel */ fvector get_ktraj(direction channel) const; private: void common_init() {traj_cache=0;} void build_seq(); float readout_npts() const; // implement virtual functions of MinimizationFunction to minimize readout duration float evaluate(const fvector& spirpar) const; unsigned int numof_fitpars() const {return 1;} SeqGradWave gx; SeqGradWave gy; SeqGradDelay gxdelay; SeqGradDelay gydelay; fvector kx; fvector ky; fvector denscomp; double spiral_dur; double predelay; // cache values for readout_npts/evaluate JDXtrajectory* traj_cache; double dt_cache; float resolution_cache; unsigned int sizeRadial_cache; float gamma_cache; }; ////////////////////////////////////////////////////////////////////////////////////////// /** @} */ #endif odin-1.8.5/odinseq/seqcmdline.cpp0000644000175000017500000001663011322062345013675 00000000000000#include "seqcmdline.h" #include "seqmeth.h" #include "seqplatform.h" #include #ifndef NO_CMDLINE class SeqTreeCallbackConsole : public SeqTreeCallbackAbstract { public: SeqTreeCallbackConsole() {} private: // implementing virtual function of SeqTreeCallbackAbstract void display_node(const SeqClass* thisnode, const SeqClass* parentnode, int treelevel, const svector& columntext) { STD_string space = ""; for (int i = 0; i<(treelevel-1); i++) space+="| "; if(treelevel>0) space+="|- "; STD_cout << space; for(unsigned int icol=0; icol odinlog("SeqCmdLine","process"); SeqMethodProxy method; SeqPlatformProxy platform; char value[ODIN_MAXCHAR]; bool valid_command=false; // try to find a suitable platform to switch to #ifdef STANDALONE_PLUGIN platform.set_current_platform(standalone); // default #else #ifdef PARAVISION_PLUGIN platform.set_current_platform(paravision); #else #ifdef IDEA_PLUGIN platform.set_current_platform(numaris_4); #else #ifdef EPIC_PLUGIN platform.set_current_platform(epic); #else #error No valid platform plugin available #endif #endif #endif #endif JDXfileName methlabel(argv[0]); // do we have at least one action argument ? if (argc<2) { STD_cout << usage(methlabel.get_basename(),method->get_description()) << STD_endl; return 0; } // switch on error tracing // set_tracing(Error); // setting up stuff for different test cases of seqtest // do this before anything else if(getCommandlineOption(argc,argv,"-testcase",value,ODIN_MAXCHAR)) { int testcase=atoi(value); ODINLOG(odinlog,normalDebug) << "testcase=" << testcase << STD_endl; method->set_current_testcase(testcase); if(testcase) { STD_string newlabel(method->get_label()); if(newlabel.length()) newlabel[newlabel.length()-1]=char('0'+testcase); method->set_label(newlabel); } } if(!method->init()) { ODINLOG(odinlog,errorLog) << "method->init() failed" << STD_endl; return -1; } STD_string action(argv[1]); // switch to platform which offers the requested action int pfact=platform.get_platform_for_action(action); ODINLOG(odinlog,normalDebug) << "action/pfact=" << action << "/" << pfact << STD_endl; if(pfact>=0) platform.set_current_platform(odinPlatform(pfact)); else platform.set_current_platform(standalone); // used as default for non-platform-specific actions STD_string scandir="."; if(getCommandlineOption(argc,argv,"-scandir",value,ODIN_MAXCHAR)) { scandir=value; ODINLOG(odinlog,normalDebug) << "scandir=" << scandir << STD_endl; } SystemInterface()->set_scandir(scandir); // analyze command line options and perform the requested action: if(action=="description") { STD_cout << methlabel.get_basename()<< STD_endl << justificate(method->get_description()) << STD_endl; valid_command=true; } if(action=="ntests") { STD_cout << method->numof_testcases() << STD_endl; exit(0); } if(action=="events") { if(getCommandlineOption(argc,argv,"-p",value,ODIN_MAXCHAR)) method->load_protocol(value); if(method->prepare()) { eventContext context; context.action=printEvent; SeqTreeCallbackConsole display; context.event_display=&display; STD_cout << "---------- Events: -------------------" << STD_endl; method->event(context); STD_cout << STD_endl; } else { ODINLOG(odinlog,errorLog) << "method->prepare() failed" << STD_endl; return -1; } valid_command=true; } if(action=="tree") { if(getCommandlineOption(argc,argv,"-p",value,ODIN_MAXCHAR)) method->load_protocol(value); if(method->build()) { SeqTreeCallbackConsole display; method->tree(&display); } else { ODINLOG(odinlog,errorLog) << "method->build() failed" << STD_endl; return -1; } valid_command=true; } if(!valid_command) { ODINLOG(odinlog,normalDebug) << "handind over control to platform" << STD_endl; int result=platform->process(argc,argv); ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; if(result<0) return -1; if(result>0) valid_command=true; } ODINLOG(odinlog,normalDebug) << "valid_command=" << valid_command << STD_endl; if(!valid_command) { JDXfileName methlabel(argv[0]); STD_cout << usage(methlabel.get_basename(),method->get_description()) << STD_endl; return -1; } // clean up SeqMethodProxy::delete_methods(); #endif return 0; // return 0 to shell on success } STD_string SeqCmdLine::usage(const STD_string& meth, const STD_string& description) { STD_string result; #ifndef NO_CMDLINE STD_string separator=n_times(" ",USAGE_INDENTION_FACTOR); result+="\nODIN method: "+meth+"\n\n"; result+="DESCRIPTION:\n"+justificate(description,USAGE_INDENTION_FACTOR)+"\n\n"; result+="USAGE:"+separator+meth+" action [options]"+"\n"; result+=separator+"where 'action' can be one of the following:\n\n"; SeqCmdlineActionList global_actions; SeqCmdlineAction descr("description","Prints a description of sequence."); global_actions.push_back(descr); SeqCmdlineAction ntests("ntests","Prints number of test cases. Exits immediately thereafter."); global_actions.push_back(ntests); SeqCmdlineAction events("events","Prints all events in the sequence. "); events.add_opt_arg("p","The file with the measurement protocol"); global_actions.push_back(events); SeqCmdlineAction tree("tree","Prints the tree of sequence objects. "); tree.add_opt_arg("p","The file with the measurement protocol"); global_actions.push_back(tree); result+="GLOBAL ACTIONS:\n\n"; result+=format_actions(global_actions); result+=SeqPlatformProxy::get_platforms_usage(); result+="ADDITIONAL OPTIONS:\n\n"; #ifdef ODIN_DEBUG result+=justificate(LogBase::get_usage(),USAGE_INDENTION_FACTOR)+"\n"; #endif result+=justificate("-scandir : Sets the directory where experimental data is stored.",USAGE_INDENTION_FACTOR)+"\n"; result+=justificate("-testcase : Uses the default sequence parameters from the given test case.",USAGE_INDENTION_FACTOR)+"\n"; result+="\n"; #endif return result; } STD_string SeqCmdLine::format_actions(const SeqCmdlineActionList& actions) { STD_string result; #ifndef NO_CMDLINE STD_string separator=n_times(" ",USAGE_INDENTION_FACTOR); STD_string argline; STD_map::const_iterator argit; for(STD_list::const_iterator it=actions.begin(); it!=actions.end(); ++it) { result+=separator+it->action+"\n"; result+=justificate(it->description,USAGE_INDENTION_FACTOR); if(it->req_args.size()) result+=separator+"Required arguments:\n"; for(argit=it->req_args.begin(); argit!=it->req_args.end(); ++argit) { argline=separator+"-"+argit->first+" <"+argit->second+">"; result+=separator+justificate(argline,USAGE_INDENTION_FACTOR,true); } if(it->opt_args.size()) result+=separator+"Optional arguments:\n"; for(argit=it->opt_args.begin(); argit!=it->opt_args.end(); ++argit) { argline=separator+"-"+argit->first+" <"+argit->second+">\n"; result+=separator+justificate(argline,USAGE_INDENTION_FACTOR,true); } result+="\n"; } #endif return result; } odin-1.8.5/odinseq/seqgradchan.h0000644000175000017500000001425711322062345013501 00000000000000/*************************************************************************** seqgradchan.h - description ------------------- begin : Mon Aug 19 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADCHAN_H #define SEQGRADCHAN_H #include #include #include #include #define _GRADROTMATRIX_LIMIT_ 1.0e-5 /** * @addtogroup odinseq_internals * @{ */ /** * The base class for platform specific drivers of gradient channel objects */ class SeqGradChanDriver : public SeqDriverBase { public: SeqGradChanDriver() {} virtual ~SeqGradChanDriver() {} virtual STD_string get_const_program (float strength, float matrixfactor) const = 0; virtual STD_string get_onepoint_program(float strength, float matrixfactor) const = 0; virtual STD_string get_delay_program (float strength, float matrixfactor) const = 0; virtual STD_string get_wave_program (float strength, float matrixfactor) const = 0; virtual STD_string get_trapez_program (float strength, float matrixfactor) const = 0; virtual STD_string get_vector_program (float strength, float matrixfactor, int reordercount) const = 0; virtual svector get_vector_commands(const STD_string& iterator) const = 0; virtual svector get_reord_commands() const = 0; virtual bool prep_const(float strength, const fvector& strengthfactor, double gradduration) = 0; virtual bool prep_onepoint(float strength, const fvector& strengthfactor, double gradduration) = 0; virtual bool prep_wave(float strength, const fvector& strengthfactor, double gradduration, const fvector& wave) = 0; virtual void update_wave(const fvector& wave) = 0; virtual bool prep_vector(float strength, const fvector& strengthfactor, double gradduration, const fvector& gradvec, const iarray& index_matrix, nestingRelation nr) = 0; virtual bool prep_vector_iteration(unsigned int count) = 0; virtual bool prep_trapez(float strength, const fvector& strengthfactor, double ruptime, const fvector& rupshape, double consttime, double rdowntime, const fvector& rdownshape) = 0; virtual void event(eventContext& context, double starttime) const = 0; virtual float check_strength(float strength) const = 0; virtual SeqGradChanDriver* clone_driver() const = 0; }; /////////////////////////////////////////////////////////////////////////////// /** * This is the base class for all objects that represent a single gradient object */ class SeqGradChan : public virtual SeqGradInterface, public ListItem, public SeqDur { public: /** * Constructs a gradient channel object labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - gradstrength: The gradient strength for this object * - gradduration: The duration of this gradient object */ SeqGradChan(const STD_string& object_label,direction gradchannel, float gradstrength, double gradduration); /** * Construct an empty gradient channel object with the given label */ SeqGradChan(const STD_string& object_label = "unnamedSeqGradChan" ); /** * Constructs a copy of 'sgc' */ SeqGradChan(const SeqGradChan& sgc); /** * Destructor */ virtual ~SeqGradChan() {} /** * Assignment operator that makes this gradient channel object become a copy of 'sgc' */ SeqGradChan& operator = (const SeqGradChan& sgc); /** * Returns the occupied channel */ virtual direction get_channel() const; /** * Overload this function to return the size of the used waveform, if any */ virtual int get_wavesize() const {return 0;} /** * Overload this function to resize the current waveform, if any */ virtual void resize(unsigned int newsize) {} // overwriting virtual functions from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); SeqGradInterface& invert_strength(); float get_strength() const; double get_gradduration() const {return get_duration();} SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); fvector get_gradintegral() const; // overwriting virtual functions from SeqTreeObj STD_string get_properties() const; unsigned int event(eventContext& context) const; STD_string get_grdpart_rot(direction chan) const; protected: /** * returns element [channel][chan] val. from the current rot. Matrix */ float get_grdfactor(direction chan) const; /** * returns element [channel][chan] val. from the current rot. Matrix without considering * the rotation matrix of the current event block (for IDEA) */ fvector get_grdfactors_norot() const; mutable SeqDriverInterface graddriver; private: friend class SeqGradChanList; friend class SeqGradChanParallel; /** * Overload this function to return a cut-out of this object in the interval [starttime,endtime] */ virtual SeqGradChan& get_subchan(double starttime, double endtime) const = 0; /** * Overload this function to return this objects part in the (gradient) program */ virtual STD_string get_grdpart(float matrixfactor) const = 0; /** * Overload this function to returns this objects gradient integral */ virtual float get_integral() const = 0; RotMatrix get_total_rotmat() const; float strength; direction channel; // Do not change this once it it is initialised RotMatrix gradrotmatrix; }; /** @} */ #endif odin-1.8.5/odinseq/seqsat.cpp0000644000175000017500000001253611322062345013052 00000000000000#include "seqsat.h" SeqPulsarSat::SeqPulsarSat(const STD_string& object_label,satNucleus nuc,float bandwidth) : SeqPulsar(object_label,false,false) { Log odinlog(this,"SeqPulsarSat"); double offset_ppm=0.0; if(nuc==fat) offset_ppm=-3.28; double offset_freq=systemInfo->get_nuc_freq("")*offset_ppm*1.0e-6; set_dim_mode(zeroDeeMode); ODINLOG(odinlog,normalDebug) << "offset_freq=" << offset_freq << STD_endl; set_Tp(secureDivision(3.0,bandwidth)); resize(128); SeqPulsar::set_flipangle(114.0); // flipangle determined experimentally with oil phantom (do NOT call virtual function in constructor) set_shape("Const"); set_trajectory("Const(0.0,1.0)"); set_filter("Gauss"); set_freqoffset( offset_freq ); SeqPulsar::set_pulse_type(saturation); // do NOT call virtual function in constructor refresh(); set_interactive(true); } SeqPulsarSat::SeqPulsarSat(const STD_string& object_label,float bandwidth, double freqoffset, float flipangle, float rel_filterwidth) : SeqPulsar(object_label,false,false) { Log odinlog(this,"SeqPulsarSat"); ODINLOG(odinlog,normalDebug) << "SeqPulsarSat.." << STD_endl; double effectiv_bandwidth; ODINLOG(odinlog,normalDebug) << "SeqPulsarSat bandwidth/ satoffset_freq / flipangle / rel_filterwidth" <get_max_grad(),2.0), spoiler_slice_neg(object_label+"_spoiler_slice_neg",sliceDirection,-0.6*systemInfo->get_max_grad(),2.0), spoiler_read_neg(object_label+"_spoiler_read_neg",readDirection,-0.6*systemInfo->get_max_grad(),2.0), spoiler_slice_pos(object_label+"_spoiler_slice_pos",sliceDirection,0.6*systemInfo->get_max_grad(),2.0), spoiler_phase_pos(object_label+"_spoiler_phase_pos",phaseDirection,0.6*systemInfo->get_max_grad(),2.0), npulses_cache(npulses) { SeqPulsInterface::set_marshall(&puls); SeqFreqChanInterface::set_marshall(&puls); build_seq(); } SeqSat::SeqSat(const SeqSat& spg) { SeqPulsInterface::set_marshall(&puls); SeqFreqChanInterface::set_marshall(&puls); SeqSat::operator = (spg); } SeqSat& SeqSat::operator = (const SeqSat& spg) { SeqObjList::operator = (spg); puls=spg.puls; spoiler_read_pos=spg.spoiler_read_pos; spoiler_slice_neg=spg.spoiler_slice_neg; spoiler_read_neg=spg.spoiler_read_neg; spoiler_slice_pos=spg.spoiler_slice_pos; spoiler_phase_pos=spg.spoiler_phase_pos; npulses_cache=spg.npulses_cache; build_seq(); return *this; } void SeqSat::build_seq() { clear(); (*this)+=(spoiler_read_pos/spoiler_slice_neg); for(unsigned int i=0; i #include #include #include #include #include #include struct SeqFieldMapPars { JcampDxBlock parblock; JDXint NumOfEchoes; JDXfloat Resolution; JDXdouble T1Ernst; JDXint DummyCycles; JDXint ReadSize; JDXint PhaseSize; JDXint SliceSize; JDXdouble FlashFlipAngle; JDXdouble ExtraDelay; }; struct SeqFieldMapObjects { SeqPulsar exc; SeqAcqEPI epi; SeqAcqDeph deph; SeqGradPhaseEnc pe3d; SeqGradConstPulse crusher; SeqDelay extradelay; SeqObjList pepart; SeqObjLoop peloop; SeqObjLoop peloop3d; SeqObjLoop sliceloop; SeqDelay acqdummy; SeqObjLoop dummyloop; }; void SeqFieldMap::alloc_data() { if(!pars) pars=new SeqFieldMapPars; if(!objs) objs=new SeqFieldMapObjects; } SeqFieldMap::~SeqFieldMap() { if(pars) delete pars; if(objs) delete objs; } void SeqFieldMap::init(const STD_string& objlabel) { alloc_data(); set_label(objlabel); pars->parblock.set_embedded(false).set_label(objlabel+"_parblock"); pars->parblock.clear(); pars->NumOfEchoes.set_description("Number of ecoes for fieldmap calculation").set_label("NumOfEchoes"); pars->NumOfEchoes=8; pars->parblock.append(pars->NumOfEchoes); pars->Resolution.set_description("Spatial in-plane resolution").set_unit(ODIN_SPAT_UNIT).set_label("Resolution"); pars->Resolution=3.0; pars->parblock.append(pars->Resolution); pars->T1Ernst.set_description("For optimum SNR, the flip angle will be set to the Ernst angle using this T1").set_unit(ODIN_TIME_UNIT).set_label("T1Ernst"); pars->T1Ernst=1300.0; pars->parblock.append(pars->T1Ernst); pars->DummyCycles.set_description("Number of dummy repetions").set_label("DummyCycles"); pars->DummyCycles=3; pars->parblock.append(pars->DummyCycles); pars->ExtraDelay.set_description("Extra TR delay").set_unit(ODIN_TIME_UNIT).set_label("ExtraDelay"); pars->parblock.append(pars->ExtraDelay); pars->FlashFlipAngle.set_description("Flip-angle of excitation pulse").set_parmode(noedit).set_label("FlashFlipAngle"); pars->parblock.append(pars->FlashFlipAngle); pars->ReadSize.set_description("Size in read direction").set_parmode(noedit).set_label("ReadSize"); pars->parblock.append(pars->ReadSize); pars->PhaseSize.set_description("Size in phase direction").set_parmode(noedit).set_label("PhaseSize"); pars->parblock.append(pars->PhaseSize); pars->SliceSize.set_description("Size in slice direction").set_parmode(noedit).set_label("SliceSize"); pars->parblock.append(pars->SliceSize); } void SeqFieldMap::build_seq(double sweepwidth, float os_factor, const SeqObjList& prep, double min_relaxdelay) { alloc_data(); STD_string objlabel(get_label()); if(geometryInfo->get_Mode()==voxel_3d) { // Same settings as in swi sequence float spatres=3.0; float slicethick=geometryInfo->get_FOV(sliceDirection)-2.0*spatres; if(slicethickexc=SeqPulsarSinc(objlabel+"_exc", slicethick, true, 4.0, 90.0, spatres, 512); // flip angle will be adjusted later objs->exc.set_filter("Gauss"); objs->exc.set_freqoffset(systemInfo->get_gamma() * objs->exc.get_strength() / (2.0*PII) * geometryInfo->get_offset(sliceDirection) ); } else { objs->exc=SeqPulsarSinc(objlabel+"_exc",geometryInfo->get_sliceThickness()); objs->exc.set_freqlist( systemInfo->get_gamma() * objs->exc.get_strength() / (2.0*PII) * geometryInfo->get_sliceOffsetVector() ); } objs->exc.set_pulse_type(excitation); pars->ReadSize= int(secureDivision(geometryInfo->get_FOV(readDirection) ,pars->Resolution)+0.5); pars->PhaseSize=int(secureDivision(geometryInfo->get_FOV(phaseDirection),pars->Resolution)+0.5); if(geometryInfo->get_Mode()==voxel_3d) { pars->SliceSize=int(secureDivision(geometryInfo->get_FOV(sliceDirection),pars->Resolution)+0.5); } else { pars->SliceSize=1; } if(pars->NumOfEchoes%2) pars->NumOfEchoes++; objs->epi=SeqAcqEPI(objlabel+"_epi",sweepwidth, pars->ReadSize,geometryInfo->get_FOV(readDirection), pars->PhaseSize,geometryInfo->get_FOV(phaseDirection), pars->PhaseSize,1,os_factor,"",0,0,linear,false,1.0,0.0,pars->NumOfEchoes/2); objs->epi.set_template_type(fieldmap_template); objs->deph=SeqAcqDeph(objlabel+"_deph",objs->epi,FID); // Does the phase encoding in one dimension objs->pepart=SeqObjList(objlabel+"_pepart"); if(geometryInfo->get_Mode()==voxel_3d) { objs->pe3d=SeqGradPhaseEnc(objlabel+"_pe3d",pars->SliceSize,geometryInfo->get_FOV(sliceDirection),sliceDirection,0.25*systemInfo->get_max_grad()); objs->pepart=objs->deph/objs->pe3d; } else { objs->pepart=objs->deph; } double crusher_strength=0.4*systemInfo->get_max_grad(); double crusher_integral=2.0*fabs(objs->deph.get_gradintegral().sum()); double crusher_dur=secureDivision(crusher_integral,crusher_strength); objs->crusher=SeqGradConstPulse(objlabel+"_crusher",readDirection,crusher_strength,crusher_dur); pars->ExtraDelay=STD_max(double(pars->ExtraDelay),min_relaxdelay); objs->extradelay=SeqDelay(objlabel+"_extradelay",pars->ExtraDelay); double readoutdur = objs->pepart.get_duration() + objs->epi.get_duration(); double kerneldur = prep.get_duration()+objs->exc.get_duration()+readoutdur+objs->crusher.get_duration()+objs->extradelay.get_duration(); float TR=double(geometryInfo->get_nSlices())*kerneldur; pars->FlashFlipAngle=180.0/PII * acos( exp ( -secureDivision ( TR, pars->T1Ernst) ) ); objs->exc.set_flipangle( pars->FlashFlipAngle ); objs->acqdummy=SeqDelay(objlabel+"_acqdummy",readoutdur); objs->peloop=SeqObjLoop(objlabel+"_peloop"); objs->peloop3d=SeqObjLoop(objlabel+"_peloop3d"); objs->sliceloop=SeqObjLoop(objlabel+"_sliceloop"); objs->dummyloop=SeqObjLoop(objlabel+"_dummyloop"); SeqObjList::clear(); if(pars->DummyCycles>0) { (*this)+= (objs->dummyloop) ( (objs->sliceloop) ( prep + objs->exc + objs->acqdummy + objs->crusher + objs->extradelay )[objs->exc] )[pars->DummyCycles]; } if(geometryInfo->get_Mode()==voxel_3d) { (*this)+= (objs->peloop3d) ( (objs->peloop) ( prep + objs->exc + objs->pepart + objs->epi + objs->crusher + objs->extradelay )[objs->deph.get_epi_segment_vector()] )[objs->pe3d]; objs->epi.set_reco_vector(line3d,objs->pe3d); } else { (*this)+= (objs->peloop) ( (objs->sliceloop) ( prep + objs->exc + objs->pepart + objs->epi + objs->crusher + objs->extradelay )[objs->exc] )[objs->deph.get_epi_segment_vector()]; objs->epi.set_reco_vector(slice,objs->exc); } // objs->epi.set_te_offset(objs->exc.get_duration()-objs->exc.get_magnetic_center()+objs->pepart.get_duration()); } JcampDxBlock& SeqFieldMap::get_parblock() { alloc_data(); return pars->parblock; } odin-1.8.5/odinseq/seqveciter.cpp0000644000175000017500000000557211455553540013737 00000000000000#include "seqveciter.h" #include "seqdelay.h" SeqVecIter::SeqVecIter(const STD_string& object_label, unsigned int start) : SeqCounter(object_label), SeqObjBase(object_label), startindex(start) { } SeqVecIter::SeqVecIter(const SeqVecIter& svi) : startindex(0) { SeqVecIter::operator = (svi); } SeqVecIter& SeqVecIter::operator = (const SeqVecIter& svi) { SeqCounter::operator = (svi); SeqObjBase::operator = (svi); startindex=svi.startindex; return *this; } STD_string SeqVecIter::get_program(programContext& context) const { counterdriver->outdate_cache(); counterdriver->update_driver(this,0,&vectors); return counterdriver->get_program_iterator(context); } double SeqVecIter::get_duration() const { counterdriver->update_driver(this,0,&vectors); return counterdriver->get_postduration_inloop(); } unsigned int SeqVecIter::event(eventContext& context) const { Log odinlog(this,"event"); unsigned int result=0; counterdriver->update_driver(this,0,&vectors); if(context.action==seqRun) { if(!context.seqcheck ) { // do not increment in test run increment_counter(); if(get_counter()>=get_times()) init_counter(); // cyclical iteration } // prep next iteration counterdriver->pre_vecprepevent(context); prep_veciterations(); counterdriver->post_vecprepevent(context,-1); } double iteratordur=counterdriver->get_postduration_inloop(); if(iteratordur) { SeqDelay sd("iteratordur",iteratordur); result+=sd.event(context); } return result; } STD_string SeqVecIter::get_properties() const { return "VecSize="+itos(get_times())+", NumOfVectors="+itos(n_vectors())+", "+SeqObjBase::get_properties(); } bool SeqVecIter::is_acq_iterator() const { Log odinlog(this,"is_acq_iterator"); bool result=false; for(veciter=get_vecbegin(); veciter!=get_vecend(); ++veciter) { if((*veciter)->is_acq_vector()) { result=true; ODINLOG(odinlog,normalDebug) << "detected acq iterator" << STD_endl; break; } } return result; } void SeqVecIter::query(queryContext& context) const { Log odinlog(this,"query"); SeqCounter::query(context); // default if(context.action==check_acq_iter) context.check_acq_iter_result=is_acq_iterator(); } RecoValList SeqVecIter::get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const { Log odinlog(this,"get_recovallist"); RecoValList dummy; if(is_acq_iterator()) { counterdriver->update_driver(this,0,&vectors); increment_counter(); if(get_counter()>=get_times()) init_counter(); // cyclical iteration // prep next iteration prep_veciterations(); } return dummy; } bool SeqVecIter::prep() { if(!SeqObjBase::prep()) return false; if(!SeqCounter::prep()) return false; init_counter(startindex); // set to first element if(!prep_veciterations()) return false;; // prep 1st iteration return true; } odin-1.8.5/odinseq/seqgradecho.h0000644000175000017500000002165311455553540013515 00000000000000/*************************************************************************** seqgradecho.h - description ------------------- begin : Mon Feb 17 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADECHO_H #define SEQGRADECHO_H #include #include #include #include #include #include /** * @addtogroup odinseq * @{ */ /** * \brief Gradient echo module * * A gradient echo module (excitation pulse + phase encoding + frequency encoding). * This is a convenience class which groups a number of low-level sequence * objects together. All objects necessary to produce a gradient echo are part * of this class, except the excitation pulse. The latter is passed per reference * (no copy is created within the module, it uses a safe pointer to the pulse). * */ class SeqGradEcho : public SeqObjList, public virtual SeqGradInterface, public virtual SeqAcqInterface { // virtual functions of SeqFreqChanInterface are marhshalled to acqread public: /** * Constructs a 2D (i.e. multi-slice) gradient echo module labeled 'object_label' with the following properties: * - exc: The excitation pulse * - sweepwidth: The sampling frequency * - readnpts: Matrix size in frequency-encoding direction * - FOVread: The FOV in frequency-encoding direction * - phasenpts: Matrix size in phase-encoding direction * - FOVphase: The FOV in phase-encoding direction * - scheme: The phase encoding scheme * - reorder: The reordering scheme * - nsegments: The number of segments for segmented reordering * - reduction: Reduction factor for parallel imaging (sparsely sampled k-space) * - acl_bands: Number of autocalibration bands (bunch of adjacent lines between actual k-space lines) for GRAPPA * - balanced: Whether rephasers (+ exc dephaser) should be added after acquisition, suitable for SSFP sequences * - partial_fourier_phase: The amount of partial Fourier undersampling in phase encoding direction (0=no undersampling, 1=half fourier) * - partial_fourier_read: The amount of partial Fourier undersampling in readout direction (0=no undersampling, 1=half fourier) * - partial_fourier_read_at_end: If set to 'true', partial Fourier will omit data at the end of the readout * - os_factor: The oversampling factor, os_factor=1 means no oversampling * - nucleus: The nucleus to observe */ SeqGradEcho(const STD_string& object_label, SeqPulsar& exc, double sweepwidth, unsigned int readnpts, float FOVread, unsigned int phasenpts, float FOVphase, encodingScheme scheme=linearEncoding, reorderScheme reorder=noReorder, unsigned int nsegments=1, unsigned int reduction=1, unsigned int acl_bands=DEFAULT_ACL_BANDS, bool balanced=false, float partial_fourier_phase=0.0, float partial_fourier_read=0.0, bool partial_fourier_read_at_end=false, float os_factor=1.0, const STD_string& nucleus=""); /** * Constructs a gradient echo module labeled 'object_label' for 3D imaging with the following properties: * - readnpts: Matrix size in frequency-encoding direction * - FOVread: The FOV in frequency-encoding direction * - phasenpts: Matrix size in phase-encoding direction * - FOVphase: The FOV in phase-encoding direction * - slicenpts: Matrix size in the 2nd phase-encoding (slice) direction * - FOVslice: The FOV in the 2nd phase-encoding (slice) direction * - exc: The excitation pulse * - sweepwidth: The sampling frequency * - reduction: Reduction factor for parallel imaging (sparsely sampled k-space), the factor applies to both phase-encoding directions * - acl_bands: Number of autocalibration bands (bunch of adjacent lines between actual k-space lines) for GRAPPA * - balanced: Whether rephasers (+ exc dephaser) should be added after acquisition, suitable for SSFP sequences * - partial_fourier_phase: The amount of partial Fourier undersampling in phase encoding direction (0=no undersampling, 1=half fourier) * - partial_fourier_read: The amount of partial Fourier undersampling in readout direction (0=no undersampling, 1=half fourier) * - partial_fourier_read_at_end: If set to 'true', partial Fourier will omit data at the end of the readout * - os_factor: The oversampling factor, os_factor=1 means no oversampling * - nucleus: The nucleus to observe */ SeqGradEcho(const STD_string& object_label, unsigned int readnpts, float FOVread, unsigned int phasenpts, float FOVphase, unsigned int slicenpts, float FOVslice, SeqPulsar& exc, double sweepwidth, unsigned int reduction=1, unsigned int acl_bands=DEFAULT_ACL_BANDS, bool balanced=false, float partial_fourier_phase=0.0, float partial_fourier_read=0.0, bool partial_fourier_read_at_end=false, float os_factor=1.0, const STD_string& nucleus=""); /** * Constructs an empty SeqGradEcho */ SeqGradEcho(const STD_string& object_label="unnamedSeqGradEcho"); /** * Constructs a copy of 'sge' */ SeqGradEcho(const SeqGradEcho& sge); /** * Assignment operator that makes this object become a copy of 'sge' */ SeqGradEcho& operator = (const SeqGradEcho& sge); /** * Returns the phase encoding vector as a sequence object (for loop insertion) */ SeqVector& get_pe_vector(); /** * Sets the reordering scheme and the number of segments for phase encoding */ SeqGradEcho& set_pe_reorder_scheme(reorderScheme scheme,unsigned int nsegments); /** * Returns the phase encoding reordering vector (for loop insertion) */ const SeqVector& get_pe_reorder_vector() const; /** * Returns the 2nd phase encoding vector as a sequence object (for loop insertion) */ SeqVector& get_pe3d_vector(); /** * Returns the excitation pulse as a sequence object (for loop insertion) */ const SeqVector& get_exc_vector() const {return *pulsptr.get_handled();} /** * Sets the reordering scheme for the frequency list of the excitation pulse */ SeqGradEcho& set_freq_reorder_scheme(reorderScheme scheme,unsigned int nsegments=1) {(*pulsptr.get_handled()).set_reorder_scheme(scheme,nsegments); return *this;} /** * Returns the reorder vector for the frequency list of the excitation pulse (for loop insertion) */ const SeqVector& get_freq_reorder_vector() const {return (*pulsptr.get_handled()).get_reorder_vector();} /** * Returns the echo time (from the middle of excitation pulse to the middle of the acquisition window) */ double get_echo_time() const; /** * Places an additional sequence object between excitation and readout */ SeqGradEcho& set_midpart(const SeqObjBase& soa); // implementing virtual functions of SeqGradInterface SeqGradInterface& set_strength(float gradstrength) {return *this;} // nothing useful float get_strength() const {return 0.0;} // nothing useful SeqGradInterface& invert_strength(); double get_gradduration() const {return get_duration();} SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); fvector get_gradintegral() const; // marshalling virtual functions of SeqAcqInterface to acqread, except: double get_acquisition_center() const {return get_preacq()+acqread.get_acquisition_center();} double get_acquisition_start() const {return get_preacq()+acqread.get_acquisition_start();} SeqAcqInterface& set_template_type(templateType type); private: double get_preacq() const; void common_init(const STD_string& objlabel); void build_seq(); // hide these functions from the user SeqAcqInterface& set_pe_vector(const SeqVector& pevec) {return *this;} Handler pulsptr; SeqPulsarReph pls_reph; SeqGradVector phase; SeqGradVector phase3d; SeqGradVector phase_rew; SeqGradVector phase3d_rew; SeqSimultanVector phasesim; SeqSimultanVector phasesim3d; SeqSimultanVector phasereordsim; SeqAcqRead acqread; SeqGradConst readdeph; SeqParallel postexcpart; SeqParallel postacqpart; SeqObjList midpart; geometryMode mode; bool balanced_grads; }; /** @} */ #endif odin-1.8.5/odinseq/Makefile.am0000644000175000017500000000543211625224370013103 00000000000000 INCLUDES = $(all_includes) $(ODINSEQ_INCLUDES) lib_LTLIBRARIES = libodinseq.la libodinseq_la_LDFLAGS = -no-undefined -release $(VERSION) libodinseq_la_LIBADD = ../odinpara/libodinpara.la library_includedir=$(includedir)/odinseq library_include_HEADERS = \ odinpulse.h \ seqacq.h \ seqacqdeph.h \ seqacqepi.h \ seqacqread.h \ seqacqspiral.h \ seqall.h \ seqclass.h \ seqcmdline.h \ seqcounter.h \ seqdec.h \ seqdelay.h \ seqdelayvec.h \ seqdiffweight.h \ seqdriver.h \ seqdur.h \ seqfreq.h \ seqgrad.h \ seqgradchan.h \ seqgradchanlist.h \ seqgradchanparallel.h \ seqgradconst.h \ seqgradecho.h \ seqgradobj.h \ seqgradphase.h \ seqgradpulse.h \ seqgradramp.h \ seqgradspiral.h \ seqgradtrapez.h \ seqgradvec.h \ seqgradwave.h \ seqlist.h \ seqloop.h \ seqmakefile.h \ seqmeth.h \ seqobj.h \ seqobjvec.h \ seqoperator.h \ seqparallel.h \ seqphase.h \ seqplatform.h \ seqplot.h \ seqpuls.h \ seqpulsar.h \ seqpulsndim.h \ seqrotmatrixvector.h \ seqsat.h \ seqsim.h \ seqtemplate.h \ seqsimvec.h \ seqtree.h \ seqtrigg.h \ seqvec.h \ seqveciter.h \ seqblsiegprep.h libodinseq_la_SOURCES = \ 00seqtest.cpp \ odinpulse.cpp odinpulse.h odinpulse_shapes.cpp odinpulse_trajectories.cpp \ seqacq.cpp seqacq.h \ seqacqdeph.cpp seqacqdeph.h \ seqacqepi.cpp seqacqepi.h \ seqacqread.cpp seqacqread.h \ seqacqspiral.cpp seqacqspiral.h \ seqall.h \ seqblsiegprep.cpp seqblsiegprep.h \ seqclass.cpp seqclass.h \ seqcmdline.cpp seqcmdline.h \ seqcounter.cpp seqcounter.h \ seqdec.cpp seqdec.h \ seqdelay.cpp seqdelay.h \ seqdelayvec.cpp seqdelayvec.h \ seqdiffweight.cpp seqdiffweight.h \ seqdriver.cpp seqdriver.h \ seqdriver_epic.cpp seqdriver_idea.cpp seqdriver_paravision.cpp seqdriver_standalone.cpp \ seqdur.cpp seqdur.h \ seqfreq.cpp seqfreq.h \ seqgrad.cpp seqgrad.h \ seqgradchan.cpp seqgradchan.h \ seqgradchanlist.cpp seqgradchanlist.h \ seqgradchanparallel.cpp seqgradchanparallel.h \ seqgradconst.cpp seqgradconst.h \ seqgradecho.cpp seqgradecho.h \ seqgradobj.cpp seqgradobj.h \ seqgradphase.cpp seqgradphase.h \ seqgradpulse.cpp seqgradpulse.h \ seqgradramp.cpp seqgradramp.h \ seqgradspiral.cpp seqgradspiral.h \ seqgradtrapez.cpp seqgradtrapez.h \ seqgradvec.cpp seqgradvec.h \ seqgradwave.cpp seqgradwave.h \ seqlist.cpp seqlist.h \ seqloop.cpp seqloop.h \ seqmakefile.cpp seqmakefile.h \ seqmeth.cpp seqmeth.h \ seqobj.cpp seqobj.h \ seqobjvec.cpp seqobjvec.h \ seqoperator.cpp seqoperator.h \ seqparallel.cpp seqparallel.h \ seqphase.cpp seqphase.h \ seqplatform.cpp seqplatform.h \ seqplot.h \ seqpuls.cpp seqpuls.h \ seqpulsar.cpp seqpulsar.h \ seqpulsndim.cpp seqpulsndim.h \ seqrotmatrixvector.cpp seqrotmatrixvector.h \ seqsat.cpp seqsat.h \ seqsim.cpp seqsim.h \ seqtemplate.cpp seqtemplate.h \ seqsimvec.cpp seqsimvec.h \ seqtree.cpp seqtree.h \ seqtrigg.cpp seqtrigg.h \ seqvec.cpp seqvec.h \ seqveciter.cpp 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tags uninstall \ uninstall-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/odinseq/seqpuls.cpp0000644000175000017500000001333511322062345013244 00000000000000#include "seqpuls.h" #include "seqdelay.h" #include SeqPulsInterface& SeqPulsInterface::set_flipangles(const fvector& flipangles) { float ang=get_flipangle(); fvector scales(flipangles.size()); if(ang) scales=flipangles/ang; else scales=0.0; set_flipscales(scales); return *this; } /////////////////////////////////////////////////////////////////////////////////// bool SeqFlipAngVector::prep_iteration() const { if(user) { return user->pulsdriver->prep_flipangle_iteration(get_current_index()); } return true; } svector SeqFlipAngVector::get_vector_commands(const STD_string& iterator) const { svector result; if(user) result=user->pulsdriver->get_flipvector_commands(iterator); return result; } /////////////////////////////////////////////////////////////////////////////////// SeqPuls::SeqPuls(const STD_string& object_label,const cvector& waveform,float pulsduration, float pulspower,const STD_string& nucleus, const dvector& phaselist,const dvector& freqlist,float rel_magnetic_center) : SeqObjBase(object_label), SeqFreqChan(object_label,nucleus,freqlist,phaselist), SeqDur(object_label,pulsduration), pulsdriver(object_label), flipvec(object_label+"_flipvec",this) { Log odinlog(this,"SeqPuls(...)"); wave=waveform; power=pulspower; system_flipangle=90.0; B1max_mT=0.0; relmagcent=rel_magnetic_center; } SeqPuls::SeqPuls(const STD_string& object_label) : SeqObjBase(object_label), SeqFreqChan(object_label), SeqDur(object_label), pulsdriver(object_label), flipvec(object_label+"_flipvec",this) { power=0.0; system_flipangle=90.0; B1max_mT=0.0; relmagcent=0.5; } SeqPuls::SeqPuls(const SeqPuls& sp) : flipvec(STD_string(sp.get_label())+"_flipvec",this) { SeqPuls::operator = (sp); } SeqPuls& SeqPuls::set_wave(const cvector& waveform) { wave=waveform; return *this; } double SeqPuls::get_duration() const { double result=get_pulsstart()+get_pulsduration(); result+=pulsdriver->get_postdelay(); return result; } SeqPulsInterface& SeqPuls::set_pulsduration(float pulsduration) { Log odinlog(this,"SeqPuls::set_pulsduration"); ODINLOG(odinlog,normalDebug) << "=" << pulsduration << STD_endl; SeqDur::set_duration(pulsduration); return *this; } double SeqPuls::get_pulsduration() const { Log odinlog(this,"SeqPuls::get_pulsduration"); ODINLOG(odinlog,normalDebug) << "=" << SeqDur::get_duration() << STD_endl; return SeqDur::get_duration(); } float SeqPuls::get_magnetic_center() const { Log odinlog(this,"get_magnetic_center"); ODINLOG(odinlog,normalDebug) << "relmagcent=" << relmagcent << STD_endl; ODINLOG(odinlog,normalDebug) << "get_pulsduration()=" << get_pulsduration() << STD_endl; ODINLOG(odinlog,normalDebug) << "get_pulsstart()=" << get_pulsstart() << STD_endl; return get_pulsstart()+relmagcent*get_pulsduration(); } bool SeqPuls::prep() { Log odinlog(this,"prep"); if(!SeqFreqChan::prep()) return false; if(wave.length()==0) ODINLOG(odinlog,warningLog) << "Empty waveform" << STD_endl; if(wave.maxabs()==STD_complex(0,0)) ODINLOG(odinlog,warningLog) << "Zero filled waveform" << STD_endl; ODINLOG(odinlog,normalDebug) << "B1max_mT=" << B1max_mT << STD_endl; fvector flipscale=flipvec.flipanglescale; ODINLOG(odinlog,normalDebug) << "flipscale=" << flipscale.printbody() << STD_endl; return pulsdriver->prep_driver(wave,get_pulsduration(),get_magnetic_center(),B1max_mT,power,system_flipangle,flipscale,plstype); } STD_string SeqPuls::get_program(programContext& context) const { STD_string result=SeqFreqChan::get_pre_program(context,pulsObj,pulsdriver->get_instr_label()); result+=pulsdriver->get_program(context,get_phaselistindex(),get_channel(),get_iteratorcommand(pulsObj)); return result; } SeqPuls& SeqPuls::set_B1max(float b1max) { Log odinlog(this,"set_B1max"); B1max_mT=b1max; ODINLOG(odinlog,normalDebug) << "B1max_mT=" << B1max_mT << STD_endl; return *this; } SeqValList SeqPuls::get_freqvallist(freqlistAction action) const { Log odinlog(this,"get_freqvallist"); SeqValList result(get_label()); double newfreq=SeqFreqChan::get_frequency(); if(action==calcDeps) pulsdriver->new_freq(newfreq); if(action==calcList) { if(pulsdriver->has_new_freq()) result.set_value(newfreq); } return result; } SeqPuls& SeqPuls::set_system_flipangle(float angle) { system_flipangle=angle; return *this; } double SeqPuls::get_rf_energy() const { return pulsdriver->get_rf_energy(); } SeqPuls& SeqPuls::operator = (const SeqPuls& sp) { Log odinlog(this,"operator = "); SeqObjBase::operator = (sp); SeqFreqChan::operator = (sp); SeqDur::operator = (sp); pulsdriver=sp.pulsdriver; wave=sp.wave; power=sp.power; system_flipangle=sp.system_flipangle; B1max_mT=sp.B1max_mT; ODINLOG(odinlog,normalDebug) << "B1max_mT=" << B1max_mT << STD_endl; relmagcent=sp.relmagcent; plstype=sp.plstype; return *this; } STD_string SeqPuls::get_properties() const { return "Samples="+itos(wave.length())+", B1="+ftos(B1max_mT); } SeqPulsInterface& SeqPuls::set_pulse_type(pulseType type) { plstype=type; return *this; } pulseType SeqPuls::get_pulse_type() const {return plstype;} unsigned int SeqPuls::event(eventContext& context) const { Log odinlog(this,"event"); double start=context.elapsed+get_pulsstart(); SeqTreeObj::event(context); if(context.action==seqRun) { ODINLOG(odinlog,normalDebug) << "start=" << start << STD_endl; SeqFreqChan::pre_event(context,start); pulsdriver->event(context,start); SeqFreqChan::post_event(context,start+get_pulsduration()); } if(context.event_progmeter) context.event_progmeter->increase_counter(); return 1; } odin-1.8.5/odinseq/seqpulsar.h0000644000175000017500000002252411322062345013234 00000000000000/*************************************************************************** seqpulsar.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPULSAR_H #define SEQPULSAR_H #include #include #include #include /** * @addtogroup odinseq * @{ */ /** * \brief Pulsar pulses, combines OdinPulse and SeqPulsNdim * * This class is an interface to the Pulsar program; * It is possible to access most of the parameters of the underlying * data structure 'OdinPulse' via get/set functions */ class SeqPulsar : public SeqPulsNdim, public OdinPulse, public StaticHandler { public: /** * Constructs an empty Pulsar pulse with the given label. * If 'rephased' is true, rephasing gradient lobes will be added to null the * zero'th order gradient moment, i.e. the integral. * If 'interactive' is true, the pulse will be updated each time a parameter * was changed, otherwise update() has to be called manually. */ SeqPulsar(const STD_string& object_label = "unnamedSeqPulsar", bool rephased=false, bool interactive=true); /** * Constructs a Pulsar pulse which is a copy of 'sp' */ SeqPulsar(const SeqPulsar& sp); /** * Destructor */ ~SeqPulsar(); /** * Specifies whether an additional gradient rephasing lobe will be added to rephase * the magnetization in case of an excitation pulse. * If strength is larger than zero, this maximum strength will be used * for the rephaser gradient. */ SeqPulsar& set_rephased(bool rephased, float strength=0.0); /** * Returns the rephasers integral on all three channels */ fvector get_reph_gradintegral() const; /** * This assignment operator will make this object become an exact copy of 'sp'. */ SeqPulsar& operator = (const SeqPulsar& sp); /** * Recalculates the pulse manually, this is only required if the pulse is not interactive */ SeqPulsar& refresh(); /** * If this flag is set to true, the pulse will be recalculated each time a parameter is changed, * otherwise it must be done manually via the refresh() function */ SeqPulsar& set_interactive(bool flag); // overloading virtual function from SeqGradInterface float get_strength() const {return OdinPulse::get_G0();} // always return strength of pulse, and not that of rephasers // reimplemented virtual functions from SeqPulsNdim int get_dims() const; // reimplemented virtual functions from SeqFreqChanInterface SeqFreqChanInterface& set_nucleus(const STD_string& nucleus); // reimplemented virtual functions from SeqPulsInterface float get_flipangle() const {return OdinPulse::get_flipangle(); } SeqPulsInterface& set_flipangle(float flipangle); SeqPulsInterface& set_pulsduration(float pulsduration); SeqPulsInterface& set_power(float pulspower); SeqPulsInterface& set_pulse_type(pulseType type); pulseType get_pulse_type() const { return SeqPulsNdim::get_pulse_type();} // overloading virtual function from SeqTreeObj STD_string get_properties() const; // initialize/destroy static members via StaticHandler static void init_static(); static void destroy_static(); // Dummy operators for vector of pulsars with STL replacement bool operator == (const SeqPulsar& sp) const {return STD_string(get_label())==STD_string(sp.get_label());} bool operator < (const SeqPulsar& sp) const {return STD_string(get_label()), public Labeled {}; static SingletonHandler active_pulsar_pulses; }; //////////////////////////////////////////////////////////////////////////////// /** * * \brief Post-pulse rephaser * * This class represents a rephasing gradient pulse for SeqPulsar, i.e. it can serve as a refocusing lobe for a SeqPulsar * pulse */ class SeqPulsarReph : public SeqGradChanParallel { public: /** * Constructs a rephasing gradient pulse labeled 'object_label' with the following properties: * - puls: The puls that should be rephased */ SeqPulsarReph(const STD_string& object_label,const SeqPulsar& puls); /** * Constructs a copy of 'spr' */ SeqPulsarReph(const SeqPulsarReph& spr); /** * Construct an empty rephasing gradient pulse with the given label */ SeqPulsarReph(const STD_string& object_label = "unnamedSeqPulsarReph"); /** * Destructor */ ~SeqPulsarReph(); /** * Assignment operator that makes this object become a copy of 'spr' */ SeqPulsarReph& operator = (const SeqPulsarReph& spr); /** * Returns the duration of the ramp that switches the gradient pulse on */ float get_onramp_duration() const; /** * Returns the duration of the rephasing part of the gradient pulse */ float get_constgrad_duration() const; /** * Returns the duration of the ramp that switches the gradient pulse on */ float get_offramp_duration() const; private: void build_seq(); unsigned int dim; SeqGradTrapez gxpulse; SeqGradTrapez gypulse; SeqGradTrapez gzpulse; }; //////////////////////////////////////////////////////////////////////////////// /** * * \brief Sinc pulse * * A sinc shaped pulse * */ class SeqPulsarSinc : public SeqPulsar { public: /** * Constructs a slice selective sinc pulse labeled 'object_label' with the following properties: * - slicethickness: The thickness of the slice that will be excited * - rephased: If true, an additional gradient lobe will be added to rephase the magnetisation * - duration: The pulse duration * - flipangle: The flip angle * - resolution: The spatial resolution, i.e. the scale on which the excitation profile is smoothed * - npoints: The number of digitised (complex) points for the pulse */ SeqPulsarSinc(const STD_string& object_label="unnamedSeqPulsarSinc", float slicethickness=5.0, bool rephased=true, float duration=2.0, float flipangle=90.0, float resolution=1.5, unsigned int npoints=256); /** * Constructs a copy of 'sps' */ SeqPulsarSinc(const SeqPulsarSinc& sps); /** * Assignment operator that makes this object become a copy of 'sps' */ SeqPulsarSinc& operator = (const SeqPulsarSinc& sps); }; //////////////////////////////////////////////////////////////////////////////// /** * * \brief Gauss pulse * * A Gaussian shaped pulse * */ class SeqPulsarGauss : public SeqPulsar { public: /** * Constructs a slice selective Gauss pulse labeled 'object_label' with the following properties: * - slicethickness: The thickness of the slice (FWHM) that will be excited * - rephased: If true, an additional gradient lobe will be added to rephase the magnetisation * - duration: The pulse duration * - flipangle: The flip angle * - npoints: The number of digitised (complex) points for the pulse */ SeqPulsarGauss(const STD_string& object_label="unnamedSeqPulsarGauss", float slicethickness=5.0, bool rephased=true, float duration=1.0, float flipangle=90.0, unsigned int npoints=128); /** * Constructs a copy of 'spg' */ SeqPulsarGauss(const SeqPulsarGauss& spg); /** * Assignment operator that makes this object become a copy of 'spg' */ SeqPulsarGauss& operator = (const SeqPulsarGauss& spg); }; //////////////////////////////////////////////////////////////////////////////// /** * * \brief Const pulse * * A block shaped shaped pulse * */ class SeqPulsarBP : public SeqPulsar { public: /** * Constructs a block shaped pulse labeled 'object_label' with the following properties: * - duration: The pulse duration * - flipangle: The flip angle */ SeqPulsarBP(const STD_string& object_label="unnamedSeqPulsarBP", float duration=1.0, float flipangle=90.0, const STD_string& nucleus=""); /** * Constructs a copy of 'spb' */ SeqPulsarBP(const SeqPulsarBP& spb); /** * Assignment operator that makes this object become a copy of 'spb' */ SeqPulsarBP& operator = (const SeqPulsarBP& spb); }; /** @} */ #endif odin-1.8.5/odinseq/seqgradchan.cpp0000644000175000017500000001137611322062345014033 00000000000000#include "seqgradchan.h" #include "seqparallel.h" #include #include SeqGradChan::SeqGradChan(const STD_string& object_label,direction gradchannel, float gradstrength, double gradduration) : SeqDur(object_label), graddriver(object_label) { channel=gradchannel; SeqGradChan::set_strength(gradstrength); // perform strength checking, do NOT call virtual function in constructor set_duration(gradduration); } SeqGradChan::SeqGradChan(const STD_string& object_label) : SeqDur(object_label), graddriver(object_label) { SeqGradChan::set_strength(0.0); // perform strength checking, do NOT call virtual function in constructor channel=readDirection; } SeqGradChan::SeqGradChan(const SeqGradChan& sgc) { SeqGradChan::operator = (sgc); } SeqGradChan& SeqGradChan::operator = (const SeqGradChan& sgc) { SeqDur::operator = (sgc); graddriver=sgc.graddriver; gradrotmatrix=sgc.gradrotmatrix; channel=sgc.channel; strength=sgc.strength; return *this; } SeqGradInterface& SeqGradChan::set_strength(float gradstrength) { Log odinlog(this,"set_strength"); ODINLOG(odinlog,normalDebug) << "gradstrength(pre)=" << gradstrength << STD_endl; gradstrength=graddriver->check_strength(gradstrength); ODINLOG(odinlog,normalDebug) << "gradstrength(post)=" << gradstrength << STD_endl; float maxgrad=systemInfo->get_max_grad(); ODINLOG(odinlog,normalDebug) << "maxgrad=" << maxgrad << STD_endl; if(gradstrength>maxgrad) { float oldstrength=gradstrength; gradstrength=maxgrad; ODINLOG(odinlog,warningLog) << "Gradient strength (" << oldstrength << ") exceeds maximum, setting to " << gradstrength << STD_endl; } strength=gradstrength; return *this; } SeqGradInterface& SeqGradChan::invert_strength() { strength=-strength; return *this; } float SeqGradChan::get_strength() const { return strength; } direction SeqGradChan::get_channel() const {return channel;} SeqGradInterface& SeqGradChan::set_gradrotmatrix(const RotMatrix& matrix) { Log odinlog(this,"set_gradrotmatrix"); for(unsigned int i=0;i1.0) { gradrotmatrix[j][i]=1.0; ODINLOG(odinlog,warningLog) << "exceeded 1.0 in gradrotmatrix[" << j << "][" << i << "], setting to 1.0" << STD_endl; } if(gradrotmatrix[j][i]<-1.0) { gradrotmatrix[j][i]=-1.0; ODINLOG(odinlog,warningLog) << "exceeded -1.0 in gradrotmatrix[" << j << "][" << i << "], setting to -1.0" << STD_endl; } } } return *this; } STD_string SeqGradChan::get_grdpart_rot(direction chan) const { Log odinlog(this,"get_grdpart_rot"); STD_string result; float matrixfactor=get_grdfactor(chan); ODINLOG(odinlog,normalDebug) << "matrixfactor[" << int(chan) << "][" << int(get_channel()) << "]=" << matrixfactor << STD_endl; if(fabs(matrixfactor)>_GRADROTMATRIX_LIMIT_) { result+=get_grdpart(matrixfactor); } ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } RotMatrix SeqGradChan::get_total_rotmat() const { RotMatrix result; const SeqRotMatrixVector* rotvec=SeqObjList::current_gradrotmatrixvec.get_handled(); if(rotvec) result=rotvec->get_current_matrix(); result=result*gradrotmatrix; // Multiplying the matrix coming from the vector with the local matrix return result; } float SeqGradChan::get_grdfactor(direction chan) const { return get_total_rotmat()[chan][get_channel()]; } fvector SeqGradChan::get_grdfactors_norot() const { fvector result(n_directions); for(int i=0; ievent(context,startelapsed); } context.elapsed=startelapsed+get_gradduration(); if(context.event_progmeter) context.event_progmeter->increase_counter(); return 1; } // Template instantiations template class ListItem; template class List; odin-1.8.5/odinseq/seqdur.cpp0000644000175000017500000000150411322062345013046 00000000000000#include "seqdur.h" SeqDur::SeqDur(const STD_string& object_label, float duration) : SeqTreeObj() { set_label(object_label); // this is neccessary because SeqClass is a virtual base class set_duration(duration); } SeqDur::SeqDur(const STD_string& object_label) : SeqTreeObj() { set_label(object_label); // this is neccessary because SeqClass is a virtual base class set_duration(0.0); } SeqDur::SeqDur(const SeqDur& sd) { SeqDur::operator = (sd); } SeqDur& SeqDur::operator = (const SeqDur& sd) { SeqTreeObj::operator = (sd); set_duration(sd.dur); return *this; } double SeqDur::get_duration() const { return dur; } SeqDur& SeqDur::set_duration(float duration) { dur=duration; if (durationget_min_duration(delayObj)) { dur=systemInfo->get_min_duration(delayObj); } return *this; } odin-1.8.5/odinseq/seqsimvec.h0000644000175000017500000000525611322062345013217 00000000000000/*************************************************************************** seqsimvec.h - description ------------------- begin : Mon Aug 9 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQSIMVEC_H #define SEQSIMVEC_H #include /** * @ingroup odinseq_internals * This vector class is used to group other vector objects together so that * they can be updated simultaneously at each iteration. */ class SeqSimultanVector : public SeqVector, public virtual SeqClass, public List { public: /** * Construct an empty vector of sequence objects with the given label */ SeqSimultanVector(const STD_string& object_label="unnamedSeqSimultanVector") : SeqClass(), SeqVector(object_label) {set_label(object_label);} /** * Constructs a copy of 'ssv' */ SeqSimultanVector(const SeqSimultanVector& ssv); /** * Assignment operator that makes this vector object become a copy of 'ssv' */ SeqSimultanVector& operator = (const SeqSimultanVector& ssv); /** * Appends sv to the list of managed vectors */ SeqSimultanVector& operator += (const SeqVector& sv); /** * clears the list of managed vectors */ SeqSimultanVector& clear() { List::clear(); return *this;} // implemented virtual functions from SeqVector svector get_vector_commands(const STD_string& iterator) const; unsigned int get_vectorsize() const; unsigned int get_numof_iterations() const; STD_string get_loopcommand() const; nestingRelation get_nesting_relation() const; bool needs_unrolling_check() const; bool prep_iteration() const; // bool is_acq_vector() const; const SeqVector& set_vechandler(const SeqCounter* sc) const; bool is_qualvector() const; private: // implemented virtual functions from SeqClass void clear_container(); }; #endif odin-1.8.5/odinseq/seqsim.cpp0000644000175000017500000011144011712547771013063 00000000000000#include #include #include "seqsim.h" /////////////////////////////////////////////////////////////////////////// void SeqSimMagsi::common_init() { magsi=false; nthreads=1; Mamp.set_filemode(compressed); Mpha.set_filemode(compressed); Mz.set_filemode(compressed); online=true; time_intervals_cache=0; xpos_cache=0; ypos_cache=0; zpos_cache=0; freqoffset_cache=0; ppm_cache=0; spin_density_cache=0; B1map_transm_cache=0; B1map_receiv_cache=0; Dcoeff_cache=0; num_rec_channel_cache=0; r1_cache=0; r2_cache=0; has_relax_cache=0; spat_rotmatrix=0; initial_vector[0]=0.0; initial_vector[1]=0.0; initial_vector[2]=1.0; online.set_description("Perform simulation online, i.e. each time a pulse parameter has been changed"); update_now.set_description("Recalculate magnetization"); initial_vector.set_description("Magnetization at beginning of pulse"); // intra-voxel magn gradients for(unsigned int k=0; k<4; k++) { dMx[k]=0; dMy[k]=0; dMz[k]=0; if(k<3) dppm[k]=0; } // init cache, must be called after setting pointers to zero outdate_simcache(); // set defaults on axes Sample default_sample; set_axes_cache(default_sample); } void SeqSimMagsi::outdate_simcache() { if(time_intervals_cache) delete[] time_intervals_cache; time_intervals_cache=0; if(xpos_cache) delete[] xpos_cache; xpos_cache=0; if(ypos_cache) delete[] ypos_cache; ypos_cache=0; if(zpos_cache) delete[] zpos_cache; zpos_cache=0; if(freqoffset_cache) delete[] freqoffset_cache; freqoffset_cache=0; if(ppm_cache) delete[] ppm_cache; ppm_cache=0; if(spin_density_cache) delete[] spin_density_cache; spin_density_cache=0; if(B1map_transm_cache) delete[] B1map_transm_cache; B1map_transm_cache=0; if(B1map_receiv_cache) { for(unsigned int ichan=0; ichan odinlog(this,"update_axes"); unsigned int nz=Mx.size(zDim); unsigned int nfreq=Mx.size(freqDim); ODINLOG(odinlog,normalDebug) << "nz/nfreq=" << nz << "/" << nfreq << STD_endl; GuiProps gp; if(nfreq>1) { gp.scale[xPlotScale]=ArrayScale("Frequency Offset",ODIN_FREQ_UNIT,freq_low,freq_upp); } if(nz>1) { gp.scale[xPlotScale]=ArrayScale("Spatial Offset",ODIN_SPAT_UNIT,x_low,x_upp); } Mx. set_gui_props(gp); My. set_gui_props(gp); Mz. set_gui_props(gp); Mamp.set_gui_props(gp); Mpha.set_gui_props(gp); } bool SeqSimMagsi::do_simulation() { bool action=false; if(update_now) action=true; if(online) action=true; return action; } void SeqSimMagsi::set_axes_cache(const Sample& sample) { Log odinlog(this,"create_simcache"); x_low=sample.get_spatial_offset(xAxis)-0.5*sample.get_FOV(xAxis); x_upp=sample.get_spatial_offset(xAxis)+0.5*sample.get_FOV(xAxis); ODINLOG(odinlog,normalDebug) << "x_low/x_upp=" << x_low << "/" << x_upp << STD_endl; y_low=sample.get_spatial_offset(yAxis)-0.5*sample.get_FOV(yAxis); y_upp=sample.get_spatial_offset(yAxis)+0.5*sample.get_FOV(yAxis); ODINLOG(odinlog,normalDebug) << "y_low/y_upp=" << y_low << "/" << y_upp << STD_endl; z_low=sample.get_spatial_offset(zAxis)-0.5*sample.get_FOV(zAxis); z_upp=sample.get_spatial_offset(zAxis)+0.5*sample.get_FOV(zAxis); ODINLOG(odinlog,normalDebug) << "z_low/z_upp=" << z_low << "/" << z_upp << STD_endl; freq_low=sample.get_freqoffset()-0.5*sample.get_freqrange(); // in kHz freq_upp=sample.get_freqoffset()+0.5*sample.get_freqrange(); // in kHz ODINLOG(odinlog,normalDebug) << "freq_low/freq_upp=" << freq_low << "/" << freq_upp << STD_endl; } void SeqSimMagsi::prepare_simulation(const Sample& sample, CoilSensitivity* transmit_coil, CoilSensitivity* receive_coil, ProgressMeter* progmeter) { if(simcache_up2date) return; Log odinlog(this,"create_simcache"); outdate_simcache(); // delete old pointers ndim extent=sample.get_extent(); unsigned int nx=extent[xDim]; unsigned int ny=extent[yDim]; unsigned int nz=extent[zDim]; unsigned int nfreq=extent[freqDim]; // unsigned int n=extent.total(); oneframe_size_cache=nx*ny*nz*nfreq; // size of one frame ODINLOG(odinlog,normalDebug) << "extent/oneframe_size=" << (STD_string)extent << "/" << oneframe_size_cache << STD_endl; resize(nx, ny, nz, nfreq); // will call reset_magnetization() and outdate_simcache() if(progmeter) progmeter->new_task(extent.total(),"Initializing Simulation"); elapsed_time=0.0; time_index_cache=0; numof_time_intervals_cache=0; dvector ti(sample.get_frame_durations()); unsigned int nti=ti.size(); if(nti>1) { numof_time_intervals_cache=nti; ODINLOG(odinlog,normalDebug) << "numof_time_intervals_cache=" << numof_time_intervals_cache << STD_endl; time_intervals_cache=new double[numof_time_intervals_cache]; for(unsigned int iti=0; iti1) L[3]=2.0*PII*sample.get_freqrange()/float(nfreq); // in rad*kHz ODINLOG(odinlog,normalDebug) << "L=" << L[0] << "/" << L[1] << "/" << L[2] << "/" << L[3]<< STD_endl; B0_ppm=1.0e-6*systemInfo->get_B0(); if(spat_rotmatrix) ODINLOG(odinlog,normalDebug) << "spat_rotmatrix=" << spat_rotmatrix->print() << STD_endl; ODINLOG(odinlog,normalDebug) << "ppmMap.get_extent()=" << ppmMap.get_extent() << STD_endl; ODINLOG(odinlog,normalDebug) << "spinDensity.get_extent()=" << spinDensity.get_extent() << STD_endl; ODINLOG(odinlog,normalDebug) << "spinDensity.sum()=" << spinDensity.sum() << STD_endl; extent[frameDim]=1; // iterate over time dim for each map separately unsigned int iframe; for(unsigned int i=0; i1) freqoffset_cache[i] = 2.0*PII*freq_low + (float(ifreq)+0.5)*L[3]; float x=sample.get_spatial_offset(xAxis); if(nx>1) x = x_low + (float(ix)+0.5)*L[0]; float y=sample.get_spatial_offset(yAxis); if(ny>1) y = y_low + (float(iy)+0.5)*L[1]; float z=sample.get_spatial_offset(zAxis); if(nz>1) z = z_low + (float(iz)+0.5)*L[2]; if(spat_rotmatrix) { dvector srcvec(3); srcvec[0]=x; srcvec[1]=y; srcvec[2]=z; dvector targetvec=(*spat_rotmatrix)*srcvec; xpos_cache[i]=targetvec[0]; ypos_cache[i]=targetvec[1]; zpos_cache[i]=targetvec[2]; } else { xpos_cache[i]=x; ypos_cache[i]=y; zpos_cache[i]=z; } for(iframe=0; iframeget_numof_channels(); ichan++) { chansum+=transmit_coil->get_sensitivity_value(ichan,xpos_cache[i],ypos_cache[i],zpos_cache[i]); } B1map_transm_cache[i]*=chansum; } if(receive_coil) { // separate B1map for different channels of coil for(ichan=0; ichanget_sensitivity_value(ichan,xpos_cache[i],ypos_cache[i],zpos_cache[i]); } if(sim_diffusion) { for(iframe=0; iframet1) t2=t1; if(iframe==0) has_relax_cache[i]=false; // reset only in 1st frame if(t1>0.0) has_relax_cache[i]=true; r1_cache[it1]=secureDivision( 1.0 , t1 ); r2_cache[it2]=secureDivision( 1.0 , t2 ); iframe++; } if(magsi || sim_diffusion) { for(k=0; k<4; k++) { dMx[k][i]=0.0; dMy[k][i]=0.0; dMz[k][i]=0.0; } for(k=0; k<3; k++) { // iterate through 3 spat dims to calc spat grads from ppmMap dppm[k][i]=0.0; bool calc_grads=true; // if(!have_ppmMap) calc_grads=false; // if(have_spinDensity && spinDensity(indexvec)<=0.0) calc_grads=false; if(spinDensity(indexvec)<=0.0) calc_grads=false; // use only first frame if(calc_grads) { bool have_low=false; bool have_upp=false; float lowval=0.0; float uppval=0.0; float currval=ppmMap(indexvec); // use only first frame int index=indexvec[xDim-k]; if(index>0) { ndim indexvec_low(indexvec); indexvec_low[xDim-k]--; // if(!have_spinDensity) have_low=true; if(/*have_spinDensity && */ spinDensity(indexvec_low)>0.0) have_low=true; if(have_low) lowval=ppmMap(indexvec_low); } if(index0.0) have_upp=true; if(have_upp) uppval=ppmMap(indexvec_upp); } if(have_upp && have_low) dppm[k][i]=secureDivision(uppval-lowval, 2.0*L[k]); if(!have_upp && have_low) dppm[k][i]=secureDivision(currval-lowval, L[k]); if(have_upp && !have_low) dppm[k][i]=secureDivision(uppval-currval, L[k]); } } } if(progmeter) progmeter->increase_counter(); } update_axes(); if(!ThreadedLoop::init(nthreads, oneframe_size_cache)) { ODINLOG(odinlog,errorLog) << "cannot init multithreading" << STD_endl; } simcache_up2date=true; } cvector SeqSimMagsi::simulate(const SeqSimInterval& simvals, double gamma) { Log odinlog(this,"simulate"); cvector result(num_rec_channel_cache); // initialized with zeroes gamma_cache=gamma; if(numof_time_intervals_cache) { elapsed_time+=simvals.dt; while(elapsed_time>=time_intervals_cache[time_index_cache]) { elapsed_time-=time_intervals_cache[time_index_cache]; time_index_cache++; if(time_index_cache>=numof_time_intervals_cache) time_index_cache=0; ODINLOG(odinlog,normalDebug) << "Switching to time_index=" << time_index_cache << STD_endl; } } STD_vector outvec; if(!ThreadedLoop::execute(simvals, outvec)) { ODINLOG(odinlog,errorLog) << "cannot start multithreading" << STD_endl; return result; } if(simvals.rec>0.0) { for(unsigned int i=0; i odinlog(this,"kernel"); if(simvals.dt<=0.0) return true; unsigned int ichan; // doubles to sum up signal, and use local (thread-specific) storage double* reSig; double* imSig; if(simvals.rec>0.0) { reSig=new double[num_rec_channel_cache]; imSig=new double[num_rec_channel_cache]; for(ichan=0; ichan0.0) A2= exp(-Dval * bval2); // Check for round-off errors when bval2 was calculated Mxnew *= A2; Mynew *= A2; Mznew *= A1; for(k=0; k<4; k++) { dMxnew[k] *= A2; dMynew[k] *= A2; dMznew[k] *= A1; } } ////////////////// Relaxation /////////////////////////////////////////////// if ( has_relax_cache[i] ) { //with relaxation E1=exp(-simvals.dt*r1_cache[(time_index_cache%nframes_r1_cache)*oneframe_size_cache+i]); E2=exp(-simvals.dt*r2_cache[(time_index_cache%nframes_r2_cache)*oneframe_size_cache+i]); Mxnew *= E2; Mynew *= E2; Mznew = (Mznew-1.0) * E1 + 1.0; // intra-voxel deph if(sim_intravoxel_grads) { for(k=0; k<4; k++) { dMxnew[k] *= E2; dMynew[k] *= E2; dMznew[k] *= E1; } } } ////////////////// Store Results /////////////////////////////////////////////// // store new values Mx[i]=Mxnew; My[i]=Mynew; Mz[i]=Mznew; // store intra-voxel magn gradients if(sim_intravoxel_grads) { for(k=0; k<4; k++) { dMx[k][i]=dMxnew[k]; dMy[k][i]=dMynew[k]; dMz[k][i]=dMznew[k]; } } ////////////////// Calculate signal //////////////////////////////////////////// if(simvals.rec>0.0) { // create signal by accumulating transverse magnetization STD_complex Mtrans(Mxnew,Mynew); if(magsi) { weight=1.0; for(k=0; k<4; k++) { float Mabs2=Mxnew*Mxnew + Mynew*Mynew; if(Mabs2) { // check before division dphi = (dMynew[k]*Mxnew - Mynew*dMxnew[k]) / Mabs2; if(dphi && (L[k]>0.0)) { weight *= sinc(0.5*dphi*L[k]); } } } Mtrans *= STD_complex(weight); } STD_complex sigMagn=s0*conj(Mtrans); for(ichan=0; ichan0.0) } // end loop over Mx,My,.. arrays if(simvals.rec>0.0) { signal.resize(num_rec_channel_cache); for(ichan=0; ichanget_B0(); if(!ThreadedLoop::init(numof_threads, particle.size())) { ODINLOG(odinlog,errorLog) << "cannot init multithreading" << STD_endl; } } unsigned int SeqSimMonteCarlo::linear_index(const float pos[3]) const { unsigned int index[3]; for(unsigned int k=0; k<3; k++) index[k]=((unsigned int)pos[k])%size_cache[k]; // assuming periodic pattern of spatial maps unsigned int result= index[2]*size_cache[0]*size_cache[1] + index[1]*size_cache[0] + index[0]; return result; } cvector SeqSimMonteCarlo::simulate(const SeqSimInterval& simvals, double gamma) { Log odinlog(this,"simulate"); cvector result(1); if(simvals.dt<=0.0) return result; gamma_cache=gamma; STD_vector outvec; if(!ThreadedLoop::execute(simvals, outvec)) { ODINLOG(odinlog,errorLog) << "cannot start multithreading" << STD_endl; return result; } if(simvals.rec>0.0) { for(unsigned int i=0; i odinlog(this,"kernel"); if(simvals.dt<=0.0) return true; float phase_rad=simvals.phase * PII / 180.0; float d_rf[3][3]; float b = 0.0; // Uniform B1 field for all particles float B1amp=cabs(simvals.B1); if(B1amp) { // float B1phase=phase(simvals.B1); // STD_complex b1_pulse= float(gamma_cache) * B1amp * STD_complex( cos(B1phase+phase_rad), sin(B1phase+phase_rad)); STD_complex b1_pulse= float(gamma_cache) * simvals.B1 * expc(STD_complex(0.0,phase_rad)); float bx=b1_pulse.real(); float by=b1_pulse.imag(); b = norm(bx,by); // Uniform B1 rotation matrix for all particles float ax = bx / b; float ay = by / b; float ph_rf = b*simvals.dt; // the precession angle around the effective field float si_rf = sin (ph_rf); float co_rf = cos (ph_rf); float axx= ax * ax; float ayy= ay * ay; float u= ax * ay * (1 - co_rf); float v= ay * si_rf; float w= ax * si_rf; // rotation matrix d_rf[0][0]= axx + ayy * co_rf; d_rf[0][1]= u; d_rf[0][2]= -v; d_rf[1][0]= u; d_rf[1][1]= ayy + axx * co_rf; d_rf[1][2]= w; d_rf[2][0]= v; d_rf[2][1]= -w; d_rf[2][2]= co_rf; } float w0_ppm=gamma_cache*B0_ppm_cache; // Use double precision to avoid round-off error when summing up signal double reSig=0.0; double imSig=0.0; for(unsigned int i=begin; i SeqTrigger::SeqTrigger(const STD_string& object_label, double duration) : SeqObjBase(object_label), triggdriver(object_label), triggdur(duration) { } SeqTrigger::SeqTrigger(const STD_string& object_label) : SeqObjBase(object_label), triggdriver(object_label), triggdur(0.0) { } SeqTrigger& SeqTrigger::operator = (const SeqTrigger& st) { SeqObjBase::operator = (st); triggdriver=st.triggdriver; triggdur=st.triggdur; return *this; } STD_string SeqTrigger::get_program(programContext& context) const { return triggdriver->get_program(context); } double SeqTrigger::get_duration() const { return triggdur+triggdriver->get_postduration(); } unsigned int SeqTrigger::event(eventContext& context) const { Log odinlog(this,"event"); double startelapsed=context.elapsed; SeqObjBase::event(context); ODINLOG(odinlog,normalDebug) << "context.action/startelapsed=" << context.action << "/" << startelapsed << STD_endl; if(context.action==seqRun) { triggdriver->event(context,startelapsed); } if(context.event_progmeter) context.event_progmeter->increase_counter(); return 1; } bool SeqTrigger::prep() { if(!SeqObjBase::prep()) return false; return triggdriver->prep_exttrigger(triggdur); } ///////////////////////////////////////////////////////////////////////////// SeqHalt::SeqHalt(const STD_string& object_label) : SeqObjBase(object_label), triggdriver(object_label) { } SeqHalt& SeqHalt::operator = (const SeqHalt& sh) { SeqObjBase::operator = (sh); triggdriver=sh.triggdriver; return *this; } STD_string SeqHalt::get_program(programContext& context) const { return triggdriver->get_program(context); } double SeqHalt::get_duration() const { return triggdriver->get_postduration(); } unsigned int SeqHalt::event(eventContext& context) const { Log odinlog(this,"event"); double startelapsed=context.elapsed; SeqObjBase::event(context); ODINLOG(odinlog,normalDebug) << "context.action/startelapsed=" << context.action << "/" << startelapsed << STD_endl; if(context.action==seqRun) { triggdriver->event(context,startelapsed); } if(context.event_progmeter) context.event_progmeter->increase_counter(); return 1; } bool SeqHalt::prep() { if(!SeqObjBase::prep()) return false; return triggdriver->prep_halttrigger(); } ///////////////////////////////////////////////////////////////////////////// SeqSnapshot::SeqSnapshot(const STD_string& object_label, const STD_string& snapshot_fname) : SeqObjBase(object_label), triggdriver(object_label) { magn_fname=snapshot_fname; } SeqSnapshot::SeqSnapshot(const STD_string& object_label) : SeqObjBase(object_label), triggdriver(object_label) { } SeqSnapshot& SeqSnapshot::operator = (const SeqSnapshot& ss) { SeqObjBase::operator = (ss); triggdriver=ss.triggdriver; magn_fname=ss.magn_fname; return *this; } unsigned int SeqSnapshot::event(eventContext& context) const { double startelapsed=context.elapsed; SeqObjBase::event(context); if(context.action==seqRun) { triggdriver->event(context,startelapsed); } if(context.event_progmeter) context.event_progmeter->increase_counter(); return 1; } bool SeqSnapshot::prep() { if(!SeqObjBase::prep()) return false; return triggdriver->prep_snaptrigger(magn_fname); } ///////////////////////////////////////////////////////////////////////////// SeqMagnReset::SeqMagnReset(const STD_string& object_label) : SeqObjBase(object_label), triggdriver(object_label) { } SeqMagnReset& SeqMagnReset::operator = (const SeqMagnReset& smr) { SeqObjBase::operator = (smr); triggdriver=smr.triggdriver; return *this; } unsigned int SeqMagnReset::event(eventContext& context) const { double startelapsed=context.elapsed; SeqObjBase::event(context); if(context.action==seqRun) { triggdriver->event(context,startelapsed); } if(context.event_progmeter) context.event_progmeter->increase_counter(); return 1; } bool SeqMagnReset::prep() { if(!SeqObjBase::prep()) return false; return triggdriver->prep_resettrigger(); } odin-1.8.5/odinseq/seqpulsndim.cpp0000644000175000017500000001345011322062345014112 00000000000000#include "seqpulsndim.h" #include "seqgradwave.h" #include "seqgradconst.h" #include "seqdelay.h" #include "seqgradchanparallel.h" #include struct SeqPulsNdimObjects { SeqPulsNdimObjects() {} SeqPulsNdimObjects(const STD_string& object_label, double gradshift_delay) : gx(object_label+"_Gx",readDirection,0.0,0.0,fvector()), gy(object_label+"_Gy",phaseDirection,0.0,0.0,fvector()), gz(object_label+"_Gz",sliceDirection,0.0,0.0,fvector()), sgh(object_label+"_handler"), rftrain(object_label+"_rftrain"), sp(object_label+"_rf"), dgs(object_label+"_shift_delay",gradshift_delay-sp.get_pulsstart()) {} SeqGradWave gx; SeqGradWave gy; SeqGradWave gz; SeqGradDelay gx_delay; SeqGradDelay gy_delay; SeqGradDelay gz_delay; SeqGradChanParallel sgh; SeqObjList rftrain; SeqPuls sp; SeqDelay dgs; }; ///////////////////////////////////////////////////////////////// SeqPulsNdim::SeqPulsNdim(const STD_string& object_label ) : SeqParallel(object_label), objs(new SeqPulsNdimObjects(object_label,systemInfo->get_grad_shift_delay())) { SeqPulsInterface::set_marshall(&(objs->sp)); SeqFreqChanInterface::set_marshall(&(objs->sp)); dims=0; gradshift=0.0; build_seq(); } SeqPulsNdim::SeqPulsNdim(const SeqPulsNdim& spnd) : objs(new SeqPulsNdimObjects) { SeqPulsInterface::set_marshall(&(objs->sp)); SeqFreqChanInterface::set_marshall(&(objs->sp)); SeqPulsNdim::operator = (spnd); } SeqPulsNdim::~SeqPulsNdim() { Log odinlog(this,"~SeqPulsNdim()"); delete objs; } SeqPulsNdim& SeqPulsNdim::set_rfwave(const cvector& waveform) { objs->sp.set_wave(waveform); return *this; } SeqPulsNdim& SeqPulsNdim::set_gradwave(direction dir, const fvector& waveform) { if(dir==readDirection) objs->gx.set_wave(waveform); if(dir==phaseDirection) objs->gy.set_wave(waveform); if(dir==sliceDirection) objs->gz.set_wave(waveform); return *this; } SeqPulsNdim& SeqPulsNdim::set_B1max(float b1max) { objs->sp.set_B1max(b1max); return *this; } cvector SeqPulsNdim::get_rfwave() const {return objs->sp.get_wave();} fvector SeqPulsNdim::get_gradwave(direction dir) const { if(dir==readDirection) return objs->gx.get_wave(); if(dir==phaseDirection) return objs->gy.get_wave(); if(dir==sliceDirection) return objs->gz.get_wave(); return fvector(); } int SeqPulsNdim::get_dims() const {return dims;} SeqPulsInterface& SeqPulsNdim::set_pulsduration(float pulsduration) { Log odinlog(this,"SeqPulsNdim::set_pulsduration"); ODINLOG(odinlog,normalDebug) << "=" << pulsduration << STD_endl; objs->sp.set_pulsduration(pulsduration); objs->gx.set_duration(pulsduration); objs->gy.set_duration(pulsduration); objs->gz.set_duration(pulsduration); return *this; } float SeqPulsNdim::get_magnetic_center() const { Log odinlog(this,"get_magnetic_center"); ODINLOG(odinlog,normalDebug) << "dgs.get_duration()=" << objs->dgs.get_duration() << STD_endl; ODINLOG(odinlog,normalDebug) << "sp.get_magnetic_center()=" << objs->sp.get_magnetic_center() << STD_endl; if(get_dims()) return objs->sgh.get_pulprogduration()+objs->dgs.get_duration()+objs->sp.get_magnetic_center(); else return objs->sp.get_magnetic_center(); } SeqVector& SeqPulsNdim::set_indexvec(const ivector& iv) {objs->sp.set_indexvec(iv); return objs->sp;} SeqPulsNdim& SeqPulsNdim::operator += (SeqGradChanList& sgcl) {objs->sgh+=sgcl; return *this;} SeqPulsNdim& SeqPulsNdim::set_system_flipangle(float angle) {objs->sp.set_system_flipangle(angle); return *this;} SeqPulsNdim& SeqPulsNdim::set_grad_shift_offset(float grad_shift_offset) { gradshift=grad_shift_offset; return *this; } SeqPulsNdim& SeqPulsNdim::operator = (const SeqPulsNdim& spnd) { Log odinlog(this,"operator = (...)"); SeqParallel::operator = (spnd); dims=spnd.get_dims(); gradshift=spnd.gradshift; objs->gx=spnd.objs->gx; objs->gy=spnd.objs->gy; objs->gz=spnd.objs->gz; objs->gx_delay=spnd.objs->gx_delay; objs->gy_delay=spnd.objs->gy_delay; objs->gz_delay=spnd.objs->gz_delay; objs->sgh=spnd.objs->sgh; objs->rftrain=spnd.objs->rftrain; objs->dgs=spnd.objs->dgs; objs->sp=spnd.objs->sp; build_seq(); return *this; } SeqPulsNdim& SeqPulsNdim::build_seq() { Log odinlog(this,"build_seq"); int dimensionality=get_dims(); ODINLOG(odinlog,normalDebug) << "dimensionality=" << dimensionality << STD_endl; objs->sgh.clear(); objs->rftrain.clear(); clear_gradptr(); double shift=systemInfo->get_grad_shift_delay()+gradshift-objs->sp.get_pulsstart(); bool have_dgs=false; bool have_grad_delays=false; if(shift>0.0) { have_dgs=true; objs->dgs.set_duration(shift); } if(shift<0.0) { have_grad_delays=true; objs->gx_delay=SeqGradDelay("gx_delay",readDirection,-shift); objs->gy_delay=SeqGradDelay("gy_delay",phaseDirection,-shift); objs->gz_delay=SeqGradDelay("gz_delay",sliceDirection,-shift); } if(dimensionality==3) { if(have_grad_delays) objs->sgh+=((objs->gx_delay+objs->gx)/(objs->gy_delay+objs->gy)/(objs->gz_delay+objs->gz)); else objs->sgh+=(objs->gx/objs->gy/objs->gz); } if(dimensionality==2) { if(have_grad_delays) objs->sgh+=((objs->gx_delay+objs->gx)/(objs->gy_delay+objs->gy)/(objs->gz_delay)); else objs->sgh+=(objs->gx/objs->gy); } if(dimensionality==1) { if(have_grad_delays) objs->sgh+=((objs->gx_delay)/(objs->gy_delay)/(objs->gz_delay+objs->gz)); else objs->sgh+=(objs->gz); double dummydur=objs->gz.get_gradduration(); ODINLOG(odinlog,normalDebug) << "dummydur=" << dummydur << STD_endl; } if(dimensionality) { if(have_dgs) objs->rftrain.append(objs->dgs); set_gradptr((SeqGradObjInterface*)&(objs->sgh)); } objs->rftrain.append(objs->sp); set_pulsptr(&(objs->rftrain)); return *this; } template class Handled; template class Handler; odin-1.8.5/odinseq/seqacqdeph.cpp0000644000175000017500000000312311322062345013660 00000000000000#include "seqacqdeph.h" #include "seqacq.h" void SeqAcqDeph::common_init() { dummyvec=SeqVector("dummyvec",1); // make one iteration the default, for dephasing of non-segmented EPI } SeqAcqDeph::SeqAcqDeph(const STD_string& object_label,const SeqAcqInterface& acq, dephaseMode mode) : SeqGradChanParallel(object_label) { Log odinlog(this,"SeqAcqDeph(...)"); common_init(); SeqGradChanParallel::clear(); const SeqVector* vec=acq.get_dephgrad(*this, mode==rephase); segvec.clear_handledobj(); if(vec) segvec.set_handled(vec); if(mode==spinEcho) { SeqGradChanParallel::invert_strength(); } ODINLOG(odinlog,normalDebug) << "integral(" << acq.get_label() << ")=" << SeqGradChanParallel::get_gradintegral().printbody() << STD_endl; } SeqAcqDeph::SeqAcqDeph(const SeqAcqDeph& sad) { common_init(); SeqAcqDeph::operator = (sad); } SeqAcqDeph::SeqAcqDeph(const STD_string& object_label) : SeqGradChanParallel(object_label) { common_init(); } SeqAcqDeph& SeqAcqDeph::operator = (const SeqAcqDeph& sad) { SeqGradInterface::operator = (sad); SeqGradChanParallel::operator = (sad); segvec=sad.segvec; return *this; } const SeqVector& SeqAcqDeph::get_epi_segment_vector() const { Log odinlog(this,"get_epi_segment_vector"); ODINLOG(odinlog,normalDebug) << "segvec.get_handled()=" << (void*)segvec.get_handled() << STD_endl; if(segvec.get_handled()) return *(segvec.get_handled()); return dummyvec; } const SeqVector& SeqAcqDeph::get_epi_reduction_vector() const { if(segvec.get_handled()) return segvec.get_handled()->get_reorder_vector(); return dummyvec; } odin-1.8.5/odinseq/seqgradramp.h0000644000175000017500000001451111322062345013520 00000000000000/*************************************************************************** seqgradramp.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADRAMP_H #define SEQGRADRAMP_H #include /** * @addtogroup odinseq * @{ */ /** * This enum is used to specify the shape of gradient ramp: * - linear: A ramp that linearly increases/decreases the gradient field. * The first ramp point has the initial gradient strength, the last point * the final gradient strength. With this selection, the integral over the * ramp is the same as that over a continuous triangular function, i.e * Integral = 1/2 * strength_difference * duration. * - sinusoidal: The sinus between -pi/2 and pi/2 is used for the gradient shape * - half_sinusoidal: The sinus between 0 and pi/2 is used for the gradient shape */ enum rampType {linear, sinusoidal, half_sinusoidal}; /////////////////////////////////////////////////////////// /** * \brief Gradient Ramp * * This class represents a digitized gradient ramp. */ class SeqGradRamp : public SeqGradWave { public: /** * Constructs a gradient ramp labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - initgradstrength: The initial gradient strength, i.e. the strength at the beginning of the ramp * - finalgradstrength: The final gradient strength, i.e. the strength at the end of the ramp * - timestep: The time between adjecent points of the ramp * - type: The shape for the ramp * - steepnessfactor: This parameter in the range of ]0,1] determines the relative rising * speed of the gradient strength, i.e. with 1 the gradients are switched * as fast as possible * - reverse: Reverse ramp calculation (only relevant for asymmetric ramps) */ SeqGradRamp(const STD_string& object_label,direction gradchannel, float initgradstrength, float finalgradstrength, double timestep,rampType type = linear, float steepnessfactor=1.0, bool reverse = false); /** * Constructs a gradient ramp labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - gradduration: The duration of this gradient object * - initgradstrength: The initial gradient strength, i.e. the strength at the beginning of the ramp * - finalgradstrength: The final gradient strength, i.e. the strength at the end of the ramp * - timestep: The time between adjecent points of the ramp * - type: The shape for the ramp * - reverse: Reverse ramp calculation (only relevant for asymmetric ramps) */ SeqGradRamp(const STD_string& object_label,direction gradchannel,double gradduration, float initgradstrength, float finalgradstrength, double timestep, rampType type = linear, bool reverse = false); /** * Constructs a copy of 'sgr' */ SeqGradRamp(const SeqGradRamp& sgr); /** * Construct an empty gradient object with the given label */ SeqGradRamp(const STD_string& object_label = "unnamedSeqGradRamp"); /** * Sets the ramp according to the following parameters: * - initgradstrength: The initial gradient strength, i.e. the strength at the beginning of the ramp * - finalgradstrength: The final gradient strength, i.e. the strength at the end of the ramp * - timestep: The time between adjecent points of the ramp * - type: The shape for the ramp * - steepnessfactor: This parameter in the range of ]0,1] determines the relative rising * speed of the gradient strength, i.e. with 1 the gradients are switched * as fast as possible * - reverse: Reverse ramp calculation (only relevant for asymmetric ramps) */ SeqGradRamp& set_ramp(float initgradstrength, float finalgradstrength, double timestep,rampType type = linear,float steepnessfactor=1.0, bool reverse = false); /** * Sets the ramp according to the following parameters: * - gradduration: The duration of this gradient object * - initgradstrength: The initial gradient strength, i.e. the strength at the beginning of the ramp * - finalgradstrength: The final gradient strength, i.e. the strength at the end of the ramp * - timestep: The time between adjecent points of the ramp * - type: The shape for the ramp * - reverse: Reverse ramp calculation (only relevant for asymmetric ramps) */ SeqGradRamp& set_ramp(double gradduration,float initgradstrength, float finalgradstrength, double timestep,rampType type = linear, bool reverse = false); /** * Returns the shape for the ramp */ rampType get_ramptype() const {return ramptype;} /** * Assignment operator that makes this gradient channel object become a copy of 'sgr' */ SeqGradRamp& operator = (const SeqGradRamp& sgr); // helper functions static fvector makeGradRamp(rampType type, float beginVal, float endVal, unsigned int n_vals, bool reverseramp); static unsigned int npts4ramp(rampType type, float beginVal, float endVal, float maxIncrement); static unsigned int npts4ramp(double totaldur, double timestep); // overloading functions from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); private: void generate_ramp(); float initstrength; float finalstrength; double dt; float steepness; bool steepcontrol; rampType ramptype; bool reverseramp; }; /** @} */ #endif odin-1.8.5/odinseq/seqplatform.h0000644000175000017500000001725211625224370013560 00000000000000/*************************************************************************** seqplatform.h - description ------------------- begin : Sat Apr 3 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPLATFORM_H #define SEQPLATFORM_H #include #include #include #include // Global Bruker stuff #define REFGAIN_FILE "odin_refgain" #define MAINNUC_FILE "odin_mainnuc" // forward declarations for hardware drivers class SeqAcqDriver; class SeqEpiDriver; class SeqDecouplingDriver; class SeqDelayDriver; class SeqDelayVecDriver; class SeqFreqChanDriver; class SeqGradChanDriver; class SeqGradChanParallelDriver; class SeqGradTrapezDriver; class SeqListDriver; class SeqCounterDriver; class SeqParallelDriver; class SeqPhaseDriver; class SeqPulsDriver; class SeqTriggerDriver; class eventContext; // forward declaration class ProgressMeter; // forward declaration ///////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Enum to specify data processing on the platform: * - odinReco: Store raw data on disk and call odinreco * - rawData: Store raw data on disk * - recoInfoOnly: Story only recoInfo file. Raw data has to be copied manually using Twix */ enum recoMode {odinReco=0, rawData, recoInfoOnly}; ///////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * This class is used only for resolving ambiguities in constructors * of other classes during platform registration */ class PlatformRegistration {}; ///////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Virtual base class for all classes that represent an ODIN platform, * i.e. that deal with platform specific peculiarities */ class SeqPlatform : public virtual SeqClass { public: enum eventLogging {noLogging=0,loggEvent}; /** * Initialize platform, is called whenever a method is initialized. */ virtual void init() = 0; /** * This function is overloaded to clean up the platform interface before a new sequence is prepared. */ virtual void reset_before_prep() = 0; /** * This function is overloaded to prepare all the global stuff which is needed to start an experiment. * 'nacqs_total' must contain the total number of acqusition events in the the sequence. */ virtual void prepare_measurement(unsigned int nacqs_total) = 0; // functions for driver factory virtual SeqAcqDriver* create_driver(SeqAcqDriver*) const = 0; virtual SeqEpiDriver* create_driver(SeqEpiDriver*) const = 0; virtual SeqDecouplingDriver* create_driver(SeqDecouplingDriver*) const = 0; virtual SeqDelayDriver* create_driver(SeqDelayDriver*) const = 0; virtual SeqDelayVecDriver* create_driver(SeqDelayVecDriver*) const = 0; virtual SeqFreqChanDriver* create_driver(SeqFreqChanDriver*) const = 0; virtual SeqGradChanDriver* create_driver(SeqGradChanDriver*) const = 0; virtual SeqGradChanParallelDriver* create_driver(SeqGradChanParallelDriver*) const = 0; virtual SeqGradTrapezDriver* create_driver(SeqGradTrapezDriver*) const = 0; virtual SeqListDriver* create_driver(SeqListDriver*) const = 0; virtual SeqCounterDriver* create_driver(SeqCounterDriver*) const = 0; virtual SeqParallelDriver* create_driver(SeqParallelDriver*) const = 0; virtual SeqPhaseDriver* create_driver(SeqPhaseDriver*) const = 0; virtual SeqPulsDriver* create_driver(SeqPulsDriver*) const = 0; virtual SeqTriggerDriver* create_driver(SeqTriggerDriver*) const = 0; virtual int process(int argc, char *argv[]) = 0; virtual SeqCmdlineActionList get_actions_usage() const = 0; virtual void pre_event (eventContext& context) const = 0; virtual void post_event(eventContext& context) const = 0; virtual fvector get_acq_channel_scale_factors() const = 0; virtual STD_string get_program(programContext& context) const = 0; virtual STD_string get_rawfile() const = 0; virtual STD_string get_rawdatatype() const = 0; virtual unsigned int get_rawheader_size() const = 0; virtual STD_string get_image_proc() const = 0; virtual bool create_recoInfo() const = 0; virtual int write_rf_waveform (const STD_string& filename, const cvector& waveform) const = 0; virtual int load_rf_waveform (const STD_string& filename, cvector& result) const = 0; virtual int get_max_methodname_length() const = 0; virtual void set_eventlogging(eventLogging loggflag) = 0; // Paravision specific virtual bool pv_pilot(ProgressMeter* progmeter) {return true;} virtual STD_string pv_pilot_scan() const {return "";} virtual bool pv_gop(bool autorg, ProgressMeter* progmeter) {return true;} virtual bool pv_stop() {return true;} // IDEA specific virtual void set_idea_pars(void* pMrProt,void* pSeqLim,void* pSeqExpo, recoMode reco_mode) {} // StandAlone specific virtual SeqPlotDataAbstract* get_plot_data() {return 0;} virtual bool create_plot_events(ProgressMeter* progmeter) {return true;} virtual ~SeqPlatform() {} protected: SeqPlatform() {} }; ///////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Singleton to hold platform instances (driver factories) */ class SeqPlatformInstances : public SeqClass { public: SeqPlatformInstances(); ~SeqPlatformInstances(); bool set_current(odinPlatform pf); SeqPlatform* get_current() {return instance[get_current_platform_id()];} odinPlatform get_current_platform_id() {return SystemInterface::get_current_pf();} private: friend class SeqPlatformProxy; SeqPlatform* instance[numof_platforms]; static odinPlatform pf_during_platform_construction; }; //////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The proxy class for platform specific classes */ class SeqPlatformProxy : public virtual SeqClass, public StaticHandler { public: SeqPlatformProxy() {set_label("SeqPlatformProxy");} static void set_current_platform(odinPlatform pF); static odinPlatform get_current_platform(); static int load_systemInfo(const STD_string& filename); static STD_string get_platform_str(odinPlatform pF); static svector get_possible_platforms(); static STD_string get_platforms_usage(); static int get_platform_for_action(const STD_string& action); SeqPlatform& operator * () {return *get_platform_ptr();} SeqPlatform* operator -> () {return get_platform_ptr();} // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); private: friend class SeqPlatform; // manually allocate of platform instances static void create_platform_instances(); static SeqPlatform* get_platform_ptr(); // manage platform instances (driver factories) static SingletonHandler platforms; }; #endif odin-1.8.5/odinseq/seqgradchanparallel.cpp0000644000175000017500000002263311322062345015546 00000000000000#include "seqgradchanparallel.h" #include "seqgradconst.h" SeqGradChanParallel::SeqGradChanParallel(const STD_string& object_label) : SeqGradObjInterface(object_label), paralleldriver(object_label) { } SeqGradChanParallel::SeqGradChanParallel(const SeqGradChanParallel& sgcp) : paralleldriver(sgcp.get_label()) { Log odinlog(this,"SeqGradChanParallel"); SeqGradChanParallel::operator = (sgcp); } SeqGradChanParallel::~SeqGradChanParallel() { Log odinlog(this,"~SeqGradChanParallel"); for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(get_gradchan(chanNo)) get_gradchan(chanNo)->clear(); } } SeqGradChanParallel& SeqGradChanParallel::operator = (const SeqGradChanParallel& sgcp) { Log odinlog(this,"operator = (...)"); SeqGradObjInterface::operator = (sgcp); paralleldriver=sgcp.paralleldriver; clear(); // create deep copy for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); SeqGradChanList* sgcl=sgcp.get_gradchan(chanNo); if(sgcl) { SeqGradChanList* my_sgcl=get_gradchan(chanNo); if(my_sgcl) (*my_sgcl)=(*sgcl); else { ODINLOG(odinlog,normalDebug) << "creating copy of " << sgcl->get_label() << STD_endl; SeqGradChanList* sgcl_copy=new SeqGradChanList(*sgcl); sgcl_copy->set_temporary(); set_gradchan(chanNo,sgcl_copy); } } } return *this; } SeqGradChanParallel& SeqGradChanParallel::operator /= (SeqGradChan& sgc) { Log odinlog(this,"operator /= (SeqGradChan&)"); direction chanNo=sgc.get_channel(); SeqGradChanList* sgcl=get_gradchan(chanNo); if(sgcl) { sgcl->clear(); } else { sgcl=new SeqGradChanList("("+sgc.get_label()+")"); sgcl->set_temporary(); set_gradchan(chanNo,sgcl); } (*sgcl)+=sgc; return *this; } SeqGradChanParallel& SeqGradChanParallel::operator /= (SeqGradChanList& sgcl) { Log odinlog(this,"operator /= (SeqGradChanList&)"); set_gradchan(sgcl.get_channel(),&sgcl); return *this; } STD_string SeqGradChanParallel::get_program(programContext& context) const { return paralleldriver->get_program(context); } bool SeqGradChanParallel::prep() { Log odinlog(this,"prep"); if(!SeqGradObjInterface::prep()) return false; SeqGradChanList* chanlists[3]; for(unsigned int i=0; i<3; i++) chanlists[i]=get_gradchan(direction(i)); return paralleldriver->prep_driver(chanlists); } SeqGradInterface& SeqGradChanParallel::set_strength(float gradstrength) { Log odinlog(this,"set_strength"); for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(get_gradchan(chanNo)) get_gradchan(chanNo)->set_strength(gradstrength); } return *this; } SeqGradInterface& SeqGradChanParallel::invert_strength() { Log odinlog(this,"invert_strength"); for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(get_gradchan(chanNo)) get_gradchan(chanNo)->invert_strength(); } return *this; } float SeqGradChanParallel::get_strength() const { Log odinlog(this,"get_strength"); float result=0.0; for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); float tmp=0.0; if(get_gradchan(chanNo)) tmp=get_gradchan(chanNo)->get_strength(); if(fabs(tmp)>fabs(result)) result=tmp; } return result; } double SeqGradChanParallel::get_gradduration() const { Log odinlog(this,"get_gradduration"); double result=0.0; for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); double chandur=0.0; if(get_gradchan(chanNo)) chandur=fabs(get_gradchan(chanNo)->get_gradduration()); if( chandur > result) result=chandur; } return result; } SeqGradInterface& SeqGradChanParallel::set_gradrotmatrix(const RotMatrix& matrix) { Log odinlog(this,"set_gradrotmatrix"); for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(get_gradchan(chanNo)) get_gradchan(chanNo)->set_gradrotmatrix(matrix); } return *this; } fvector SeqGradChanParallel::get_gradintegral() const { Log odinlog(this,"get_gradintegral"); fvector result(3); result=0.0; for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(get_gradchan(chanNo)) result=result+(get_gradchan(chanNo)->get_gradintegral()); } ODINLOG(odinlog,normalDebug) << "result=" << result.printbody() << STD_endl; return result; } SeqGradChanParallel& SeqGradChanParallel::operator += (SeqGradChan& sgc) { Log odinlog(this,"SeqGradChanParallel::operator += (SeqGradChan)"); ODINLOG(odinlog,normalDebug) << "appending " << sgc.get_label() << STD_endl; direction chanNo=sgc.get_channel(); padd_channel_with_delay(chanNo, get_gradduration()); if(get_gradchan(chanNo)) { (*get_gradchan(chanNo))+=sgc; } else { SeqGradChanList* sgcl=new SeqGradChanList(STD_string("(")+get_label()+")"); sgcl->set_temporary(); (*sgcl)+=sgc; set_gradchan(chanNo,sgcl); } return *this; } SeqGradChanParallel& SeqGradChanParallel::operator += (SeqGradChanList& sgcl) { Log odinlog(this,"SeqGradChanParallel::operator += (SeqGradChanList)"); direction chanNo=sgcl.get_channel(); padd_channel_with_delay(chanNo, get_gradduration()); if(get_gradchan(chanNo)) { ODINLOG(odinlog,normalDebug) << "appending " << sgcl.get_label() << STD_endl; (*get_gradchan(chanNo))+=sgcl; } else { ODINLOG(odinlog,normalDebug) << "creating copy of " << sgcl.get_label() << STD_endl; SeqGradChanList* sgcl_copy=new SeqGradChanList(sgcl); sgcl_copy->set_temporary(); set_gradchan(chanNo,sgcl_copy); } return *this; } SeqGradChanParallel& SeqGradChanParallel::operator += (SeqGradChanParallel& sgcp) { Log odinlog(this,"operator += (SeqGradChanParallel)"); ODINLOG(odinlog,normalDebug) << "appending " << sgcp.get_label() << STD_endl; double maxdur=get_gradduration(); for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(sgcp.get_gradchan(chanNo)) { padd_channel_with_delay(chanNo,maxdur); if(get_gradchan(chanNo)) (*get_gradchan(chanNo))+=(*sgcp.get_gradchan(chanNo)); else { ODINLOG(odinlog,normalDebug) << "creating copy of " << sgcp.get_label() << STD_endl; SeqGradChanList* sgcl_copy=new SeqGradChanList(*(sgcp.get_gradchan(chanNo))); sgcl_copy->set_temporary(); set_gradchan(chanNo,sgcl_copy); } } } return *this; } void SeqGradChanParallel::clear() { Log odinlog(this,"clear"); for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { gradchan[cn].clear_handledobj(); } } unsigned int SeqGradChanParallel::event(eventContext& context) const { unsigned int result=0; double startelapsed=context.elapsed; double maxelapsed=context.elapsed; for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { context.elapsed=startelapsed; direction chanNo=direction(cn); if(get_gradchan(chanNo)) { result+=get_gradchan(chanNo)->event(context); if(context.elapsed>maxelapsed) maxelapsed=context.elapsed; } } context.elapsed=maxelapsed; return result; } void SeqGradChanParallel::clear_container() {clear();} void SeqGradChanParallel::query(queryContext& context) const { SeqTreeObj::query(context); // defaults if(context.action==count_acqs) return; // nothing to do context.treelevel++; for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { context.parentnode=this; // reset to this because it might changed by last query SeqGradChanList* sgcl=get_gradchan(direction(cn)); if(sgcl) sgcl->query(context); } context.treelevel--; } STD_string SeqGradChanParallel::get_properties() const { STD_string result="ChanListSize="; for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(get_gradchan(chanNo)) result+=itos(get_gradchan(chanNo)->size()); else result+="-"; if(cn!=sliceDirection) result+="/"; } return result; } void SeqGradChanParallel::padd_channel_with_delay(direction chanNo, double maxdur) { Log odinlog(this,"padd_channel_with_delay"); ODINLOG(odinlog,normalDebug) << "maxdur=" << maxdur << STD_endl; if(!maxdur) return; double chandur=0.0; if(get_gradchan(chanNo)) chandur=fabs(get_gradchan(chanNo)->get_gradduration()); if( chandur < maxdur) { ODINLOG(odinlog,normalDebug) << "chandur[" << chanNo << "]=" << chandur << STD_endl; SeqGradDelay* graddelay=new SeqGradDelay(STD_string(get_label())+"_paddelay",chanNo,maxdur-chandur); graddelay->set_temporary(); if(get_gradchan(chanNo)) { ODINLOG(odinlog,normalDebug) << "appending to existing SeqGradChanList" << STD_endl; (*get_gradchan(chanNo))+=(*graddelay); } else { ODINLOG(odinlog,normalDebug) << "creating new SeqGradChanList" << STD_endl; SeqGradChanList* sgcl=new SeqGradChanList(STD_string("(")+graddelay->get_label()+")"); sgcl->set_temporary(); (*sgcl)+=(*graddelay); set_gradchan(chanNo,sgcl); } } } SeqGradChanList* SeqGradChanParallel::get_gradchan(direction channel) const { return (gradchan[channel]).get_handled(); } SeqGradChanParallel& SeqGradChanParallel::set_gradchan(direction channel, SeqGradChanList* sgcl) { if(sgcl) (gradchan[channel]).set_handled(sgcl); return *this; } odin-1.8.5/odinseq/seqdelayvec.h0000644000175000017500000000662511322062345013526 00000000000000/*************************************************************************** seqdelayvec.h - description ------------------- begin : Mon Oct 7 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDELAYVEC_H #define SEQDELAYVEC_H #include #include #include /** * @ingroup odinseq_internals * The base class for platform specific drivers of delay vectors */ class SeqDelayVecDriver : public SeqDriverBase { public: SeqDelayVecDriver() {} virtual ~SeqDelayVecDriver() {} virtual bool prep_driver() = 0; virtual STD_string get_program(programContext& context, double duration) const = 0; virtual bool unroll_program() const = 0; virtual SeqDelayVecDriver* clone_driver() const = 0; }; /////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * \brief Vector of variable timing delays * * This class represents a vector of delay (delay list) that can be attached to a loop. */ class SeqDelayVector : public SeqObjBase, public SeqVector { public: /** * Constructs a delay vector labeled 'object_label' with the following properties: * - delaylist: The list of delays that will be played out subsequently when looping * over this object */ SeqDelayVector(const STD_string& object_label,const dvector& delaylist); /** * Constructs an empty delay vector labeled 'object_label' */ SeqDelayVector(const STD_string& object_label = "unnamedSeqDelayVector"); /** * Constructs a delay which is a copy of 'sdv' */ SeqDelayVector(const SeqDelayVector& sdv); /** * This assignment operator will make this object become an exact copy of 'sdv'. */ SeqDelayVector& operator = (const SeqDelayVector& sdv); /** * Specifies the list of delays that will be played out subsequently when looping * over this object */ SeqDelayVector& set_delayvector(const dvector& delaylist); /** * Returns the list of delays that will be played out subsequently when looping * over this object */ dvector get_delayvector() const; // overloading virtual function from SeqTreeObj double get_duration() const; STD_string get_program(programContext& context) const; SeqValList get_delayvallist() const; private: // overwriting virtual functions from SeqClass bool prep(); // overloading virtual function from SeqVector unsigned int get_vectorsize() const; bool needs_unrolling_check() const {return delayvecdriver->unroll_program();} mutable SeqDriverInterface delayvecdriver; dvector delayvec; }; /** @} */ #endif odin-1.8.5/odinseq/seqacq.h0000644000175000017500000002707511455553540012511 00000000000000/*************************************************************************** seqacq.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQACQ_H #define SEQACQ_H #include #include #include #include #include class SeqGradChanParallel; // forward declaration //////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * This is the abstract base class for all objects that have the * property of acquiring a signal */ class SeqAcqInterface : public virtual SeqFreqChanInterface { public: /** * Returns the duration of the acquisition window without padding delays. */ virtual double get_acquisition_duration() const {if(marshall) return marshall->get_acquisition_duration(); else marshall_error(); return 0.0;} /** * Returns the the duration from the the beginnig of the acquisition * object to the middle of the acquisition window. */ virtual double get_acquisition_center() const {if(marshall) return marshall->get_acquisition_center(); else marshall_error(); return 0.0;} /** * Returns the the duration from the the beginnig of the acquisition * object to the beginnig of the acquisition window (the point * of time where data starts to be acquired). */ virtual double get_acquisition_start() const {if(marshall) return marshall->get_acquisition_start(); else marshall_error(); return 0.0;} /** * Returns the total number of sampling points, without oversampling */ virtual unsigned int get_npts() const {if(marshall) return marshall->get_npts(); else marshall_error(); return 0;} /** * Sets the sweepwidth 'sw' without oversampling and oversampling factor 'os_factor' for this acquisition object, os_factor=1 means no oversampling. */ virtual SeqAcqInterface& set_sweepwidth(double sw, float os_factor) {if(marshall) marshall->set_sweepwidth(sw,os_factor); else marshall_error(); return *this;} /** * Returns the sweepwidth factor */ virtual double get_sweepwidth() const {if(marshall) return marshall->get_sweepwidth(); else marshall_error(); return 0.0;} /** * Returns the oversampling factor */ virtual float get_oversampling() const {if(marshall) return marshall->get_oversampling(); else marshall_error(); return 0.0;} /** * Specifies a regridding matrix for this ADC (for automatic reconstruction) */ virtual SeqAcqInterface& set_readout_shape(const fvector& shape, unsigned int dstsize) {if(marshall) marshall->set_readout_shape(shape, dstsize); else marshall_error(); return *this;} /** * Specifies a vector 'vec' which indexes the data dimension 'dim'. * The current index for each acquisition is retrieved from the vector. * This is relevant for automatic reconstruction. * An additional vector 'valvec' of double values can be given, * which is attached to this dimension, e.g. different TEs in the echo * dimension. */ virtual SeqAcqInterface& set_reco_vector(recoDim dim, const SeqVector& vec, const dvector& valvec=dvector()) {if(marshall) marshall->set_reco_vector(dim, vec, valvec); else marshall_error(); return *this;} /** * Sets the default value 'index' for the reco index in dimension 'dim'. * This is relevant for automatic reconstruction. */ virtual SeqAcqInterface& set_default_reco_index(recoDim dim, unsigned int index) {if(marshall) marshall->set_default_reco_index(dim, index); else marshall_error(); return *this;} /** * Sets the template mode of this acquisition object. * This is also relevant for automatic reconstruction. */ virtual SeqAcqInterface& set_template_type(templateType type) {if(marshall) marshall->set_template_type(type); return set_default_reco_index(templtype,type);} /** * Specifies whether the data points should be reversed, only relevant * for automatic reconstruction */ virtual SeqAcqInterface& set_reflect_flag(bool flag) {if(marshall) marshall->set_reflect_flag(flag); else marshall_error(); return *this;} protected: SeqAcqInterface() : marshall(0) {} virtual ~SeqAcqInterface() {} void set_marshall(SeqAcqInterface* mymarshall) {marshall=mymarshall;} // to be used in constructor code private: friend class SeqAcqDeph; // to be used by SeqAcqDeph to retrieve pre-dephasing gradients from acquisition object. // Overload this function if your acq needs pre-dephasers, return them by appending them to 'dephobj'. // Returns any possible vector object as the return value. virtual const SeqVector* get_dephgrad(SeqGradChanParallel& dephobj, bool rephase) const {if(marshall) return marshall->get_dephgrad(dephobj,rephase); return 0;} SeqAcqInterface* marshall; // for marshalling member functions to a sub-object }; ///////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The base class for platform specific drivers of acquisition windows */ class SeqAcqDriver : public SeqDriverBase { public: SeqAcqDriver() {} virtual ~SeqAcqDriver() {} /** * Returns possible sweepwidth closest to 'desired_sweep_widht' */ virtual double adjust_sweepwidth(double desired_sweep_widht) const = 0; /** * Prepare driver, let driver adjust reco coordinate 'recoindex' */ virtual bool prep_driver(kSpaceCoord& recoindex, double sweepwidth, unsigned int nAcqPoints, double acqcenter, int freqchannel) = 0; /** * Delay prior to actual acquisition */ virtual double get_predelay() const = 0; /** * Delay following actual acquisition depending on 'sweepwidth' */ virtual double get_postdelay(double sweepwidth) const = 0; virtual void event(eventContext& context, double start) const = 0; virtual STD_string get_program(programContext& context, unsigned int phaselistindex) const = 0; virtual STD_string get_instr_label() const = 0; virtual unsigned int get_numof_channels() const = 0; virtual SeqAcqDriver* clone_driver() const = 0; }; ///////////////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * \brief Acquisition * * This class represents an acquisition window */ class SeqAcq : public virtual SeqAcqInterface, public SeqObjBase, public SeqFreqChan { public: /** * Constructs an acquisition window labeled 'object_label' with the following properties: * - nAcqPoints: The number of sampling points that will be acquired during the acquisition * - sweepwidth: The sampling frequency without oversampling * - os_factor: The oversampling factor, os_factor=1 means no oversampling * - nucleus: The nucleus for which the acquisition should be performed. The default * is to acquire on the protons resonance freuency. * - phaselist: This is an array of phases at which the acquired signal will be * demodulated. The actual phase for each acquisition is determined * by cycling through this array of phases which are represented * in degree. * - freqlist: This is an array of frequency offsets at which the acquired signal * will be demodulated. */ SeqAcq(const STD_string& object_label, unsigned int nAcqPoints, double sweepwidth, float os_factor=1.0, const STD_string& nucleus="", const dvector& phaselist=0,const dvector& freqlist=0); /** * Constructs an acquisition window which is a copy of 'sa' */ SeqAcq(const SeqAcq& sa); /** * Constructs an empty acquisition window with the given label. */ SeqAcq(const STD_string& object_label="unnamedSeqAcq"); /** * Destructor */ ~SeqAcq(); /** * Sets the number of sampling points that will be acquired during the acquisition */ SeqAcq& set_npts(unsigned int nAcqPoints); /** * Returns the sweep width */ double get_sweep_width() const {return sweep_width;} /** * This assignment operator will make this object become an exact copy of 'sa'. */ SeqAcq& operator = (const SeqAcq& sa); /** * Specifies a an explicit k-space Trajectory for this ADC (for automatic reconstruction) */ void set_kspace_traj(const farray& kspaceTraj); /** * Specifies a complex vector which is is used to weight each point in this ADC (for automatic reconstruction) */ void set_weight_vec(const cvector& weightVec); /** * Sets the relative point in time (between 0 and 1) when k-space center is passed, the default is 0.5. * Will be used in get_acquisition_center(). */ SeqAcq& set_rel_center(double relative_kspace_center) {rel_center=relative_kspace_center; return *this;} /** * Returns the k-space index of this ADCs */ const kSpaceCoord& get_kcoord() const; // overwriting virtual functions of SeqAcqInterface double get_acquisition_duration() const {return secureDivision(npts,sweep_width);} double get_acquisition_center() const; double get_acquisition_start() const {return acqdriver->get_predelay();} unsigned int get_npts() const {return npts;} SeqAcqInterface& set_sweepwidth(double sw, float os_factor); double get_sweepwidth() const {return sweep_width;} float get_oversampling() const {return oversampl;} SeqAcqInterface& set_readout_shape(const fvector& shape, unsigned int dstsize); SeqAcqInterface& set_reco_vector(recoDim dim, const SeqVector& vec, const dvector& valvec=dvector()); SeqAcqInterface& set_default_reco_index(recoDim dim, unsigned int index); SeqAcqInterface& set_reflect_flag(bool flag) {reflect_flag=flag; return *this;} // overwriting virtual functions of SeqTreeObj STD_string get_program(programContext& context) const; double get_duration() const; SeqValList get_freqvallist(freqlistAction action) const; void query(queryContext& context) const {SeqTreeObj::query(context); context.numof_acqs=1;} RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const; unsigned int event(eventContext& context) const; STD_string get_properties() const; private: friend class SeqMethod; friend class SeqEpiDriverParavision; friend class SeqEpiDriverEpic; void common_init(); // overwriting virtual functions of SeqFreqChan double get_freqchan_duration() const {return get_acquisition_duration();} STD_string get_driver_instr_label() const {return acqdriver->get_instr_label();} // overwriting virtual functions of SeqClass bool prep(); mutable kSpaceCoord kcoord; mutable SeqDriverInterface acqdriver; double sweep_width; unsigned int npts; float oversampl; double rel_center; bool reflect_flag; int readoutIndex; int trajIndex; int weightIndex; // safe pointers to vectors to create indices for the ADC // pointer to pointer is used here to avoid delete[] bug in GCC2.9 Handler** dimvec; int default_recoindex[n_recoIndexDims]; }; /** @} */ #endif odin-1.8.5/odinseq/seqall.h0000644000175000017500000000211411625224370012473 00000000000000#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include odin-1.8.5/odinseq/seqdec.h0000644000175000017500000001220111322062345012450 00000000000000/*************************************************************************** seqdec.h - description ------------------- begin : Fri Sep 7 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDEC_H #define SEQDEC_H #include #include #include #include #include /** * @ingroup odinseq_internals * The base class for platform specific drivers of decoupling periods */ class SeqDecouplingDriver : public SeqDriverBase { public: SeqDecouplingDriver() {} virtual ~SeqDecouplingDriver() {} virtual bool prep_driver(double decdur, int channel, float decpower, const STD_string& program, double pulsedur) = 0; virtual void event(eventContext& context, double start) const = 0; virtual double get_preduration() const = 0; virtual double get_postduration() const = 0; virtual STD_string get_preprogram(programContext& context, const STD_string& iteratorcommand) const = 0; virtual STD_string get_postprogram(programContext& context) const = 0; virtual SeqDecouplingDriver* clone_driver() const = 0; }; //////////////////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * \brief Decoupling period * * This class represents a decoupling container which can hold a part * of the sequence where decoupling is switched on. */ class SeqDecoupling : public SeqObjList, public Embed, public SeqFreqChan { public: /** * Constructs a container for a sequence part at which decoupling will be switched on * with the following properties: * - nucleus: The nucleus for which the decoupling should be performed. * - decpower: The maximum power for the decoupling program. * - freqlist: Frequency list for the decoupler. * - decprog: The file name of the decoupling program which will be used. If none * is specified, continuous wave decouling will be used. * - decpulsduration: If a decoupling program is given, this parameter determines * the pulse duration of each single pulse in a composite pulse * decoupling scheme. */ SeqDecoupling(const STD_string& object_label,const STD_string& nucleus,float decpower,const dvector& freqlist=0, const STD_string decprog="",float decpulsduration=0.0); /** * Constructs a decoupling container which is a copy of 'sd' */ SeqDecoupling(const SeqDecoupling& sd); /** * Constructs an empty decoupling container with the given label. */ SeqDecoupling(const STD_string& object_label="unnamedSeqDecoupling"); /** * This function specifies that during the sequence part 'so' decoupling * will be switched on. */ SeqDecoupling& operator () (const SeqObjBase& so); /** * Returns the decoupling power */ float get_decpower() const {return power;} /** * Sets the decoupling power */ void set_decpower(float p) {power=p;} /** * Returns the decoupling program */ STD_string get_program() const; /** * Sets the decoupling program */ void set_program(const STD_string& p); /** * Returns the decoupling pulse duration for Composite Pulse Decoupling */ double get_pulsduration() const; /** * Sets the decoupling pulse duration for Composite Pulse Decoupling */ void set_pulsduration(float d); /** * This assignment operator will make this object become an exact copy of 'sd'. */ SeqDecoupling& operator = (const SeqDecoupling& sd); // implementing virtual functions of SeqTreeObj double get_duration() const; unsigned int event(eventContext& context) const; // overwriting virtual function from SeqFreqChan STD_string get_program(programContext& context) const; double get_freqchan_duration() const {return get_duration();} unsigned int get_freqlistindex() const {return 2;} const SeqVector& get_freqlist_vector() const; SeqValList get_freqvallist(freqlistAction action) const; void clear_container(); private: friend class Embed; int set_body(const SeqObjBase& so); // overwriting virtual functions from SeqClass bool prep(); float power; STD_string decprogram; double pulsduration; mutable SeqDriverInterface decdriver; SeqSimultanVector instvec; }; /** @} */ #endif odin-1.8.5/odinseq/seqdur.h0000644000175000017500000000432611322062345012520 00000000000000/*************************************************************************** seqdur.h - description ------------------- begin : Wed Aug 14 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDUR_H #define SEQDUR_H #include /** * @addtogroup odinseq_internals * @{ */ /** * This is the base class for all objects which have a certain * duration. This is one of the base classes for all 'sequence atoms' * i.e. those classes which cannot be devided further (e.g. SeqPuls, SeqAcq, SeqDelay, ...). * In contrast, the duration of composite objects (e.g. SeqObjList) * is calculated from their elements. */ class SeqDur : public virtual SeqTreeObj { public: /** * Construct a duration object with the given 'object_label' and the specified 'duration' */ SeqDur(const STD_string& object_label, float duration); /** * Construct an empty duration object with the given label */ SeqDur(const STD_string& object_label="unnamedSeqDur"); /** * Construct a duration object which is a copy of 'sd' */ SeqDur(const SeqDur& sd); /** * Sets the duration */ SeqDur& set_duration(float duration); // implementing virtual functions of SeqTreeObj double get_duration() const; /** * Assignment operator that makes this duration object become a copy of 'sd' */ SeqDur& operator = (const SeqDur& sd); private: double dur; }; /** @} */ #endif odin-1.8.5/odinseq/seqgradramp.cpp0000644000175000017500000001727711322062345014067 00000000000000#include "seqgradramp.h" fvector SeqGradRamp::makeGradRamp(rampType type, float beginVal, float endVal, unsigned int n_vals, bool reverseramp) { unsigned int i; fvector result(n_vals); if(n_vals==1) { result[0]=0.5*(beginVal+endVal); return result; } if(type==linear) result.fill_linear(beginVal,endVal); if(type==sinusoidal) { for(i=0; i odinlog(this,"SeqGradRamp(1...)"); initstrength=initgradstrength; finalstrength=finalgradstrength; dt=timestep; steepness=steepnessfactor; steepcontrol=true; ramptype=type; reverseramp=reverse; generate_ramp(); } SeqGradRamp::SeqGradRamp(const STD_string& object_label,direction gradchannel,double gradduration, float initgradstrength, float finalgradstrength, double timestep, rampType type, bool reverse) : SeqGradWave(object_label,gradchannel,gradduration,0.0,JDXfloatArr()) { Log odinlog(this,"SeqGradRamp(2...)"); initstrength=initgradstrength; finalstrength=finalgradstrength; dt=timestep; steepness=secureDivision(fabs(finalgradstrength-initgradstrength), gradduration*systemInfo->get_max_slew_rate()); ODINLOG(odinlog,normalDebug) << "steepness=" << steepness << STD_endl; steepcontrol=false; ramptype=type; reverseramp=reverse; generate_ramp(); } SeqGradRamp::SeqGradRamp(const SeqGradRamp& sgr) { SeqGradRamp::operator = (sgr); } SeqGradRamp::SeqGradRamp(const STD_string& object_label) : SeqGradWave(object_label) { Log odinlog(this,"SeqGradRamp(const STD_string&)"); initstrength=0.0; finalstrength=0.0; dt=0.0; steepness=1.0; steepcontrol=false; ramptype=linear; reverseramp=false; } SeqGradRamp& SeqGradRamp::set_ramp(float initgradstrength, float finalgradstrength, double timestep,rampType type,float steepnessfactor, bool reverse) { initstrength=initgradstrength; finalstrength=finalgradstrength; dt=timestep; steepness=steepnessfactor; if(steepness==0.0) steepcontrol=false; else steepcontrol=true; ramptype=type; reverseramp=reverse; generate_ramp(); return *this; } SeqGradRamp& SeqGradRamp::set_ramp(double gradduration,float initgradstrength, float finalgradstrength, double timestep,rampType type, bool reverse) { Log odinlog(this,"set_ramp"); set_duration(gradduration); initstrength=initgradstrength; finalstrength=finalgradstrength; dt=timestep; steepness=secureDivision(fabs(finalgradstrength-initgradstrength), gradduration*systemInfo->get_max_slew_rate()); ODINLOG(odinlog,normalDebug) << "steepness=" << steepness << STD_endl; steepcontrol=false; ramptype=type; reverseramp=reverse; generate_ramp(); return *this; } SeqGradRamp& SeqGradRamp::operator = (const SeqGradRamp& sgr) { SeqGradWave::operator = (sgr); initstrength=sgr.initstrength; finalstrength=sgr.finalstrength; dt=sgr.dt; steepness=sgr.steepness; steepcontrol=sgr.steepcontrol; ramptype=sgr.ramptype; reverseramp=sgr.reverseramp; return *this; } SeqGradInterface& SeqGradRamp::set_strength(float gradstrength) { Log odinlog(this,"set_strength"); float oldstrength=SeqGradWave::get_strength(); float maxstrength=secureDivision(fabs(oldstrength), steepness); float val=gradstrength; ODINLOG(odinlog,normalDebug) << "old/max/val/steepness=" << oldstrength << "/" << maxstrength << "/" << val << "/" << steepness << STD_endl; float sign=secureDivision(gradstrength, fabs(gradstrength)); if(fabs(gradstrength) > fabs(maxstrength)) { val=sign*maxstrength; ODINLOG(odinlog,warningLog) << "limiting strength to " << val << STD_endl; } SeqGradWave::set_strength(val); return *this; } void SeqGradRamp::generate_ramp() { Log odinlog(this,"generate_ramp"); if(steepness<=0.0) { steepness=1.0; } if(steepness>1.0) { ODINLOG(odinlog,warningLog) << "steepness(" << steepness << ")>1, setting to 1" << STD_endl; steepness=1.0; } float gradstrength=0.0; bool init_is_max=false; if(fabs(initstrength) > fabs(gradstrength)) {init_is_max=true; gradstrength=initstrength;} if(fabs(finalstrength) > fabs(gradstrength)) gradstrength=finalstrength; SeqGradWave::set_strength(gradstrength); ODINLOG(odinlog,normalDebug) << "get_duration()/dt=" << get_duration() << "/" << dt << STD_endl; unsigned int npts; if (steepcontrol) { ODINLOG(odinlog,normalDebug) << "in steepcontrol mode" << STD_endl; double maxIncr=steepness*dt*systemInfo->get_max_slew_rate(); ODINLOG(odinlog,normalDebug) << "maxIncr=" << maxIncr << STD_endl; npts=npts4ramp(ramptype,initstrength,finalstrength,maxIncr); ODINLOG(odinlog,normalDebug) << "npts=" << npts << STD_endl; set_duration(npts*dt); } else { ODINLOG(odinlog,normalDebug) << "NOT in steepcontrol mode" << STD_endl; npts=npts4ramp(get_duration(),dt); double maxIncr=dt*systemInfo->get_max_slew_rate(); unsigned int npts_ramp=npts4ramp(ramptype,initstrength,finalstrength,maxIncr); ODINLOG(odinlog,normalDebug) << "initstrength/finalstrength=" << initstrength << "/" << finalstrength << STD_endl; ODINLOG(odinlog,normalDebug) << "npts/maxIncr/npts_ramp=" << npts << "/" << maxIncr << "/" << npts_ramp << STD_endl; if(npts_ramp>npts) { ODINLOG(odinlog,warningLog) << "ramp too short (" << (npts*dt) << "), setting to " << (npts_ramp*dt) << STD_endl; npts=npts_ramp; set_duration(npts*dt); } } fvector rampwav(npts); float rel_initstrength=secureDivision(initstrength,gradstrength); float rel_finalstrength=secureDivision(finalstrength,gradstrength); if(init_is_max) { if(rel_initstrength<0.0) { rel_initstrength=-rel_initstrength; rel_finalstrength=-rel_finalstrength; } } else { if(rel_finalstrength<0.0) { rel_initstrength=-rel_initstrength; rel_finalstrength=-rel_finalstrength; } } ODINLOG(odinlog,normalDebug) << "rel_initstrength/rel_finalstrength=" << rel_initstrength << "/" << rel_finalstrength << STD_endl; rampwav=makeGradRamp(ramptype,rel_initstrength,rel_finalstrength,npts,reverseramp); ODINLOG(odinlog,normalDebug) << "max/minvalue=" << rampwav.maxvalue() << "/" << rampwav.minvalue() << STD_endl; set_wave(rampwav); } odin-1.8.5/odinseq/seqobj.h0000644000175000017500000000304311322062345012473 00000000000000/*************************************************************************** seqobj.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQOBJ_H #define SEQOBJ_H #include #include #include /** * @addtogroup odinseq_internals * @{ */ /** * Base class for elements in a list of sequence objects. */ class SeqObjBase : public ListItem, public virtual SeqTreeObj, public Handled { protected: SeqObjBase(const STD_string& object_label="unnamedSeqObjBase"); SeqObjBase(const SeqObjBase& soa); SeqObjBase& operator = (const SeqObjBase& soa); }; /** @} */ #endif odin-1.8.5/odinseq/seqdriver_epic.cpp0000644000175000017500000000167111322062345014554 00000000000000#ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif #ifdef EPIC_PLUGIN #include "../platforms/EPIC/odinseq_epic/seqepic.cpp" #include "../platforms/EPIC/odinseq_epic/seqacq_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqacqepi_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqcounter_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqdec_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqdelay_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqfreq_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqgradchan_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqgradtrapez_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqlist_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqparallel_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqphase_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqpuls_epic.cpp" #include "../platforms/EPIC/odinseq_epic/seqtrigg_epic.cpp" #endif odin-1.8.5/odinseq/seqsat.h0000644000175000017500000000776211322062345012524 00000000000000/*************************************************************************** seqsat.h - description ------------------- begin : Tue Oct 19 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQSAT_H #define SEQSAT_H #include #include /** * @addtogroup odinseq * @{ */ /** * * Enum to specifiy saturation component: * - fat: lipid protons will be saturated * - water: water protons will be saturated */ enum satNucleus {fat=0,water}; //////////////////////////////////////////////////////////////////////////// /** * * \brief Saturation pulse * * A 90deg Gaussian shaped saturation pulse * */ class SeqPulsarSat : public SeqPulsar { public: /** * Constructs saturation pulse labeled 'object_label' with the following properties: * - nuc: the nucleus to saturate * - bandwidth: The bandwidth in kHz */ SeqPulsarSat(const STD_string& object_label="unnamedSeqPulsarSat", satNucleus nuc=fat,float bandwidth=0.3); /** * Constructs a saturation pulse labeled 'object_label' with the following properties: * - bandwidth: The bandwidth in kHz * - freqoffset: Frequency offset relative to the base frequency * - flipangle: The flipangle * - rel_filterwidth: Pulse width */ SeqPulsarSat(const STD_string& object_label,float bandwidth, double freqoffset=0.0, float flipangle=90.0, float rel_filterwidth=0.3); /** * Constructs a copy of 'spg' */ SeqPulsarSat(const SeqPulsarSat& spg); /** * Assignment operator that makes this object become a copy of 'spg' */ SeqPulsarSat& operator = (const SeqPulsarSat& spg); }; //////////////////////////////////////////////////////////////////////////// /** * * \brief Saturation pulse + spoilers * * A saturation pulse + spoiler gradient pulse * */ class SeqSat : public SeqObjList, public virtual SeqPulsInterface, public virtual SeqGradInterface { // virtual functions of SeqPulsInterface are marshalled to puls // virtual functions of SeqFreqChanInterface are marshalled to puls public: /** * Constructs saturation pulse labeled 'object_label' with the following properties: * - nuc: the nucleus to saturate * - bandwidth: The bandwidth in kHz * - npulses: The number of consecutive pulses */ SeqSat(const STD_string& object_label="unnamedSeqSat",satNucleus nuc=fat,float bandwidth=0.3, unsigned int npulses=1); /** * Constructs a copy of 'spg' */ SeqSat(const SeqSat& spg); /** * Assignment operator that makes this object become a copy of 'spg' */ SeqSat& operator = (const SeqSat& spg); // overloading virtual function from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); SeqGradInterface& invert_strength(); float get_strength() const; fvector get_gradintegral() const; double get_gradduration() const; SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); private: void build_seq(); SeqPulsarSat puls; SeqGradConstPulse spoiler_read_pos; SeqGradConstPulse spoiler_slice_neg; SeqGradConstPulse spoiler_read_neg; SeqGradConstPulse spoiler_slice_pos; SeqGradConstPulse spoiler_phase_pos; unsigned int npulses_cache; }; /** @} */ #endif odin-1.8.5/odinseq/seqsim.h0000644000175000017500000002464111712547771012536 00000000000000/*************************************************************************** seqsim.h - description ------------------- begin : Tue Jun 11 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQSIM_H #define SEQSIM_H #include #include // for RandomDist #include #include /** * @ingroup odinseq * \brief Time interval for simulation * * Data structure to hold the values for a single interval with constant fields * - dt: Duration of the interval * - B1: Complex RF field * - freq: Transmit/receive frequency * - phase: Transmit/receive phase in deg * - rec: Receiver (>0 means on) * - Gx: Gradient in read direction * - Gy: Gradient in phase direction * - Gz: Gradient in slice direction */ struct SeqSimInterval { SeqSimInterval() : dt(0.0), B1(0.0), freq(0.0), phase(0.0), rec(0.0), Gx(0.0), Gy(0.0), Gz(0.0) {} float dt; STD_complex B1; float freq; float phase; float rec; float Gx; float Gy; float Gz; }; ///////////////////////////////////////////////////////////////////// class ProgressMeter; // forward declaration /** * @ingroup odinseq_internals * Interface for Simulators */ class SeqSimAbstract : public virtual SeqClass { public: virtual ~SeqSimAbstract() {} /** * Prepare a simulation (i.e. before successive calls to simulate() ) with the parameters: * - sample: The virtual sample * - transmit_coil: Transmitter coil, 0 for none * - receive_coil: Receiver coil, 0 for none * - progmeter: Status indicator to trace progress, 0 for none */ virtual void prepare_simulation(const Sample& sample, CoilSensitivity* transmit_coil=0, CoilSensitivity* receive_coil=0, ProgressMeter* progmeter=0) = 0; /** * Simulation with * - simvals: The magnetic fields during a time interval * - gamma: Gyromagnetic ration of the nucleus observed * Return value: Signal in each receiver channel */ virtual cvector simulate(const SeqSimInterval& simvals, double gamma) = 0; /** * Call this function after a simulation (i.e. after successive calls to simulate() ) */ virtual void finalize_simulation() = 0; }; ///////////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * \brief MAGSI-based Magnetization Simulator * * This is a simulator to calculate the time evolution of a magnetization grid * in 4 dimension (frequency and three spatial dimensions). This simulation of the * Bloch-Torrey equations is performed by means of the MAGSI algorith * (c.f. Journal of Magnetic Resonance 180:29-38, 2006). * Simulation usually involves the following steps: * - Initialize the simulator by prepare_simulation() using a virtual sample. * - Iterative simulation by simulate() using a structure with piece-wise constant fields. * - Finish simulation by calling finalize_simulation(). */ class SeqSimMagsi : public JcampDxBlock, public ThreadedLoop, public virtual SeqSimAbstract { public: /** * Constructs a simulator labeled 'object_label'. */ SeqSimMagsi(const STD_string& label="unnamedSeqSimMagsi"); /** * Copy constructor */ SeqSimMagsi(const SeqSimMagsi& ssm); /** * Destructor */ ~SeqSimMagsi(); /** * Assignment operator */ SeqSimMagsi& operator = (const SeqSimMagsi& ssm); /** * Returns the overall size of the array */ unsigned int get_total_size() const {return Mx.total();} /** * Set each magnetization to initial state 'initial_vector', which is (0,0,1) by default */ SeqSimMagsi& reset_magnetization(); /** * Set the vector for the initial magnetization */ SeqSimMagsi& set_initial_vector(float Mx, float My, float Mz); /** * Returns the real part of the transverse magnetisation */ const farray& get_Mx() const {return Mx;} /** * Returns the imaginary part of the transverse magnetisation */ const farray& get_My() const {return My;} /** * Returns the longitudinal magnetisation */ const farray& get_Mz() const {return Mz;} /** * Returns the amplitude of the transverse magnetisation */ const farray& get_Mamp() const {return Mamp;} /** * Returns the phase of the transverse magnetisation */ const farray& get_Mpha() const {return Mpha;} /** * Updates all parameter relations */ SeqSimMagsi& update(); /** * Specifies whether simulation should be performed everytime update() is called */ SeqSimMagsi& set_online_simulation(bool onlineflag) { online=onlineflag; return *this;} /** * Specifies whether intra-voxel magnetzation gradients are considered during simulation */ SeqSimMagsi& set_intravoxel_simulation(bool ivflag) { magsi=ivflag; return *this;} /** * Specifies the number of threads used during simulation */ SeqSimMagsi& set_numof_threads(unsigned int n) { nthreads=n; return *this;} /** * Specifies a rotation matrix for the spatial domain, i.e. the magnetization * array will be rotated in space using the specified rotation matrix. */ SeqSimMagsi& set_spat_rotmatrix(const RotMatrix& rotmatrix); /** * Returns whether simulation should be performed, i.e. whether the 'online' flag * is true or 'update' was activated. */ bool do_simulation(); // implementing virtual functions of SeqSimAbstract void prepare_simulation(const Sample& sample, CoilSensitivity* transmit_coil=0, CoilSensitivity* receive_coil=0, ProgressMeter* progmeter=0); cvector simulate(const SeqSimInterval& simvals, double gamma); void finalize_simulation(); // implementing virtual functions of ThreadedLoop bool kernel(const SeqSimInterval& simvals, cvector& signal, int&, unsigned int begin, unsigned int end); private: friend class SeqTimecourse; /** * Resize the array in the four dimensions according to the given sizes */ SeqSimMagsi& resize(unsigned int xsize, unsigned int ysize, unsigned int zsize, unsigned int freqsize=1); void common_init(); int append_all_members(); SeqSimMagsi& MampMpha2MxMy(); SeqSimMagsi& MxMy2MampMpha(); void update_axes(); void set_axes_cache(const Sample& sample); JDXfloatArr Mx; JDXfloatArr My; JDXfloatArr Mz; JDXfloatArr Mamp; JDXfloatArr Mpha; JDXbool online; JDXaction update_now; JDXtriple initial_vector; bool iactive; bool magsi; unsigned int nthreads; RotMatrix* spat_rotmatrix; double gamma_cache; double elapsed_time; // within current time frame unsigned int time_index_cache; unsigned int numof_time_intervals_cache; double* time_intervals_cache; // cache for update_axes() float x_low; float x_upp; float y_low; float y_upp; float z_low; float z_upp; float freq_low; // in rad/s float freq_upp; // in rad/s // intra-voxel magn gradients float *dMx[4]; float *dMy[4]; float *dMz[4]; float *dppm[3]; // readonly // use raw pointers to avoid slower []-operator of STD_vector unsigned int oneframe_size_cache; // size of one frame float* xpos_cache; float* ypos_cache; float* zpos_cache; float* freqoffset_cache; // in rad*kHz unsigned int nframes_ppm_cache; float* ppm_cache; unsigned int nframes_spin_density_cache; float* spin_density_cache; STD_complex* B1map_transm_cache; unsigned int num_rec_channel_cache; STD_complex** B1map_receiv_cache; unsigned int nframes_Dcoeff_cache; float* Dcoeff_cache; bool sim_diffusion; unsigned int nframes_r1_cache; float* r1_cache; unsigned int nframes_r2_cache; float* r2_cache; bool* has_relax_cache; float L[4]; float B0_ppm; bool simcache_up2date; void outdate_simcache(); }; ///////////////////////////////////////////////////////////////////// #ifdef STANDALONE_PLUGIN // exclude from Siemens DLLs /** * \brief Monte-Carlo-based Magnetization Simulator * * Monte-Carlo Simulator for diffusional averaging */ class SeqSimMonteCarlo : public ThreadedLoop, public virtual SeqSimAbstract { public: /** * Constructs a simulator labeled 'object_label' to simulate 'nparticles' diffusion trajectories using 'nthreads' threads. */ SeqSimMonteCarlo(const STD_string& label="unnamedSeqSimMonteCarlo", unsigned int nparticles=10000, unsigned int nthreads=1); /** * Copy constructor */ SeqSimMonteCarlo(const SeqSimMonteCarlo& ssmc) {common_init(); SeqSimMonteCarlo::operator = (ssmc);} /** * Assignment operator */ SeqSimMonteCarlo& operator = (const SeqSimMonteCarlo& ssmc); /** * Get spatial distribution of particles after simulation */ farray get_spatial_dist() const; // implementing virtual functions of SeqSimAbstract void prepare_simulation(const Sample& sample, CoilSensitivity* transmit_coil=0, CoilSensitivity* receive_coil=0, ProgressMeter* progmeter=0); cvector simulate(const SeqSimInterval& simvals, double gamma); void finalize_simulation(); // implementing virtual functions of ThreadedLoop bool kernel(const SeqSimInterval& simvals, cvector& signal, RandomDist& local_rng, unsigned int begin, unsigned int end); private: struct Particle { float pos[3]; float Mx, My, Mz; }; void common_init(); void clear_cache(); unsigned int linear_index(const float pos[3]) const; STD_vector particle; unsigned int numof_threads; RandomDist rng; // seed only once per simulator double gamma_cache; unsigned int size_cache[3]; // use raw pointers to avoid slower []-operator of STD_vector float* Dcoeff_cache; float* ppmMap_cache; float* R1map_cache; float* R2map_cache; float* spinDensity_cache; float pixelspacing_cache[3]; float B0_ppm_cache; }; #endif ///////////////////////////////////////////////////////////////////// /** @} */ #endif odin-1.8.5/odinseq/odinpulse.cpp0000644000175000017500000010464711322062345013561 00000000000000#include "odinpulse.h" #include "seqsim.h" #include "seqdriver.h" #include "seqplatform.h" /////////////////////////////////////////////////////////////////////// const kspace_coord& JDXtrajectory::calculate(float s) const { JDXfunctionPlugIn::coord_retval=kspace_coord(); if(allocated_function) return allocated_function->calculate_traj(s); else return JDXfunctionPlugIn::coord_retval; } const traj_info& JDXtrajectory::get_traj_info() const { JDXfunctionPlugIn::traj_info_retval=traj_info(); if(allocated_function) return allocated_function->get_traj_properties(); else return JDXfunctionPlugIn::traj_info_retval; } /////////////////////////////////////////////////////////////////////// STD_complex JDXshape::calculate(const kspace_coord& coord ) const { if(allocated_function) return allocated_function->calculate_shape(coord); return STD_complex(0.0); } STD_complex JDXshape::calculate(float s, float Tp) const { if(allocated_function) return allocated_function->calculate_shape(s,Tp); return STD_complex(0.0); } const shape_info& JDXshape::get_shape_info() const { JDXfunctionPlugIn::shape_info_retval=shape_info(); if(allocated_function) return allocated_function->get_shape_properties(); else return JDXfunctionPlugIn::shape_info_retval; } /////////////////////////////////////////////////////////////////////// struct OdinPulseData { bool intactive; JDXenum dim_mode; JDXenum nucleus; JDXshape shape; JDXtrajectory trajectory; JDXfilter filter; JDXint npts; JDXdouble Tp; JDXcomplexArr B1; JDXfloatArr Gr; JDXfloatArr Gp; JDXfloatArr Gs; JDXdouble B10; JDXdouble G0; JDXbool consider_system_cond_flag; JDXbool consider_Nyquist_cond_flag; JDXbool take_min_smoothing_kernel; JDXdouble smoothing_kernel_size; JDXtriple spatial_offset; JDXdouble field_of_excitation; JDXenum pulse_type; JDXformula composite_pulse; JDXint npts_1pulse; JDXdouble Tp_1pulse; JDXdouble pulse_gain; JDXdouble pulse_power; JDXdouble flipangle; float flip_corr; funcMode old_mode; bool ready; }; /////////////////////////////////////////////////////////////////////// // Calculate maximum possible gradient strengt which is either given by the slew rate or max gradient strength float OdinPulse::gradient_system_max (const fvector& Gvec, float Gmax, float maxslew, float Tp) { Log odinlog("","gradient_system_max"); float dGmax = 0.0; int npuls=Gvec.size(); for (int i = 1; i < npuls; i++) dGmax=STD_max(dGmax, float(fabs(Gvec[i - 1] - Gvec[i]))); if(dGmax>0.0 && npuls>0 ) { float Gmax_slew = maxslew * Tp / (float(npuls) * dGmax); // Gradient strength which would have to be used in order to stay within slew-rate limits return STD_min(Gmax_slew, Gmax); } else { return Gmax; } } float OdinPulse::max_kspace_step (const fvector& Gz,float gamma,float Tp,float G0) { float kz = 0.0, kzold = 0.0, maxstep = 0.0; int npuls=Gz.size(); for (int i = npuls - 1; i >= 0; i--) { kz -= gamma * Tp * G0 / float(npuls) * Gz[i]; maxstep = STD_max(maxstep, float(fabs(kz - kzold))); kzold = kz; } return maxstep; } float OdinPulse::max_kspace_step2 (const fvector& Gx, const fvector& Gy, float gamma,float Tp,float G0) { float kx = 0.0, ky = 0.0, kxold = 0.0, kyold = 0.0, maxstep = 0.0; int npuls=Gx.size(); for (int i = npuls - 1; i >= 0; i--) { kx -= gamma * Tp * G0 / float(npuls) * Gx[i]; ky -= gamma * Tp * G0 / float(npuls) * Gy[i]; maxstep = STD_max(maxstep, float(norm(kx - kxold, ky - kyold))); kxold = kx; kyold = ky; } return maxstep; } ////////////////////////////////////////////////////////////////////////////////////////// OdinPulse::OdinPulse(const STD_string& pulse_label,bool interactive) : JcampDxBlock(pulse_label), data(new OdinPulseData) { set_label(pulse_label); // because SeqClass is a virtual base class Log odinlog(this,"OdinPulse(...)"); data->shape.set_label("shape"); data->trajectory.set_label("trajectory"); data->filter.set_label("filter"); data->ready=false; data->intactive=interactive; data->flip_corr=1.0; data->dim_mode.add_item("0D"); data->dim_mode.add_item("1D"); data->dim_mode.add_item("2D"); data->dim_mode.set_actual(oneDeeMode); data->old_mode=funcMode(int(data->dim_mode)); ODINLOG(odinlog,normalDebug) << "old_mode=" << int(data->old_mode) << STD_endl; data->nucleus=systemInfo->get_nuc_enum(); data->nucleus.set_actual(0); data->shape.set_function_mode(funcMode(int(data->dim_mode))); data->trajectory.set_function_mode(funcMode(int(data->dim_mode))); data->npts_1pulse=256; data->npts_1pulse.set_minmaxval(1,systemInfo->get_max_rf_samples()); data->npts=data->npts_1pulse; resize_noupdate(data->npts); data->Tp_1pulse=2.0; data->Tp_1pulse.set_minmaxval(0.001,30.0); data->Tp_1pulse.set_unit(ODIN_TIME_UNIT); data->Tp=data->Tp_1pulse; data->take_min_smoothing_kernel=true; data->smoothing_kernel_size=0.001;// smoothing_kernel_size.set_minmaxval(0.001,20.0); data->smoothing_kernel_size.set_unit(ODIN_SPAT_UNIT); data->field_of_excitation=200.0; data->field_of_excitation.set_unit(ODIN_SPAT_UNIT); data->flipangle=90.0; data->flipangle.set_minmaxval(0.0,360.0); data->flipangle.set_unit(ODIN_ANGLE_UNIT); data->consider_system_cond_flag=true; data->consider_Nyquist_cond_flag=true; data->spatial_offset.set_unit(ODIN_SPAT_UNIT); for(int i=0; ipulse_type.add_item(pulseTypeLabel[i],i); data->pulse_type.set_actual(0); data->composite_pulse.set_syntax("A composite pulse can be specified by a string of the form a1(x2) a2(x2) ... where a1,a2,... are the flipangles in degree and x1,x2,... are the axes, .e.g. X,-X,Y or -Y"); data->pulse_gain=0.0; data->pulse_gain.set_parmode(noedit); data->pulse_gain.set_unit("dB"); data->pulse_power=0.0; data->pulse_power.set_parmode(noedit); data->pulse_power.set_unit(STD_string(ODIN_FIELD_UNIT)+"^2*"+ODIN_TIME_UNIT); data->B10=0.0; data->B10.set_parmode(noedit); data->B10.set_unit(ODIN_FIELD_UNIT); data->G0=0.0; data->G0.set_parmode(noedit); data->G0.set_unit(ODIN_GRAD_UNIT); data->B1.set_filemode(exclude); GuiProps gp; gp.scale[xPlotScale]=ArrayScale("time",ODIN_TIME_UNIT,0.0,data->Tp); data->B1.set_gui_props(gp); data->Gr.set_filemode(exclude); data->Gp.set_filemode(exclude); data->Gs.set_filemode(exclude); data->shape.set_function(0); data->trajectory.set_function(0); data->filter.set_function(0); unsigned int capacity=systemInfo->get_max_rf_samples(); data->B1.reserve(capacity); data->Gr.reserve(capacity); data->Gp.reserve(capacity); data->Gs.reserve(capacity); append_all_members(); data->ready=true; OdinPulse::update(); } OdinPulse::OdinPulse(const OdinPulse& pulse) : data(new OdinPulseData) { OdinPulse::operator = (pulse); } OdinPulse::~OdinPulse() { Log odinlog(this,"~OdinPulse()"); delete data; } int OdinPulse::append_all_members() { clear(); append_member(data->dim_mode,"Mode"); append_member(data->nucleus,"Nucleus"); append_member(data->shape,"Shape"); append_member(data->trajectory,"Trajectory"); append_member(data->filter,"Filter"); append_member(data->npts_1pulse,"NumberOfPoints"); append_member(data->Tp_1pulse,"PulseDuration"); if(int(data->dim_mode)>zeroDeeMode) append_member(data->take_min_smoothing_kernel,"TakeMinSmoothingKernel"); if(int(data->dim_mode)>zeroDeeMode) append_member(data->smoothing_kernel_size,"SmoothingKernelSize"); append_member(data->flipangle,"FlipAngle"); if(int(data->dim_mode)>zeroDeeMode) append_member(data->consider_system_cond_flag,"ConsiderSystem"); if(int(data->dim_mode)>zeroDeeMode) append_member(data->consider_Nyquist_cond_flag,"ConsiderNyquist"); if(int(data->dim_mode)>zeroDeeMode) append_member(data->spatial_offset,"SpatialOffset"); if(int(data->dim_mode)>zeroDeeMode) append_member(data->field_of_excitation,"FieldOfExcitation"); if(int(data->dim_mode)pulse_type,"PulseType"); append_member(data->composite_pulse,"CompositePulse"); append_member(data->B1,"B1"); if(int(data->dim_mode)==twoDeeMode) append_member(data->Gr,"x_Gradient"); if(int(data->dim_mode)==twoDeeMode) append_member(data->Gp,"y_Gradient"); if(int(data->dim_mode)==oneDeeMode) append_member(data->Gs,"z_Gradient"); append_member(data->pulse_gain,"PulseGain"); append_member(data->pulse_power,"PulsePower"); append_member(data->B10,"B1_Max"); append_member(data->G0,"GradientMax"); return 0; } OdinPulse& OdinPulse::operator = (const OdinPulse& pulse) { Log odinlog(this,"operator = (...)"); SeqClass::operator = (pulse); JcampDxBlock::operator = (pulse); ODINLOG(odinlog,normalDebug) << "operator of base classes called" << STD_endl; (*data)=(*(pulse.data)); OdinPulse::append_all_members(); update(); return *this; } OdinPulse& OdinPulse::set_dim_mode(funcMode dmode) { Log odinlog(this,"set_dim_mode"); data->old_mode=funcMode(int(data->dim_mode)); ODINLOG(odinlog,normalDebug) << "old_mode/dmode=" << int(data->old_mode) << "/" << int(dmode) << STD_endl; data->dim_mode.set_actual(dmode); data->shape.set_function_mode(funcMode(int(data->dim_mode))); data->trajectory.set_function_mode(funcMode(int(data->dim_mode))); update(); return *this; } funcMode OdinPulse::get_dim_mode() const { return funcMode(int(data->dim_mode)); } unsigned int OdinPulse::get_size() const {return data->npts;} OdinPulse& OdinPulse::resize(unsigned int newsize) { data->npts_1pulse=newsize; resize_noupdate(newsize); return update(); } OdinPulse& OdinPulse::resize_noupdate(unsigned int newsize) { data->B1.resize(newsize); data->Gr.resize(newsize); data->Gp.resize(newsize); data->Gs.resize(newsize); return *this; } OdinPulse& OdinPulse::set_Tp(double duration) { data->Tp_1pulse=duration; data->Tp=duration; return update(); } double OdinPulse::get_Tp() const { return data->Tp; } double OdinPulse::get_Tp_1pulse() const { return data->Tp_1pulse; } OdinPulse& OdinPulse::set_consider_system_cond(bool flag) { data->consider_system_cond_flag=flag; update(); return *this; } bool OdinPulse::get_consider_system_cond() const {return data->consider_system_cond_flag;} OdinPulse& OdinPulse::set_consider_Nyquist_cond(bool flag) { data->consider_Nyquist_cond_flag=flag; update(); return *this; } bool OdinPulse::get_consider_Nyquist_cond() const { return data->consider_Nyquist_cond_flag;} OdinPulse& OdinPulse::set_spat_resolution(double sigma) { data->smoothing_kernel_size=sigma; data->take_min_smoothing_kernel=false; update(); return *this; } double OdinPulse::get_spat_resolution() const {return data->smoothing_kernel_size;} OdinPulse& OdinPulse::use_min_spat_resolution(bool flag) { data->take_min_smoothing_kernel=flag; update(); return *this; } OdinPulse& OdinPulse::set_field_of_excitation(double fox) { data->field_of_excitation=fox; update(); return *this; } double OdinPulse::get_field_of_excitation() const {return data->field_of_excitation;} OdinPulse& OdinPulse::set_spatial_offset(direction direction, double offset) { data->spatial_offset[direction]=offset; update(); return *this; } double OdinPulse::get_spatial_offset(direction direction) const {return data->spatial_offset[direction];} OdinPulse& OdinPulse::set_nucleus(const STD_string& nucleusname) { data->nucleus.set_actual(nucleusname); update(); return *this; } STD_string OdinPulse::get_nucleus() const { return data->nucleus; } OdinPulse& OdinPulse::set_pulse_type(pulseType type) { data->pulse_type.set_actual(type); update(); return *this; } pulseType OdinPulse::get_pulse_type() const {return pulseType(int(data->pulse_type));} OdinPulse& OdinPulse::set_composite_pulse(const STD_string& cpstring) { Log odinlog(this,"set_composite_pulse"); data->composite_pulse=cpstring; ODINLOG(odinlog,normalDebug) << "composite_pulse=>" << STD_string(data->composite_pulse) << "<" << STD_endl; update(); return *this; } farray OdinPulse::get_composite_pulse_parameters() const { Log odinlog(this,"get_composite_pulse_parameters"); if(!is_composite_pulse()) return farray(); ODINLOG(odinlog,normalDebug) << "composite_pulse=>" << STD_string(data->composite_pulse) << "<" << STD_endl; svector subpulses=tokens(data->composite_pulse); unsigned int n_pulses=subpulses.size(); ODINLOG(odinlog,normalDebug) << "n_pulses=" << n_pulses << STD_endl; farray result(n_pulses,2); for(unsigned int i=0;i" << subpulses[i] << "<" << STD_endl; result(i,0)=atof(rmblock(subpulses[i],"(",")",true,true).c_str()); } return result; } bool OdinPulse::is_composite_pulse() const { Log odinlog(this,"is_composite_pulse"); bool result=true; if(data->composite_pulse=="") result=false; ODINLOG(odinlog,normalDebug) << "composite_pulse/result=" << STD_string(data->composite_pulse) << "/" << result << STD_endl; return result; } OdinPulse& OdinPulse::set_flipangle(double angle) { data->flipangle=angle; update_B10andPower(); return *this; } double OdinPulse::get_flipangle() const {return data->flipangle;} int OdinPulse::load(const STD_string& filename) { Log odinlog(this,"load"); // determine the dim mode first and set the functions accordingly data->dim_mode.load(filename); ODINLOG(odinlog,normalDebug) << "dim_mode/old_mode=" << int(data->dim_mode) << "/" << int(data->old_mode) << STD_endl; // switch before loading so that plugin parameters can be assigned properly data->shape.set_function_mode(funcMode(int(data->dim_mode))); data->trajectory.set_function_mode(funcMode(int(data->dim_mode))); // then load the whole set of parameters and update the pulse int result=JcampDxBlock::load(filename); update(); return result; } int OdinPulse::write(const STD_string& filename) const {return JcampDxBlock::write(filename);} float OdinPulse::ensure_unit_range(float x) { x=STD_min(float(1.0),x); x=STD_max(float(-1.0),x); return x; } OdinPulse& OdinPulse::generate() { Log odinlog(this,"generate"); if(!data->ready) { ODINLOG(odinlog,normalDebug) << "not ready" << STD_endl; return *this; } int i; float knew; float dkmax=0.0; if(data->take_min_smoothing_kernel) data->smoothing_kernel_size=0.001; // Reset so that it will be increased to min in a later step data->smoothing_kernel_size=STD_max(0.001, double(data->smoothing_kernel_size)); data->shape.init_shape(); data->trajectory.init_trajectory(this); // For loaded pulses int fixedsize=data->shape.get_shape_info().fixed_size; if(fixedsize>=0) data->npts_1pulse=fixedsize; // Calculate pulse using fixed rastertime, if necessary double rastime=systemInfo->get_rastertime(pulsObj); if(rastime) { data->npts_1pulse=int(secureDivision(data->Tp_1pulse,rastime)+0.5); data->Tp_1pulse=double(data->npts_1pulse)*rastime; } // reset to the size of one pulse data->npts=data->npts_1pulse; data->Tp=data->Tp_1pulse; resize_noupdate(data->npts_1pulse); ODINLOG(odinlog,normalDebug) << "resize done" << STD_endl; float gamma=systemInfo->get_gamma(data->nucleus); funcMode mode=funcMode(int(data->dim_mode)); // Zero gradients before calculating the selectively data->Gr=JDXfloat(0.0); data->Gp=JDXfloat(0.0); data->Gs=JDXfloat(0.0); data->G0=0.0; float g0=0.0; // The scaling factor for the time-strength-independent gradient shape bool spatsel_mode=(mode>=oneDeeMode) && (mode<=twoDeeMode); if(spatsel_mode) { // generate gradients if in spatial-selective mode if(mode==oneDeeMode) { // calculate gradient: for(i=0; inpts_1pulse; i++) { const kspace_coord& tds=data->trajectory.calculate (float(i)/float(data->npts_1pulse-1)); data->Gs[i] = tds.Gz; } // normalize_gradient: g0 = data->Gs.normalize(); } // end oneDeeMode if(mode==twoDeeMode) { // calculate gradient: for(i=0; inpts_1pulse; i++) { const kspace_coord& tds=data->trajectory.calculate (float(i)/float(data->npts_1pulse-1)); data->Gr[i] = tds.Gx; data->Gp[i] = tds.Gy; } // normalize_gradient: g0 = STD_max (data->Gr.maxabs(), data->Gp.maxabs()); if (g0) { data->Gr/=g0; data->Gp/=g0; } } } // The following calculations are based on these notations: // // k(t) = kr * f(t/Tp) = gamma * integral{ G(t') dt'} = gamma * G0 * integral{ G(t')/G0 dt'} = gamma * G0 * Tp * integral{ g(s)/g0 ds} = gamma * G0/g0 * Tp * f(s) // // => kr = gamma * Tp * G0/g0 // // with // k(t): Physical k-space trajectory // kr: Maximum k-space radius (distance from center) // f(s): Trajectory as provided by plugin // G(t): Physical gradient shape // G0: Scaling factor for physical gradient strength // g(s): Gradient shape as provided by plugin, f(s) = integral{ g(s) ds} // g0: Scaling factor for gradient shape as provided by plugin // // Please note: the vectors G(t)/G0 and g(s)/g0 have the same normalized values. double nyquist_factor = sqrt (-2.0 * log (_BOUNDARY_VALUE_)) * 2.0; // TODO: replace this by PII // double nyquist_factor = PII; // set_gradient_max_scale: if(spatsel_mode) { // set G0 according to smoothing scale: float kr = secureDivision(nyquist_factor , data->smoothing_kernel_size); data->G0 = secureDivision(kr * g0 , gamma * data->Tp_1pulse); } ODINLOG(odinlog,normalDebug) << "set_gradient_max_scale done" << STD_endl; // calculate the maximum gradient strength of the pulse according to the system constrains float Gmax_system=systemInfo->get_max_grad(); float maxslew_system=systemInfo->get_max_slew_rate(); ODINLOG(odinlog,normalDebug) << "systemInfo stuff done" << STD_endl; float Gsystem=0.0; if(mode==oneDeeMode) { ODINLOG(odinlog,normalDebug) << "calling gradient_system_max in 1D mode" << STD_endl; Gsystem = gradient_system_max (data->Gs, Gmax_system, maxslew_system, data->Tp_1pulse); } if(mode==twoDeeMode) { ODINLOG(odinlog,normalDebug) << "calling gradient_system_max in 2D mode" << STD_endl; Gsystem = STD_min(gradient_system_max (data->Gr, Gmax_system, maxslew_system, data->Tp_1pulse), gradient_system_max (data->Gp, Gmax_system, maxslew_system, data->Tp_1pulse)); } ODINLOG(odinlog,normalDebug) << "gradient scaling done" << STD_endl; // check to above calculated max gradient strength against the actual and correct if neccessary if (data->G0 >= Gsystem) { if (data->consider_system_cond_flag) { data->G0 = Gsystem; if(spatsel_mode) { knew = secureDivision(gamma * data->G0 * data->Tp_1pulse , g0); data->smoothing_kernel_size = STD_max( double(data->smoothing_kernel_size), nyquist_factor / knew); } } else ODINLOG(odinlog,warningLog) << "system conditions violated !" << STD_endl; } ODINLOG(odinlog,normalDebug) << "system constraints done" << STD_endl; // precalculations for Nyquist check float max_spatial_extension=0.5*data->field_of_excitation; // Assume single point as the excitation shape, so that, in contrast to a shape that fills the whole FOX, aliases would appear at (+/- FOX). Therefore, we can effectively use half the FOX without aliasing. max_spatial_extension*=sqrt(mode); // extend to diagonal direction square-shaped alias-free FOX max_spatial_extension+=data->shape.get_shape_info().spatial_extent; // If shape is not single point, add the total extent of the shape. Otherwise it aliases into the FOX. if(mode==oneDeeMode) { dkmax=max_kspace_step(data->Gs, gamma, data->Tp_1pulse, data->G0); max_spatial_extension += fabs(data->spatial_offset[zAxis]); } if(mode==twoDeeMode) { dkmax=max_kspace_step2(data->Gr, data->Gp, gamma, data->Tp_1pulse,data->G0); // max k-space step in tangential direction max_spatial_extension += norm (data->spatial_offset[xAxis], data->spatial_offset[yAxis]); // add spatial offset } float kr0 = secureDivision(gamma * data->G0 * data->Tp_1pulse , g0); // k-space radius float dkmax_trajectory=2.0*kr0*data->trajectory.get_traj_info().max_kspace_step; // max k-space step in radial direction ODINLOG(odinlog,normalDebug) << "dkmax_trajectory/dkmax=" << dkmax_trajectory << "/" << dkmax << STD_endl; dkmax=STD_max(dkmax, dkmax_trajectory); // max of both // consider Nyquist condition and correct if neccessary if(spatsel_mode) { float phase_product=dkmax * max_spatial_extension; if (phase_product > 2.0*PII) { // Nyquist condition if (data->consider_Nyquist_cond_flag) { // rescale k-space to fulfill Nyquist condition data->G0 = secureDivision( 2.0*PII * data->G0 , phase_product ); knew = secureDivision( gamma * data->G0 * data->Tp_1pulse , g0 ); data->smoothing_kernel_size = STD_max( double(data->smoothing_kernel_size), nyquist_factor / knew); } else ODINLOG(odinlog,warningLog) << "Nyquist condition violated !" << STD_endl; } } ODINLOG(odinlog,normalDebug) << "Nyquist constraints done" << STD_endl; // float kernel0D=sqrt(-32*log(_BOUNDARY_VALUE_)); //generate RF waveform: kr0 = secureDivision(gamma * data->G0 * data->Tp_1pulse , g0); ODINLOG(odinlog,normalDebug) << "dim_mode/g0/G0/kr0 = " << data->dim_mode.printvalstring() << "/" << g0 << "/" << double(data->G0) << "/" << kr0 << STD_endl; ODINLOG(odinlog,normalDebug) << "adiabatic = " << is_adiabatic() << STD_endl; kspace_coord tds; for (i=0; inpts_1pulse; i++) { float s=float(i)/float(data->npts_1pulse-1); tds=data->trajectory.calculate(s); tds.index=i; tds.kx=tds.kx*kr0; tds.ky=tds.ky*kr0; tds.kz=tds.kz*kr0; STD_complex Wk; if (mode==zeroDeeMode) Wk=data->shape.calculate(tds.traj_s,data->Tp_1pulse); else Wk=data->shape.calculate(tds); if ( !is_adiabatic() ) { if(mode==zeroDeeMode) { Wk*=data->filter.calculate(fabs(tds.traj_s-0.5)*2.0); } else { float kr = secureDivision( nyquist_factor , data->smoothing_kernel_size); float krad = sqrt(tds.kx*tds.kx+tds.ky*tds.ky+tds.kz*tds.kz); Wk*=data->filter.calculate(secureDivision( krad , kr ) ); } } if(mode==oneDeeMode) { Wk *= tds.denscomp; if (data->spatial_offset[zAxis] != 0.0) { float argument = float(data->spatial_offset[zAxis]) * tds.kz; Wk*=exp(STD_complex(0.0,-argument)); } } if(mode==twoDeeMode) { Wk *= tds.denscomp; if ((data->spatial_offset[xAxis] != 0.0) || (data->spatial_offset[yAxis] != 0.0)) { float argument = float(data->spatial_offset[xAxis]) * tds.kx + float(data->spatial_offset[yAxis]) * tds.ky; Wk*=exp(STD_complex(0.0,-argument)); } } data->B1[i]=Wk; } ODINLOG(odinlog,normalDebug) << "generate RF done" << STD_endl; // final scaling float Bmax = amplitude(data->B1).maxvalue(); ODINLOG(odinlog,normalDebug) << "Bmax=" << Bmax << STD_endl; if (Bmax <= 0.0) ODINLOG(odinlog,warningLog) << "RF-amplitude array=0.0 !" << STD_endl; for (i = 0; inpts_1pulse; i++) data->B1[i]*= secureInv(Bmax); ODINLOG(odinlog,normalDebug) << "final scaling done" << STD_endl; ODINLOG(odinlog,normalDebug) << "all done" << STD_endl; return *this; } unsigned int OdinPulse::get_numof_composite_pulse() const { return get_composite_pulse_parameters().size(0); } bool OdinPulse::is_adiabatic() const {return data->shape.get_shape_info().adiabatic;} float OdinPulse::get_rel_center() const {return data->trajectory.get_traj_info().rel_center;} double OdinPulse::get_pulse_gain() const {return data->pulse_gain;} float OdinPulse::get_flipangle_corr_factor() const {return data->flip_corr;} OdinPulse& OdinPulse::make_composite_pulse() { Log odinlog(this,"make_composite_pulse"); // reset to the size of one pulse data->npts=data->npts_1pulse; data->Tp=data->Tp_1pulse; if(!is_composite_pulse()) { ODINLOG(odinlog,normalDebug) << "no composite pulse" << STD_endl; return *this; } ODINLOG(odinlog,normalDebug) << "is composite pulse" << STD_endl; OdinPulseData datacopy(*data); farray pars=get_composite_pulse_parameters(); unsigned int npulses=pars.size(0); ODINLOG(odinlog,normalDebug) << "sdcopy & pars done" << STD_endl; unsigned int oldsize=datacopy.npts_1pulse; unsigned int newsize=npulses*oldsize; ODINLOG(odinlog,normalDebug) << "oldsize/newsize=" << oldsize << "/" << newsize << STD_endl; resize_noupdate(newsize); data->npts=newsize; data->Tp=double(data->Tp_1pulse)*double(npulses); ODINLOG(odinlog,normalDebug) << "Tp_1pulse/npulses/Tp=" << data->Tp_1pulse << "/" << npulses << "/" << data->Tp << STD_endl; unsigned int ipulse; float maxflip=0.0; for(ipulse=0; ipulsemaxflip) maxflip=flipang; } unsigned int index=0; for(ipulse=0; ipulseB1[index]=flipscale*phasefactor*datacopy.B1[i]; data->Gr[index]=datacopy.Gr[i]; data->Gp[index]=datacopy.Gp[i]; data->Gs[index]=datacopy.Gs[i]; index++; } } ODINLOG(odinlog,normalDebug) << "assignment done" << STD_endl; data->flipangle=maxflip; update_B10andPower(); ODINLOG(odinlog,normalDebug) << "B10/power done" << STD_endl; float gamma=systemInfo->get_gamma(data->nucleus); float flip_formfactor= 180.0/PII * gamma * data->B10 * abs(data->B1.sum()) * secureDivision(data->Tp,double(data->npts)); data->flip_corr=secureDivision(flip_formfactor,data->flipangle); ODINLOG(odinlog,normalDebug) << "flip_formfactor/flip_corr=" << flip_formfactor << "/" << data->flip_corr << STD_endl; return *this; } OdinPulse& OdinPulse::set_pulse_gain() { Log odinlog(this,"set_pulse_gain"); if(!data->ready) return *this; unsigned int i; SeqSimMagsi mag; //("set_pulse_gain::mag"); // mag.resize(1,1,1,1); float gamma=systemInfo->get_gamma(data->nucleus); ODINLOG(odinlog,normalDebug) << "gamma=" << gamma << STD_endl; // Field-Strength of 90,Tp BP-Pulse as starting value data->B10 = secureDivision( 0.5 * PII , (gamma * data->Tp_1pulse) ); ODINLOG(odinlog,normalDebug) << "B10=" << data->B10 << STD_endl; Sample sample; sample.set_spatial_offset(xAxis,0.0); sample.set_spatial_offset(yAxis,0.0); sample.set_spatial_offset(zAxis,0.0); if(int(data->dim_mode) == oneDeeMode) { sample.set_spatial_offset(zAxis,data->spatial_offset[zAxis]+ data->shape.get_shape_info().ref_z_pos); } if(int(data->dim_mode) == twoDeeMode) { float x_offset=data->spatial_offset[xAxis] + data->shape.get_shape_info().ref_x_pos; float y_offset=data->spatial_offset[yAxis] + data->shape.get_shape_info().ref_y_pos; ODINLOG(odinlog,normalDebug) << "x_offset=" << x_offset << STD_endl; ODINLOG(odinlog,normalDebug) << "y_offset=" << y_offset << STD_endl; sample.set_spatial_offset(xAxis,x_offset); sample.set_spatial_offset(yAxis,y_offset); } // deal with adiabatic mode first if(is_adiabatic()) { i=0; float Mzdes=-1.0+_SETREFGAIN_ADIABATIC_INTERVAL_; // inversion is default if(get_pulse_type()==saturation) Mzdes= 0.0+_SETREFGAIN_ADIABATIC_INTERVAL_; while( /* i Mzdes) { simulate_pulse(mag,sample); data->B10 = _SETREFGAIN_ADIABATIC_INCR_FACTOR_*data->B10; i++; } } // adjust 90deg pulse if(!is_adiabatic()) { for (i = 0; i < _SETREFGAIN_ITERATIONS_; i++) { simulate_pulse(mag,sample); ODINLOG(odinlog,normalDebug) << "B10(pre) [" << i << "]=" << data->B10 << STD_endl; ODINLOG(odinlog,normalDebug) << "Mz=" << (mag.get_Mz())[0] << STD_endl; data->B10 = secureDivision(0.5 * PII * data->B10 , acos ((mag.get_Mz())[0])); ODINLOG(odinlog,normalDebug) << "B10(post)[" << i << "]=" << data->B10 << STD_endl; } } float formfactor=secureDivision(abs(data->B1.sum()),double(data->npts_1pulse)); ODINLOG(odinlog,normalDebug) << "formfactor=" << formfactor << STD_endl; float B10_formfactor=secureDivision( 0.5 * PII , (formfactor * gamma * data->Tp_1pulse)); ODINLOG(odinlog,normalDebug) << "B10_formfactor=" << B10_formfactor << STD_endl; data->flip_corr=secureDivision(data->B10,B10_formfactor); ODINLOG(odinlog,normalDebug) << "flip_corr=" << data->flip_corr << STD_endl; // calculate pulse gain (formfactor) of the pulse data->pulse_gain = 20.0 * log10 (secureDivision( 0.5 * PII , (gamma * data->B10 * data->Tp_1pulse))); ODINLOG(odinlog,normalDebug) << "pulse_gain=" << float(data->pulse_gain) << STD_endl; update_B10andPower(); ODINLOG(odinlog,normalDebug) << "pulse_power=" << float(data->pulse_power) << STD_endl; return *this; } void OdinPulse::update_B10andPower() { Log odinlog(this,"update_B10andPower"); if(!is_adiabatic()) { ODINLOG(odinlog,normalDebug) << "flipangle=" << data->flipangle << STD_endl; ODINLOG(odinlog,normalDebug) << "Tp_1pulse=" << double(data->Tp_1pulse) << STD_endl; ODINLOG(odinlog,normalDebug) << "gamma=" << double(systemInfo->get_gamma(data->nucleus)) << STD_endl; ODINLOG(odinlog,normalDebug) << "pulse_gain=" << data->pulse_gain << STD_endl; data->B10 = data->flipangle / 90.0 / data->Tp_1pulse * 0.5 * PII / (systemInfo->get_gamma(data->nucleus) * pow (10.0, data->pulse_gain / 20.0)); ODINLOG(odinlog,normalDebug) << "B10=" << data->B10 << STD_endl; } data->pulse_power = get_power_depos(); } OdinPulse& OdinPulse::update() { Log odinlog(this,"update"); ODINLOG(odinlog,normalDebug) << "dim_mode/old_mode=" << int(data->dim_mode) << "/" << int(data->old_mode) << STD_endl; if(int(data->dim_mode)!=int(data->old_mode)) { data->shape.set_function_mode(funcMode(int(data->dim_mode))); data->trajectory.set_function_mode(funcMode(int(data->dim_mode))); data->old_mode=funcMode(int(data->dim_mode)); ODINLOG(odinlog,normalDebug) << "old_mode=" << int(data->old_mode) << STD_endl; append_all_members(); // append only members which are useful in the current dim_mode } if(data->intactive) recalc_pulse(); // axis range may have changed GuiProps gp; gp.scale[xPlotScale]=ArrayScale("time",ODIN_TIME_UNIT,0.0,data->Tp); data->B1.set_gui_props(gp); data->Gr.set_gui_props(gp); data->Gp.set_gui_props(gp); data->Gs.set_gui_props(gp); return *this; } OdinPulse& OdinPulse::recalc_pulse() { generate(); set_pulse_gain(); make_composite_pulse(); return *this; } float OdinPulse::get_power_depos() const { Log odinlog(this,"get_power_depos"); unsigned int n=data->B1.length(); // may differ from npts float result=0.0; float dt = secureDivision(data->Tp , n); float B1amp; for (unsigned int i=0; iB10) * cabs(data->B1[i]); result+= B1amp*B1amp * dt; } return result; // To get values in reasonable range } OdinPulse& OdinPulse::set_shape(const STD_string& shapeval) { data->shape.set_funcpars(shapeval); update(); return *this; } OdinPulse& OdinPulse::set_trajectory(const STD_string& trajval) { data->trajectory.set_funcpars(trajval); update(); return *this; } OdinPulse& OdinPulse::set_filter(const STD_string& filterval) { data->filter.set_funcpars(filterval); update(); return *this; } OdinPulse& OdinPulse::set_shape_parameter(const STD_string& parameter_label, const STD_string& value) {data->shape.set_parameter(parameter_label,value); return *this;} OdinPulse& OdinPulse::set_trajectory_parameter(const STD_string& parameter_label, const STD_string& value) {data->trajectory.set_parameter(parameter_label,value); return *this;} OdinPulse& OdinPulse::set_filter_parameter(const STD_string& parameter_label, const STD_string& value) {data->filter.set_parameter(parameter_label,value); return *this;} STD_string OdinPulse::get_shape_parameter(const STD_string& parameter_label) const {return data->shape.get_parameter(parameter_label);} STD_string OdinPulse::get_trajectory_parameter(const STD_string& parameter_label) const {return data->trajectory.get_parameter(parameter_label);} STD_string OdinPulse::get_filter_parameter(const STD_string& parameter_label) const {return data->filter.get_parameter(parameter_label);} STD_string OdinPulse::get_shape() const {return data->shape.get_function_name();} STD_string OdinPulse::get_trajectory() const {return data->trajectory.get_function_name();} STD_string OdinPulse::get_filter() const {return data->filter.get_function_name();} const fvector& OdinPulse::get_Grad(direction channel) const { if(channel==readDirection) return data->Gr; if(channel==phaseDirection) return data->Gp; if(channel==sliceDirection) return data->Gs; return data->Gr; } double OdinPulse::get_G0() const {return data->G0;} const cvector& OdinPulse::get_B1() const {return data->B1;} double OdinPulse::get_B10() const {return data->B10;} void OdinPulse::simulate_pulse(SeqSimAbstract& sim, const Sample& sample) const { Log odinlog(this,"simulate_pulse"); // sim.reset_magnetization(); // will be called in prepare_simulation unsigned int n=get_size(); double dt=secureDivision(get_Tp(),n); float gamma=systemInfo->get_gamma(data->nucleus); ODINLOG(odinlog,normalDebug) << "n/dt/gamma=" << n << "/" << dt << "/" << gamma << STD_endl; SeqSimInterval simvals; simvals.dt=dt; simvals.freq=0.0; simvals.phase=0.0; simvals.rec=0.0; sim.prepare_simulation(sample); for(unsigned int i=0; iB10)*data->B1[i]; simvals.Gx= data->G0*data->Gr[i]; simvals.Gy= data->G0*data->Gp[i]; simvals.Gz= data->G0*data->Gs[i]; sim.simulate(simvals,gamma); } sim.finalize_simulation(); } int OdinPulse::write_rf_waveform (const STD_string& filename) const { Log odinlog(this,"write_rf_waveform"); int result=SeqPlatformProxy()->write_rf_waveform(filename,data->B1); if(result<0) ODINLOG(odinlog,errorLog) << " failed" << STD_endl; return result; } int OdinPulse::load_rf_waveform (const STD_string& filename) { Log odinlog(this,"load_rf_waveform"); cvector B1load; B1load.reserve(systemInfo->get_max_rf_samples()); int n=SeqPlatformProxy()->load_rf_waveform(filename,B1load); if(n>0) { resize(n); data->B1=B1load; } if(n>=0) n=0; if(n<0) ODINLOG(odinlog,errorLog) << " failed" << STD_endl; return n; } odin-1.8.5/odinseq/seqvec.h0000644000175000017500000002430111322062345012476 00000000000000/*************************************************************************** seqvec.h - description ------------------- begin : Mon Aug 19 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQVEC_H #define SEQVEC_H #include class SeqCounter; // forward declaration class SeqReorderVector; // forward declaration /////////////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq * This enum can be used to determine the encoding scheme of a list of values: * - linearEncoding : values are played out in the same order as specified * - reverseEncoding : values are played out in the reverse order as specified * - centerOutEncoding : encoding start in the center of values and moves outwards alternatingly in positive/negative direction * - centerInEncoding : encoding starts outwards and moves inwards alternatingly in positive/negative direction * - maxDistEncoding : Maximum distance between consecutive elements */ enum encodingScheme {linearEncoding=0, reverseEncoding, centerOutEncoding, centerInEncoding, maxDistEncoding}; /** * @ingroup odinseq * This enum can be used to determine the reordering scheme of a list of values: * - noReorder : No reordering is performed, the number of reorderings is then equal one * - rotateReorder : The values will be rotated, the number of reorderings is then the number of values * - blockedSegmented : The values will be divided into segments, preserving their order * - interleavedSegmented : The values will be divided into segments like distributing game cards */ enum reorderScheme {noReorder=0,rotateReorder,blockedSegmented,interleavedSegmented}; /** * @ingroup odinseq_internals * This enum holds information about how a certain vector and its reordering * are nested in the sequence tree: * - noRelation : They are not nested * - reorderInner : The reorder vector is attached to an inner loop * - vecInner : The reorder vector is attached to an outer loop * - unrolledLoop : The loop which uses the vector will be unrolled in the program */ enum nestingRelation {noRelation=0, reorderInner, vecInner, unrolledLoop}; /////////////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * This is the base class for all vector objects, i.e. objects that can * can take different values while looping over them. */ class SeqVector : public ListItem, public Handled, public virtual SeqClass { public: /** * Default Constructor */ SeqVector(const STD_string& object_label="unnamedSeqVector"); /** * Constructs an index vector labeled 'object_label' with the following properties: * - nindices: the total number of iterations * - slope: the number of indices per iteration * - offset: the offset of the indices, i.e. the index of the first iteration */ SeqVector(const STD_string& object_label, unsigned int nindices, int slope=1, int offset=0 ); /** * Copy Constructor */ SeqVector(const SeqVector& sv); /** * Destructor */ virtual ~SeqVector(); /** * Assignment operator that makes this vector become a copy of 'sv' */ SeqVector& operator = (const SeqVector& sv); /** * Overload this function to return the number of elements in the vector * (regardless of reordering) */ virtual unsigned int get_vectorsize() const {return indexvec.size();} /** * Returns the number of iterations with proper * consideration of reordering, e.g. if the vector has N values distributed * over M reordering segments, this function will return N/M. */ virtual unsigned int get_numof_iterations() const; /** * Overload this function to trigger a check whether the loop must possibly be unrolled * in pulse or gradient program */ virtual bool needs_unrolling_check() const {return false;} /** * Overload this function to prepare objects at run-time before the execution of a loop repetition * return 'false' when preparation fails */ virtual bool prep_iteration() const {return true;} /** * Overload this function to return the current index, intended to use it in * combination with reordering of phase encoding steps or slices */ virtual int get_current_index() const; /** * Returns the current index relevant for acquisition (reco dimensions). * This is the value of the index vector (set_indexvec) at the position * returned by 'get_current_index'. */ int get_acq_index() const; /** * Overload this function to tell whether the vector qualitatively alters the * sequence concerning timings and RF power deposition. * This is useful for accelerating duration and SAR calculations (Siemens). */ virtual bool is_qualvector() const; /** * Returns whether this vector is used to specify an acquisition dimension through the * set_*_vector(...) functions of all classes derived from SeqAcqInterface */ virtual bool is_acq_vector() const; /** * Returns whether this vector uses a different set of sequence objects at each repetition */ virtual bool is_obj_vector() const {return false;} /** * If the vector is used as a variable in the code-generated pulse program, * overload this function to return a unique label/command for the vector * which is either attached to the loop (Bruker), or executed at the beginning * of the loop (EPIC). */ virtual svector get_vector_commands(const STD_string& iterator) const {return svector();} /** * Overload this function to return the command to iterate to the next item at the end of the loop */ virtual STD_string get_loopcommand() const {return "";} /** * Sets the vector of indices 'iv' which will be returned by get_acq_index, * i.e. the assign reco indices (positions in k-space) */ SeqVector& set_indexvec(const ivector& iv) {indexvec=iv; return *this;} /** * Returns the vector of indices 'iv' which will be returned by get_acq_index, * i.e. the assign reco indices (positions in k-space) */ ivector get_indexvec() const {return indexvec;} /** * Sets the reordering scheme and the number of segments */ SeqVector& set_reorder_scheme(reorderScheme scheme, unsigned int nsegments=1); /** * Sets the encoding scheme */ SeqVector& set_encoding_scheme(encodingScheme scheme); /** * Returns the reordering vector (for loop insertion) */ const SeqVector& get_reorder_vector() const; /** * Returns the nesting relation between the vector and its reordering vector */ virtual nestingRelation get_nesting_relation() const; /** * Returns a matrix whereby the elements of rows (second dimension) * contain the reordered index for each iteration. The other * dimension (first dimension) represents reordering iterations. */ iarray get_index_matrix() const; /** * Returns the current index of the reordering vector */ int get_current_reord_index() const; /** * Returns the iterator as modified by the reorder vector as C code */ STD_string get_reord_iterator(const STD_string& iterator) const; protected: /** * Tell reorder vector what to do within a loop */ virtual svector get_reord_vector_commands(const STD_string& iterator) const {return svector();} /** * Returns true if vector is actually handled by a loop */ bool is_handled() const {return vechandler.get_handled();} private: friend class SeqReorderVector; friend class SeqCounter; friend class SeqObjLoop; friend class SeqSimultanVector; #ifdef SELF_FRIEND_CLASS friend class SeqVector; // making the class itself a friend is required for MSVC6 !! #endif /** * Returns whether the loop that controls this vector is currently iterating */ bool loopcounter_is_active() const; /** * Returns the current iteration */ int get_loopcounter() const; void common_int(); virtual const SeqVector& set_vechandler(const SeqCounter *sc) const; ivector indexvec; Handler vechandler; Handler simhandler; mutable SeqReorderVector* reordvec; mutable nestingRelation nr_cache; mutable bool nr_cache_up2date; }; /////////////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * This vector class is used to change the order of a list of values, e.g. * to change the order of frequencies to reorder slice selection */ class SeqReorderVector : public SeqVector { public: SeqReorderVector(const SeqVector* user, const SeqReorderVector* copy_templ=0); unsigned int get_reordered_size(unsigned int vecsize) const; int get_reordered_index(int counter) const {return get_reordered_index(counter,get_current_index());} private: friend class SeqVector; // implemented virtual functions of SeqVector unsigned int get_vectorsize() const; bool needs_unrolling_check() const {return reord_scheme!=noReorder;} bool prep_iteration() const {return reorder_user->prep_iteration();} bool is_qualvector() const {return reorder_user->is_qualvector();} bool is_acq_vector() const {return reorder_user->is_acq_vector();} svector get_vector_commands(const STD_string& iterator) const; int get_reordered_index(int counter, int reord_iteration) const; STD_string get_reordered_iterator(const STD_string& iterator) const; void clear_cache() {reord_iterator_cache="";} reorderScheme reord_scheme; unsigned int n_reord_segments; encodingScheme encoding_scheme; const SeqVector* reorder_user; mutable STD_string reord_iterator_cache; }; #endif odin-1.8.5/odinseq/seqgradtrapez.cpp0000644000175000017500000003513111455553540014433 00000000000000#include "seqgradtrapez.h" SeqGradTrapezDefault::SeqGradTrapezDefault() { const_dur=0.0; exclude_offramp=false; } SeqGradTrapezDefault::SeqGradTrapezDefault(const SeqGradTrapezDefault& sgtd) : SeqGradTrapezDriver(sgtd), SeqGradChan(sgtd) { graddriver->set_label(STD_string(sgtd.get_label())); onramp_cache=sgtd.onramp_cache; offramp_cache=sgtd.offramp_cache; const_dur=sgtd.const_dur; exclude_offramp=sgtd.exclude_offramp; } bool SeqGradTrapezDefault::update_driver(direction channel, double onrampdur, double constdur, double offrampdur, float strength, double timestep, rampType type, bool exclude_offramp_from_timing) { Log odinlog(this,"update_driver"); STD_string objlabel(get_label()); set_duration(onrampdur+constdur+offrampdur); // Store redundant info, e.g. for correct display in sequence tree double mingraddur=0.0; if(constdurset_label(get_label()); return graddriver->prep_trapez(get_strength(),get_grdfactors_norot(), onramp_cache.get_gradduration(), onramp_cache.get_wave(), const_dur, offramp_cache.get_gradduration(), offramp_cache.get_wave()); } STD_string SeqGradTrapezDefault::get_properties() const { return SeqGradChan::get_properties()+", up/const/down="+ftos(onramp_cache.get_gradduration())+"/"+ftos(const_dur)+"/"+ftos(offramp_cache.get_gradduration()); } SeqGradInterface& SeqGradTrapezDefault::set_strength(float gradstrength) { SeqGradChan::set_strength(gradstrength); onramp_cache.set_strength(gradstrength); offramp_cache.set_strength(gradstrength); return *this; } SeqGradInterface& SeqGradTrapezDefault::invert_strength() { SeqGradChan::invert_strength(); onramp_cache.invert_strength(); offramp_cache.invert_strength(); return *this; } float SeqGradTrapezDefault::get_integral() const { return onramp_cache.get_gradintegral().sum() + get_strength()*const_dur + offramp_cache.get_gradintegral().sum(); } double SeqGradTrapezDefault::get_gradduration() const { double result=onramp_cache.get_gradduration()+const_dur; if(!exclude_offramp) result+=offramp_cache.get_gradduration(); return result; } SeqGradInterface& SeqGradTrapezDefault::set_gradrotmatrix(const RotMatrix& matrix) { SeqGradChan::set_gradrotmatrix(matrix); onramp_cache.set_gradrotmatrix(matrix); offramp_cache.set_gradrotmatrix(matrix); return *this; } SeqGradChan& SeqGradTrapezDefault::get_subchan(double starttime, double endtime) const { SeqGradTrapezDefault* sgti= new SeqGradTrapezDefault(*this); sgti->set_temporary(); return *sgti; } /////////////////////////////////////////////////////////////// void SeqGradTrapez::common_init() { rampMode=linear; dt=0.0; steepnessfactor=1.0; exclude_offramp_timing=false; trapezchannel=readDirection; onrampdur=0.0; constdur=0.0; offrampdur=0.0; trapezstrength=0.0; } SeqGradTrapez::SeqGradTrapez(const STD_string& object_label, direction gradchannel,float gradstrength, double constgradduration, double timestep,rampType type, double minrampduration, float steepness) : SeqGradChanList(object_label), trapezdriver(object_label) { Log odinlog(this,"SeqGradTrapez"); ODINLOG(odinlog,normalDebug) << "gradstrength/constgradduration=" << gradstrength << "/" << constgradduration << STD_endl; common_init(); rampMode=type; dt=timestep; steepnessfactor=steepness; trapezchannel=gradchannel; constdur=constgradduration; trapezstrength=gradstrength; check_platform(); float rampintegral; get_ramps(get_label(), rampintegral, onrampdur, offrampdur, trapezstrength, dt, rampMode, steepnessfactor, minrampduration); update_driver(); build_seq(); } SeqGradTrapez::SeqGradTrapez(const STD_string& object_label, float gradintegral, direction gradchannel, double constgradduration, double timestep,rampType type, double minrampduration, float steepness) : SeqGradChanList(object_label), trapezdriver(object_label) { Log odinlog(this,"SeqGradTrapez"); common_init(); rampMode=type; dt=timestep; steepnessfactor=steepness; trapezchannel=gradchannel; if(constgradduration<=0.0) { // ramp-only gradient constdur=0.0; float sign=secureDivision(gradintegral,fabs(gradintegral)); trapezstrength=sign*sqrt(fabs(gradintegral)*systemInfo->get_max_slew_rate()); // Assume linear ramps } else { constdur=constgradduration; trapezstrength=secureDivision(gradintegral,constgradduration); } check_platform(); float rampintegral; get_ramps(get_label(), rampintegral, onrampdur, offrampdur, trapezstrength, dt, rampMode, steepnessfactor, minrampduration); // Fine-tune gradient integral float oldintegral=rampintegral+trapezstrength*constdur; trapezstrength*=secureDivision( gradintegral, oldintegral ); update_driver(); build_seq(); } SeqGradTrapez::SeqGradTrapez(const STD_string& object_label,float gradintegral, float gradstrength, direction gradchannel, double timestep, rampType type, double minrampduration, float steepness) : SeqGradChanList(object_label), trapezdriver(object_label) { Log odinlog(this,"SeqGradTrapez"); common_init(); rampMode=type; dt=timestep; steepnessfactor=steepness; trapezchannel=gradchannel; check_platform(); // Take note of sign of integral, apply later float sign=secureDivision(gradintegral,fabs(gradintegral)); // Use magnitude gradstrength=fabs(gradstrength); gradintegral=fabs(gradintegral); float rampintegral; get_ramps(get_label(), rampintegral, onrampdur, offrampdur, gradstrength, dt, rampMode, steepnessfactor, minrampduration); if(rampintegral<0.0) { // Consistency check: should be positive ODINLOG(odinlog,warningLog) << "Polarity mismatch: rampintegral=" << rampintegral << STD_endl; } if(rampintegral>gradintegral) { // Use ramp-only gradient constdur=0.0; trapezstrength=secureDivision(gradintegral,rampintegral)*gradstrength; // scale down ramp for correct integral } else { constdur=secureDivision(gradintegral-rampintegral,gradstrength); // Use const part for remainder trapezstrength=gradstrength; double rastertime=systemInfo->get_rastertime(gradObj); if(rastertime>0.0) { int nraster=(int)secureDivision(constdur,rastertime); if(rastertime*nraster!=constdur) nraster++; // always increase length of constant part constdur=nraster*rastertime; float rastered_integral=constdur*gradstrength+rampintegral; float scalefactor=secureDivision(gradintegral,rastered_integral); // scale down amplitude if(scalefactor>1.0) { ODINLOG(odinlog,warningLog) << "scalefactor=" << scalefactor << ", setting to 1" << STD_endl; } trapezstrength*=scalefactor; } } // Apply sign trapezstrength=sign*trapezstrength; update_driver(); build_seq(); } SeqGradTrapez::SeqGradTrapez(const SeqGradTrapez& sgt) { common_init(); SeqGradTrapez::operator = (sgt); } SeqGradTrapez::SeqGradTrapez(const STD_string& object_label) : SeqGradChanList(object_label), trapezdriver(object_label) { common_init(); } SeqGradTrapez& SeqGradTrapez::set_constgrad_duration(double duration) { constdur=duration; update_driver(); return *this; } SeqGradTrapez& SeqGradTrapez::set_integral(float gradintegral) { float newstrength=secureDivision( gradintegral, get_integral() )*trapezstrength; trapezstrength=newstrength; update_driver(); return *this; } float SeqGradTrapez::get_integral() const { return get_onramp_integral()+get_constgrad_integral()+get_offramp_integral(); } unsigned int SeqGradTrapez::get_onramp_npts() const { return (unsigned int)( secureDivision(onrampdur, dt)+0.5); } unsigned int SeqGradTrapez::get_const_npts() const { return (unsigned int)( secureDivision(constdur, dt)+0.5); } unsigned int SeqGradTrapez::get_offramp_npts() const { return (unsigned int)( secureDivision(offrampdur, dt)+0.5); } unsigned int SeqGradTrapez::get_npts() const { return ( get_onramp_npts()+ get_const_npts() + get_offramp_npts() ); } fvector SeqGradTrapez::get_trapezshape() const { fvector result(get_npts()); fvector onramp(get_onramp()); fvector offramp(get_offramp()); unsigned int index=0; unsigned int i; for(i=0; i odinlog(this,"check_platform"); ODINLOG(odinlog,normalDebug) << "checking if dt is valid on current platform" << STD_endl; double min_dt=systemInfo->get_min_grad_rastertime(); if(dtget_min_grad_rastertime()) { dt=min_dt; } ODINLOG(odinlog,normalDebug) << "checking if ramptype is valid on current platform" << STD_endl; if(!trapezdriver->check_ramptype(rampMode)) { ODINLOG(odinlog,errorLog) << "rampMode not supported on this platform" << STD_endl; } } void SeqGradTrapez::get_ramps(const STD_string& label, float& rampintegral, double& rampondur, double& rampoffdur, float strength, double dwelltime, rampType ramptype, float steepness, double mindur) { Log odinlog(label.c_str(),"get_ramps"); ODINLOG(odinlog,normalDebug) << "steepness/dwelltime=" << steepness << "/" << dwelltime << STD_endl; if( (steepness<=0.0) || (steepness>1.0) ) { ODINLOG(odinlog,warningLog) << "Steepness out of range, setting to 1.0" << STD_endl; steepness=1.0; } SeqGradRamp onramp4calc (label+"_onramp4calc", readDirection,0.0,strength,dwelltime,ramptype,steepness,false); SeqGradRamp offramp4calc(label+"_offramp4calc",readDirection,strength,0.0,dwelltime,ramptype,steepness,true); ODINLOG(odinlog,normalDebug) << "on/off/mindur=" << onramp4calc.get_duration() << "/" << offramp4calc.get_duration() << "/" << mindur << STD_endl; if(onramp4calc.get_duration() odinlog(this,"update_driver"); ODINLOG(odinlog,normalDebug) << "setting label" << STD_endl; trapezdriver->set_label(STD_string(get_label())); ODINLOG(odinlog,normalDebug) << "updating driver: onrampdur/constdur/offrampdur=" << onrampdur << "/" << constdur << "/" << offrampdur << STD_endl; trapezdriver->update_driver(trapezchannel,onrampdur,constdur,offrampdur,trapezstrength,dt,rampMode,exclude_offramp_timing); } void SeqGradTrapez::build_seq() { Log odinlog(this,"build_seq"); clear(); SeqGradChanList sgcl_driver(trapezdriver->get_driverchanlist()); (*this)+=sgcl_driver; } ////////////////////////////////////////////////////////// SeqGradTrapezParallel::SeqGradTrapezParallel(const STD_string& object_label, float gradintegral_read, float gradintegral_phase, float gradintegral_slice, float maxgradstrength, double timestep, rampType type, double minrampduration) : SeqGradChanParallel(object_label) { Log odinlog(this,"build_seq"); float maxint=maxof3(fabs(gradintegral_read),fabs(gradintegral_phase),fabs(gradintegral_slice)); ODINLOG(odinlog,normalDebug) << "maxint=" << maxint << STD_endl; // first, initialize sub-pulses with max integral: readgrad =SeqGradTrapez(object_label+"_readgrad", maxint,maxgradstrength,readDirection, timestep,type,minrampduration); phasegrad=SeqGradTrapez(object_label+"_phasegrad",maxint,maxgradstrength,phaseDirection,timestep,type,minrampduration); slicegrad=SeqGradTrapez(object_label+"_slicegrad",maxint,maxgradstrength,sliceDirection,timestep,type,minrampduration); ODINLOG(odinlog,normalDebug) << "readgrad.get_gradintegral()=" << readgrad.get_gradintegral().printbody() << STD_endl; // second, adjust strength readgrad. set_strength(secureDivision(gradintegral_read, maxint)*readgrad.get_strength()); phasegrad.set_strength(secureDivision(gradintegral_phase,maxint)*phasegrad.get_strength()); slicegrad.set_strength(secureDivision(gradintegral_slice,maxint)*slicegrad.get_strength()); ODINLOG(odinlog,normalDebug) << "readgrad.get_gradintegral()=" << readgrad.get_gradintegral().printbody() << STD_endl; build_seq(); } SeqGradTrapezParallel::SeqGradTrapezParallel(const SeqGradTrapezParallel& sgtp) : SeqGradChanParallel(sgtp) { SeqGradTrapezParallel::operator = (sgtp); } SeqGradTrapezParallel::SeqGradTrapezParallel(const STD_string& object_label) : SeqGradChanParallel(object_label) { } SeqGradTrapezParallel& SeqGradTrapezParallel::operator = (const SeqGradTrapezParallel& sgtp) { SeqGradChanParallel::operator = (sgtp); readgrad =sgtp.readgrad; phasegrad=sgtp.phasegrad; slicegrad=sgtp.slicegrad; build_seq(); return *this; } void SeqGradTrapezParallel::build_seq() { clear(); (*this)+=readgrad/phasegrad/slicegrad; } odin-1.8.5/odinseq/seqgradwave.h0000644000175000017500000000715511322062345013531 00000000000000/*************************************************************************** seqgradwave.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADWAVE_H #define SEQGRADWAVE_H #include /** * @addtogroup odinseq * @{ */ /** * \brief Gradient Waveform * * This class represents a gradient object with an arbitrarily shaped gradient field * The physical gradient strengths of one data point is the product of the value * of the waveform at that point and the gradient strength of this object */ class SeqGradWave : public SeqGradChan { public: /** * Constructs a gradient waveform labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - gradduration: The duration of this gradient object * - maxgradstrength: The maximum gradient strength for this object * - waveform: The waveform that will be played out */ SeqGradWave(const STD_string& object_label,direction gradchannel, double gradduration, float maxgradstrength,const fvector& waveform); /** * Constructs a copy of 'sgw' */ SeqGradWave(const SeqGradWave& sgw); /** * Construct an empty gradient object with the given label */ SeqGradWave(const STD_string& object_label = "unnamedSeqGradWave"); /** * Specifies the waveform that will be used */ SeqGradWave& set_wave(const fvector& waveform); /** * Returns the waveform that will be used */ const fvector& get_wave() const {return wave;} /** * Returns the integral of the waveform time tmin to time tmax (relative to the starting point of the ramp) */ float get_integral(double tmin, double tmax) const; /** * Returns the number of digitised points for the waveform */ unsigned int get_npts() const; /** * Returns the number of digitised points for the waveform */ unsigned int size() const {return get_npts();} /** * Returns the sampling rate of the waveform */ double get_timestep() const {return secureDivision(get_gradduration(),double(get_npts()));} /** * Returns the i'th element of the waveform */ float operator [] (unsigned int i) const {return wave[i];} /** * Assignment operator that makes this gradient channel object become a copy of 'sgw' */ SeqGradWave& operator = (const SeqGradWave& sgw); protected: fvector wave; private: // overwriting virtual functions from SeqClass bool prep(); // overwriting virtual functions from SeqGradChan int get_wavesize() const; void resize(unsigned int newsize); SeqGradChan& get_subchan(double starttime, double endtime) const; STD_string get_grdpart(float matrixfactor) const; float get_integral() const {return get_integral(0.0,get_gradduration());} void check_wave(); }; /** @} */ #endif odin-1.8.5/odinseq/seqoperator.cpp0000644000175000017500000003563411322062345014122 00000000000000#include "seqoperator.h" #include "seqobj.h" #include "seqgradobj.h" #include "seqlist.h" #include "seqloop.h" #include "seqdec.h" #include "seqparallel.h" #include "seqgradchan.h" #include "seqgradchanlist.h" #include "seqgradchanparallel.h" void bad_parallel(const SeqGradInterface& s1, const SeqGradInterface& s2, direction chan) { Log odinlog("","bad_parallel"); ODINLOG(odinlog,errorLog) << s1.get_label() << "/" << s2.get_label() << " - same channel: " << directionLabel[chan] << STD_endl; } ///////////////////////////////////////////////////////////////// void SeqOperator::append_list2list(SeqObjList& dst, const SeqObjList& src) { if(src.gradrotmatrixvec.get_handled()) { dst+=src; // keep whole object in list for correct rotation } else { STD_list::const_iterator constiter; for(constiter=src.get_const_begin();constiter!=src.get_const_end();++constiter) { dst+=(**constiter); } } } SeqObjList& SeqOperator::create_SeqObjList_label(const STD_string& label1, const STD_string& label2, bool swap) { STD_string l1=label1; STD_string l2=label2; if(swap) { l1=label2; l2=label1; } SeqObjList* result=new SeqObjList(l1+"+"+l2); result->set_temporary(); return *result; } SeqObjList& SeqOperator::create_SeqObjList_obj(const SeqObjBase& s1, const SeqObjBase& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(!swap) result+=s1; result+=s2; if(swap) result+=s1; return result; } SeqObjList& SeqOperator::create_SeqObjList_list(const SeqObjList& s1, const SeqObjBase& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; append_list2list(result,s1); if(!swap) result+=s2; return result; } SeqGradChanList& SeqOperator::create_SeqGradChanList(const STD_string& label1, const STD_string& label2, bool swap) { STD_string l1=label1; STD_string l2=label2; if(swap) { l1=label2; l2=label1; } SeqGradChanList* result=new SeqGradChanList(l1+"+"+l2); result->set_temporary(); return *result; } SeqGradChanList& SeqOperator::create_SeqGradChanList(SeqGradChan& sgc) { SeqGradChanList* result=new SeqGradChanList("("+sgc.get_label()+")"); result->set_temporary(); (*result)+=sgc; return *result; } SeqGradChanParallel& SeqOperator::create_SeqGradChanParallel_concat(const STD_string& label1, const STD_string& label2, bool swap) { STD_string l1=label1; STD_string l2=label2; if(swap) { l1=label2; l2=label1; } SeqGradChanParallel* result=new SeqGradChanParallel(l1+"+"+l2); result->set_temporary(); return *result; } SeqParallel& SeqOperator::create_SeqParallel(const STD_string& label1, const STD_string& label2) { SeqParallel* result=new SeqParallel(label1+"/"+label2); result->set_temporary(); return *result; } SeqGradChanParallel& SeqOperator::create_SeqGradChanParallel_simultan(const STD_string& label1, const STD_string& label2) { SeqGradChanParallel* result=new SeqGradChanParallel(label1+"/"+label2); result->set_temporary(); return *result; } //////////////////////////////////////////////////////////////////////////////////////////// SeqObjList& SeqOperator::concat(const SeqObjBase& s1, const SeqObjBase& s2) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),false); result+=s1; result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqObjBase& s1, const SeqObjList& s2, bool swap) { return create_SeqObjList_list(s2,s1,!swap); } SeqObjList& SeqOperator::concat(const SeqObjBase& s1, const SeqObjLoop& s2, bool swap) { return create_SeqObjList_obj(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjBase& s1, const SeqDecoupling& s2, bool swap) { return create_SeqObjList_obj(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjBase& s1, const SeqParallel& s2, bool swap) { return create_SeqObjList_obj(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjBase& s1, SeqGradChan& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(!swap) result+=s1; result+=s2; if(swap) result+=s1; return result; } SeqObjList& SeqOperator::concat(const SeqObjBase& s1, SeqGradChanList& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(!swap) result+=s1; result+=s2; if(swap) result+=s1; return result; } SeqObjList& SeqOperator::concat(const SeqObjBase& s1, SeqGradChanParallel& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(!swap) result+=s1; result+=s2; if(swap) result+=s1; return result; } SeqObjList& SeqOperator::concat(const SeqObjList& s1, const SeqObjList& s2) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),false); append_list2list(result,s1); append_list2list(result,s2); return result; } SeqObjList& SeqOperator::concat(const SeqObjList& s1, const SeqObjLoop& s2, bool swap) { return create_SeqObjList_list(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjList& s1, const SeqDecoupling& s2, bool swap) { return create_SeqObjList_list(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjList& s1, const SeqParallel& s2, bool swap) { return create_SeqObjList_list(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjList& s1, SeqGradChan& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; append_list2list(result,s1); if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqObjList& s1, SeqGradChanList& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; append_list2list(result,s1); if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqObjList& s1, SeqGradChanParallel& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; append_list2list(result,s1); if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqObjLoop& s1, const SeqObjLoop& s2) { return create_SeqObjList_obj(s1,s2,false); } SeqObjList& SeqOperator::concat(const SeqObjLoop& s1, const SeqDecoupling& s2, bool swap) { return create_SeqObjList_obj(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjLoop& s1, const SeqParallel& s2, bool swap) { return create_SeqObjList_obj(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqObjLoop& s1, SeqGradChan& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqObjLoop& s1, SeqGradChanList& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqObjLoop& s1, SeqGradChanParallel& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqDecoupling& s1, const SeqDecoupling& s2) { return create_SeqObjList_obj(s1,s2,false); } SeqObjList& SeqOperator::concat(const SeqDecoupling& s1, const SeqParallel& s2, bool swap) { return create_SeqObjList_obj(s1,s2,swap); } SeqObjList& SeqOperator::concat(const SeqDecoupling& s1, SeqGradChan& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqDecoupling& s1, SeqGradChanList& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqDecoupling& s1, SeqGradChanParallel& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqParallel& s1, const SeqParallel& s2) { return create_SeqObjList_obj(s1,s2,false); } SeqObjList& SeqOperator::concat(const SeqParallel& s1, SeqGradChan& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqParallel& s1, SeqGradChanList& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqObjList& SeqOperator::concat(const SeqParallel& s1, SeqGradChanParallel& s2, bool swap) { SeqObjList& result=create_SeqObjList_label(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqGradChanList& SeqOperator::concat(SeqGradChan& s1, SeqGradChan& s2) { SeqGradChanList& result=create_SeqGradChanList(s1.get_label(),s2.get_label(),false); result+=s1; result+=s2; return result; } SeqGradChanList& SeqOperator::concat(SeqGradChan& s1, SeqGradChanList& s2, bool swap) { SeqGradChanList& result=create_SeqGradChanList(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqGradChanParallel& SeqOperator::concat(SeqGradChan& s1, SeqGradChanParallel& s2, bool swap) { SeqGradChanParallel& result=create_SeqGradChanParallel_concat(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqGradChanList& SeqOperator::concat(SeqGradChanList& s1, SeqGradChanList& s2) { SeqGradChanList& result=create_SeqGradChanList(s1.get_label(),s2.get_label(),false); result+=s1; result+=s2; return result; } SeqGradChanParallel& SeqOperator::concat(SeqGradChanList& s1, SeqGradChanParallel& s2, bool swap) { SeqGradChanParallel& result=create_SeqGradChanParallel_concat(s1.get_label(),s2.get_label(),swap); if(swap) result+=s2; result+=s1; if(!swap) result+=s2; return result; } SeqGradChanParallel& SeqOperator::concat(SeqGradChanParallel& s1, SeqGradChanParallel& s2) { SeqGradChanParallel& result=create_SeqGradChanParallel_concat(s1.get_label(),s2.get_label(),false); result+=s1; result+=s2; return result; } //////////////////////////////////////////////////////////////////////////////////////////// SeqParallel& SeqOperator::simultan(const SeqObjBase& s1, SeqGradObjInterface& s2) { SeqParallel& result=create_SeqParallel(s1.get_label(),s2.get_label()); result.set_pulsptr(&s1); result.set_gradptr(&s2); return result; } SeqParallel& SeqOperator::simultan(const SeqObjBase& s1, SeqGradChan& s2) { SeqParallel& result=create_SeqParallel(s1.get_label(),s2.get_label()); result.set_pulsptr(&s1); SeqGradChanParallel* sgcp=new SeqGradChanParallel("{"+s2.get_label()+"}"); sgcp->set_temporary(); (*sgcp)+=s2; result.set_gradptr((SeqGradObjInterface*)sgcp); return result; } SeqParallel& SeqOperator::simultan(const SeqObjBase& s1, SeqGradChanList& s2) { SeqParallel& result=create_SeqParallel(s1.get_label(),s2.get_label()); result.set_pulsptr(&s1); SeqGradChanParallel* sgcp=new SeqGradChanParallel("{"+s2.get_label()+"}"); sgcp->set_temporary(); (*sgcp)+=s2; result.set_gradptr((SeqGradObjInterface*)sgcp); return result; } SeqGradChanParallel& SeqOperator::simultan(SeqGradChan& s1, SeqGradChan& s2) { SeqGradChanParallel& result=create_SeqGradChanParallel_simultan(s1.get_label(),s2.get_label()); if(s1.get_channel()==s2.get_channel()) { bad_parallel(s1,s2,s1.get_channel()); return result; } result.set_gradchan(s1.get_channel(),&create_SeqGradChanList(s1)); result.set_gradchan(s2.get_channel(),&create_SeqGradChanList(s2)); return result; } SeqGradChanParallel& SeqOperator::simultan(SeqGradChan& s1, SeqGradChanList& s2) { SeqGradChanParallel& result=create_SeqGradChanParallel_simultan(s1.get_label(),s2.get_label()); if(s2.size() && s1.get_channel()==s2.get_channel()) { bad_parallel(s1,s2,s1.get_channel()); return result; } result.set_gradchan(s1.get_channel(),&create_SeqGradChanList(s1)); SeqGradChanList* s2_copy=new SeqGradChanList(s2); s2_copy->set_temporary(); result.set_gradchan(s2.get_channel(),s2_copy); return result; } SeqGradChanParallel& SeqOperator::simultan(SeqGradChan& s1, SeqGradChanParallel& s2) { SeqGradChanParallel* result=new SeqGradChanParallel(s2); result->set_label(s1.get_label()+"/"+s2.get_label()); result->set_temporary(); if(result->get_gradchan(s1.get_channel())) { bad_parallel(s1,s2,s1.get_channel()); return *result; } result->set_gradchan(s1.get_channel(),&create_SeqGradChanList(s1)); return (*result); } SeqGradChanParallel& SeqOperator::simultan(SeqGradChanList& s1, SeqGradChanList& s2) { Log odinlog("SeqOperator","simultan"); SeqGradChanParallel& result=create_SeqGradChanParallel_simultan(s1.get_label(),s2.get_label()); if(s1.size() && s2.size()) { if(s1.get_channel()==s2.get_channel()) { bad_parallel(s1,s2,s1.get_channel()); return result; } } ODINLOG(odinlog,normalDebug) << "chan1/2=" << s1.get_channel() << "/" << s2.get_channel() << STD_endl; SeqGradChanList* s1_copy=new SeqGradChanList(s1); s1_copy->set_temporary(); result.set_gradchan(s1.get_channel(),s1_copy); SeqGradChanList* s2_copy=new SeqGradChanList(s2); s2_copy->set_temporary(); result.set_gradchan(s2.get_channel(),s2_copy); return result; } SeqGradChanParallel& SeqOperator::simultan(SeqGradChanList& s1, SeqGradChanParallel& s2) { SeqGradChanParallel *result=new SeqGradChanParallel(s2); result->set_label(s1.get_label()+"/"+s2.get_label()); result->set_temporary(); if(result->get_gradchan(s1.get_channel())) { bad_parallel(s1,s2,s1.get_channel()); return *result; } else { SeqGradChanList* s1_copy=new SeqGradChanList(s1); s1_copy->set_temporary(); result->set_gradchan(s1.get_channel(),s1_copy); } return *result; } SeqGradChanParallel& SeqOperator::simultan(SeqGradChanParallel& s1, SeqGradChanParallel& s2) { SeqGradChanParallel *result=new SeqGradChanParallel(s2); result->set_label(s1.get_label()+"/"+s2.get_label()); result->set_temporary(); for(unsigned int cn=readDirection; cn <= sliceDirection; cn++) { direction chanNo=direction(cn); if(result->get_gradchan(chanNo) && s1.get_gradchan(chanNo)) { bad_parallel(s1,s2,chanNo); return *result; } else { if(s1.get_gradchan(chanNo)) { SeqGradChanList* s1_copy=new SeqGradChanList(*s1.get_gradchan(chanNo)); s1_copy->set_temporary(); result->set_gradchan(chanNo,s1_copy); } } } return *result; } odin-1.8.5/odinseq/seqoperator.h0000644000175000017500000003662611322062345013571 00000000000000/*************************************************************************** seqoperator.h - description ------------------- begin : Mon Apr 19 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQOPERATOR_H #define SEQOPERATOR_H #include // forward declarations class SeqObjBase; class SeqGradObjInterface; class SeqObjList; class SeqObjLoop; class SeqDecoupling; class SeqParallel; class SeqGradChan; class SeqGradChanList; class SeqGradChanParallel; /** * @ingroup odinseq_internals * A class for connecting sequence objects via operators. */ class SeqOperator : public SeqClass { public: static SeqObjList& concat(const SeqObjBase& s1, const SeqObjBase& s2); static SeqObjList& concat(const SeqObjBase& s1, const SeqObjList& s2, bool swap); static SeqObjList& concat(const SeqObjBase& s1, const SeqObjLoop& s2, bool swap); static SeqObjList& concat(const SeqObjBase& s1, const SeqDecoupling& s2, bool swap); static SeqObjList& concat(const SeqObjBase& s1, const SeqParallel& s2, bool swap); static SeqObjList& concat(const SeqObjBase& s1, SeqGradChan& s2, bool swap); static SeqObjList& concat(const SeqObjBase& s1, SeqGradChanList& s2, bool swap); static SeqObjList& concat(const SeqObjBase& s1, SeqGradChanParallel& s2, bool swap); static SeqObjList& concat(const SeqObjList& s1, const SeqObjList& s2); static SeqObjList& concat(const SeqObjList& s1, const SeqObjLoop& s2, bool swap); static SeqObjList& concat(const SeqObjList& s1, const SeqDecoupling& s2, bool swap); static SeqObjList& concat(const SeqObjList& s1, const SeqParallel& s2, bool swap); static SeqObjList& concat(const SeqObjList& s1, SeqGradChan& s2, bool swap); static SeqObjList& concat(const SeqObjList& s1, SeqGradChanList& s2, bool swap); static SeqObjList& concat(const SeqObjList& s1, SeqGradChanParallel& s2, bool swap); static SeqObjList& concat(const SeqObjLoop& s1, const SeqObjLoop& s2); static SeqObjList& concat(const SeqObjLoop& s1, const SeqDecoupling& s2, bool swap); static SeqObjList& concat(const SeqObjLoop& s1, const SeqParallel& s2, bool swap); static SeqObjList& concat(const SeqObjLoop& s1, SeqGradChan& s2, bool swap); static SeqObjList& concat(const SeqObjLoop& s1, SeqGradChanList& s2, bool swap); static SeqObjList& concat(const SeqObjLoop& s1, SeqGradChanParallel& s2, bool swap); static SeqObjList& concat(const SeqDecoupling& s1, const SeqDecoupling& s2); static SeqObjList& concat(const SeqDecoupling& s1, const SeqParallel& s2, bool swap); static SeqObjList& concat(const SeqDecoupling& s1, SeqGradChan& s2, bool swap); static SeqObjList& concat(const SeqDecoupling& s1, SeqGradChanList& s2, bool swap); static SeqObjList& concat(const SeqDecoupling& s1, SeqGradChanParallel& s2, bool swap); static SeqObjList& concat(const SeqParallel& s1, const SeqParallel& s2); static SeqObjList& concat(const SeqParallel& s1, SeqGradChan& s2, bool swap); static SeqObjList& concat(const SeqParallel& s1, SeqGradChanList& s2, bool swap); static SeqObjList& concat(const SeqParallel& s1, SeqGradChanParallel& s2, bool swap); static SeqGradChanList& concat(SeqGradChan& s1, SeqGradChan& s2); static SeqGradChanList& concat(SeqGradChan& s1, SeqGradChanList& s2, bool swap); static SeqGradChanParallel& concat(SeqGradChan& s1, SeqGradChanParallel& s2, bool swap); static SeqGradChanList& concat(SeqGradChanList& s1, SeqGradChanList& s2); static SeqGradChanParallel& concat(SeqGradChanList& s1, SeqGradChanParallel& s2, bool swap); static SeqGradChanParallel& concat(SeqGradChanParallel& s1, SeqGradChanParallel& s2); static SeqParallel& simultan(const SeqObjBase& s1, SeqGradObjInterface& s2); static SeqParallel& simultan(const SeqObjBase& s1, SeqGradChan& s2); static SeqParallel& simultan(const SeqObjBase& s1, SeqGradChanList& s2); static SeqGradChanParallel& simultan(SeqGradChan& s1, SeqGradChan& s2); static SeqGradChanParallel& simultan(SeqGradChan& s1, SeqGradChanList& s2); static SeqGradChanParallel& simultan(SeqGradChan& s1, SeqGradChanParallel& s2); static SeqGradChanParallel& simultan(SeqGradChanList& s1, SeqGradChanList& s2); static SeqGradChanParallel& simultan(SeqGradChanList& s1, SeqGradChanParallel& s2); static SeqGradChanParallel& simultan(SeqGradChanParallel& s1, SeqGradChanParallel& s2); private: static void append_list2list(SeqObjList& dst, const SeqObjList& src); static SeqObjList& create_SeqObjList_label(const STD_string& label1, const STD_string& label2, bool swap); static SeqObjList& create_SeqObjList_obj(const SeqObjBase& s1, const SeqObjBase& s2, bool swap); static SeqObjList& create_SeqObjList_list(const SeqObjList& s1, const SeqObjBase& s2, bool swap); static SeqGradChanList& create_SeqGradChanList(const STD_string& label1, const STD_string& label2, bool swap); static SeqGradChanList& create_SeqGradChanList(SeqGradChan& sgc); static SeqGradChanParallel& create_SeqGradChanParallel_concat(const STD_string& label1, const STD_string& label2, bool swap); static SeqParallel& create_SeqParallel(const STD_string& label1, const STD_string& label2); static SeqGradChanParallel& create_SeqGradChanParallel_simultan(const STD_string& label1, const STD_string& label2); }; inline SeqObjList& operator + (const SeqObjBase& s1, const SeqObjBase& s2){return SeqOperator::concat(s1,s2);} inline SeqObjList& operator + (const SeqObjBase& s1, const SeqObjList& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjBase& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjBase& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjBase& s1, const SeqParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjBase& s1, SeqGradChan& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjBase& s1, SeqGradChanList& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjBase& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjList& s1, const SeqObjBase& s2){return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqObjList& s1, const SeqObjList& s2) {return SeqOperator::concat(s1,s2);} inline SeqObjList& operator + (const SeqObjList& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjList& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjList& s1, const SeqParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjList& s1, SeqGradChan& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjList& s1, SeqGradChanList& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjList& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjLoop& s1, const SeqObjBase& s2){return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqObjLoop& s1, const SeqObjList& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqObjLoop& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s1,s2);} inline SeqObjList& operator + (const SeqObjLoop& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjLoop& s1, const SeqParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjLoop& s1, SeqGradChan& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjLoop& s1, SeqGradChanList& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqObjLoop& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqDecoupling& s1, const SeqObjBase& s2){return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqDecoupling& s1, const SeqObjList& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqDecoupling& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqDecoupling& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s1,s2);} inline SeqObjList& operator + (const SeqDecoupling& s1, const SeqParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqDecoupling& s1, SeqGradChan& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqDecoupling& s1, SeqGradChanList& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqDecoupling& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqParallel& s1, const SeqObjBase& s2){return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqParallel& s1, const SeqObjList& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqParallel& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqParallel& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (const SeqParallel& s1, const SeqParallel& s2) {return SeqOperator::concat(s1,s2);} inline SeqObjList& operator + (const SeqParallel& s1, SeqGradChan& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqParallel& s1, SeqGradChanList& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (const SeqParallel& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (SeqGradChan& s1, const SeqObjBase& s2){return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChan& s1, const SeqObjList& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChan& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChan& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChan& s1, const SeqParallel& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqGradChanList& operator + (SeqGradChan& s1, SeqGradChan& s2) {return SeqOperator::concat(s1,s2);} inline SeqGradChanList& operator + (SeqGradChan& s1, SeqGradChanList& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqGradChanParallel& operator + (SeqGradChan& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (SeqGradChanList& s1, const SeqObjBase& s2){return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanList& s1, const SeqObjList& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanList& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanList& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanList& s1, const SeqParallel& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqGradChanList& operator + (SeqGradChanList& s1, SeqGradChan& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqGradChanList& operator + (SeqGradChanList& s1, SeqGradChanList& s2) {return SeqOperator::concat(s1,s2);} inline SeqGradChanParallel& operator + (SeqGradChanList& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2,false);} inline SeqObjList& operator + (SeqGradChanParallel& s1, const SeqObjBase& s2){return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanParallel& s1, const SeqObjList& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanParallel& s1, const SeqObjLoop& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanParallel& s1, const SeqDecoupling& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqObjList& operator + (SeqGradChanParallel& s1, const SeqParallel& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqGradChanParallel& operator + (SeqGradChanParallel& s1, SeqGradChan& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqGradChanParallel& operator + (SeqGradChanParallel& s1, SeqGradChanList& s2) {return SeqOperator::concat(s2,s1,true);} inline SeqGradChanParallel& operator + (SeqGradChanParallel& s1, SeqGradChanParallel& s2) {return SeqOperator::concat(s1,s2);} inline SeqParallel& operator / (const SeqObjBase& s1, SeqGradObjInterface& s2) {return SeqOperator::simultan(s1,s2);} inline SeqParallel& operator / (SeqGradObjInterface& s1, const SeqObjBase& s2) {return SeqOperator::simultan(s2,s1);} inline SeqParallel& operator / (const SeqObjBase& s1, SeqGradChan& s2) {return SeqOperator::simultan(s1,s2);} inline SeqParallel& operator / (SeqGradChan& s1, const SeqObjBase& s2) {return SeqOperator::simultan(s2,s1);} inline SeqParallel& operator / (const SeqObjBase& s1, SeqGradChanList& s2) {return SeqOperator::simultan(s1,s2);} inline SeqParallel& operator / (SeqGradChanList& s1, const SeqObjBase& s2) {return SeqOperator::simultan(s2,s1);} inline SeqGradChanParallel& operator / (SeqGradChan& s1, SeqGradChan& s2) {return SeqOperator::simultan(s1,s2);} inline SeqGradChanParallel& operator / (SeqGradChan& s1, SeqGradChanList& s2) {return SeqOperator::simultan(s1,s2);} inline SeqGradChanParallel& operator / (SeqGradChanList& s1, SeqGradChan& s2) {return SeqOperator::simultan(s2,s1);} inline SeqGradChanParallel& operator / (SeqGradChan& s1, SeqGradChanParallel& s2) {return SeqOperator::simultan(s1,s2);} inline SeqGradChanParallel& operator / (SeqGradChanParallel& s1, SeqGradChan& s2) {return SeqOperator::simultan(s2,s1);} inline SeqGradChanParallel& operator / (SeqGradChanList& s1, SeqGradChanList& s2) {return SeqOperator::simultan(s1,s2);} inline SeqGradChanParallel& operator / (SeqGradChanList& s1, SeqGradChanParallel& s2) {return SeqOperator::simultan(s1,s2);} inline SeqGradChanParallel& operator / (SeqGradChanParallel& s1, SeqGradChanList& s2) {return SeqOperator::simultan(s2,s1);} inline SeqGradChanParallel& operator / (SeqGradChanParallel& s1, SeqGradChanParallel& s2) {return SeqOperator::simultan(s1,s2);} #endif odin-1.8.5/odinseq/seqdiffweight.h0000644000175000017500000002001711322062345014041 00000000000000/*************************************************************************** seqdiffweight.h - description ------------------- begin : Wed Feb 12 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDIFFWEIGHT_H #define SEQDIFFWEIGHT_H #include #include #include #include #include #include /** * @addtogroup odinseq * @{ */ /** * * \brief Diffusion Weighting * * A bipolar gradient pulse for diffusion weighting * * The b-value and the properties of the gradient pulses are connected through the equation * * b = gamma^2 * delta^2 ( Delta - delta/3 ) G^2 * * - b: b-value * - gamma: gyromagnetic ratio * - delta: gradient pulse duration * - Delta: gradient pulse separation, the duration of midpart (sequence part which is enclosed by the two gradient) is considered here * - G: gradient strength * * The order in which the series of b-values is played out can be cyclically * reordered by using the vector which is returned by the get_reorder_vector() * function: At each iteration of this vector, the b-values are exchanged cyclically. */ class SeqDiffWeight : public SeqObjList, public SeqSimultanVector, public virtual SeqGradInterface { public: /** * Constructs a bipolar gradient pulse labeled 'object_label' with the following properties: * - bvals: The b-values for diffusion weighting, a postive value means that the first * gradient pulse will have positive polarity and the second gradient pulse a negative polarity. * These polarities are swapped in case of a negative b-value. * - maxgradstrength: The maximum gradient strength to use for the maximum b-value * - midpart: The sequence part which will be enclosed by the two gradient pulses. * - chan: The gradient channel for the gradient pulses. * - stejskalTanner: If set to 'true', both gradients will have the same polarity * - nucleus: The nucleus for which the gradient pulses will be calculated */ SeqDiffWeight(const STD_string& object_label, const fvector& bvals, float maxgradstrength, const SeqObjBase& midpart, direction chan, bool stejskalTanner=false, const STD_string& nucleus = "" ); /** * Constructs a bipolar gradient pulse labeled 'object_label' with the following properties: * - ndir: Number of uniformly ditributed directions * - bvals: The b-values for diffusion weighting, a postive value means that the first * gradient pulse will have positive polarity and the second gradient pulse a negative polarity. * These polarities are swapped in case of a negative b-value. * - maxgradstrength: The maximum gradient strength to use for the maximum b-value * - midpart: The sequence part which will be enclosed by the two gradient pulses. * - baseline_rep: Repetition rate of the baseline (b=0) scan. Not repeated if zero. * - stejskalTanner: If set to 'true', both gradients will have the same polarity * - nucleus: The nucleus for which the gradient pulses will be calculated */ SeqDiffWeight(const STD_string& object_label, unsigned int ndir, const fvector& bvals, float maxgradstrength, const SeqObjBase& midpart, unsigned int baseline_rep=0, bool stejskalTanner=false, const STD_string& nucleus = "" ); /** * Default constructor */ SeqDiffWeight(const STD_string& object_label = "unnamedSeqDiffWeight" ); /** * Copy constructor */ SeqDiffWeight(const SeqDiffWeight& sgdw) {SeqDiffWeight::operator = (sgdw);} /** * Assignment operator */ SeqDiffWeight& operator = (const SeqDiffWeight& sgdw); /** * Returns the first gradient lobe */ const SeqGradInterface& get_grad1() const {return par1;} /** * Returns the second gradient lobe */ const SeqGradInterface& get_grad2() const {return par2;} /** * Returns the duration of the first gradient lobe */ double get_grad1_duration() const {return par1.get_duration();} /** * Returns the duration of the second gradient lobe */ double get_grad2_duration() const {return par2.get_duration();} /** * Returns the duration of the part in the middle between the two gradient lobes */ double get_midpart_duration() const {return middle_part.get_duration();} /** * Returns the b-vectors used in subsequent order. */ const darray& get_b_vectors() const {return b_vectors_cache;} // overloading virtual function from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); SeqGradInterface& invert_strength(); float get_strength() const; fvector get_gradintegral() const; double get_gradduration() const; SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); // final overrider of virtual functions from SeqClass void clear_container() {SeqObjList::clear(); SeqSimultanVector::clear();} // implemented virtual functions from SeqVector bool is_qualvector() const {return false;} private: void build_seq(); SeqGradVectorPulse pfg1[n_directions]; SeqGradVectorPulse pfg2[n_directions]; SeqParallel par1; SeqParallel par2; SeqObjList middle_part; darray b_vectors_cache; }; ////////////////////////////////////////////////////////////////////////////////////////// /** * * \brief Flow-Compensated Diffusion Weighting * * A flow-compensated gradient train for diffusion weighting * */ class SeqDiffWeightFlowComp : public SeqGradChanList, public SeqSimultanVector { public: /** * Constructs a flow-compensated gradient train labeled 'object_label' with the following properties: * - bvals: The b-values for diffusion weighting, a postive value means that the first * gradient pulse will have positive polarity and the second gradient pulse a negative polarity. * These polarities are swapped in case of a negative b-value * - maxgradstrength: The maximum gradient strength to use for the maximum b-value * - chan: The gradient channel for the gradient pulses * - stimdelay: Extra delay between gradient sub-pulses to avoid stimulation * - nucleus: The nucleus for which the gradient pulses will be calculated */ SeqDiffWeightFlowComp(const STD_string& object_label, const fvector& bvals, float maxgradstrength, direction chan, double stimdelay=1.0, const STD_string& nucleus = "" ); /** * Default constructor */ SeqDiffWeightFlowComp(const STD_string& object_label = "unnamedSeqDiffWeightFlowComp" ); /** * Copy constructor */ SeqDiffWeightFlowComp(const SeqDiffWeightFlowComp& sgdwfc) {SeqDiffWeightFlowComp::operator = (sgdwfc);} /** * Assignment operator */ SeqDiffWeightFlowComp& operator = (const SeqDiffWeightFlowComp& sgdwfc); // final overrider of virtual functions from SeqClass void clear_container() {SeqGradChanList::clear(); SeqSimultanVector::clear();} // implemented virtual functions from SeqVector bool is_qualvector() const {return false;} private: void build_seq(); SeqGradVectorPulse pfg1; SeqGradVectorPulse pfg2; SeqGradVectorPulse pfg3; SeqGradDelay delay; }; /** @} */ #endif odin-1.8.5/odinseq/seqdriver.h0000644000175000017500000000654211322062345013223 00000000000000/*************************************************************************** seqdriver.h - description ------------------- begin : Sat Apr 3 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQDRIVER_H #define SEQDRIVER_H #include #include class SeqDriverBase : public virtual SeqClass { public: SeqDriverBase() {} virtual ~SeqDriverBase() {} virtual odinPlatform get_driverplatform() const = 0; }; ///////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The interface class for all driver (platform specific) classes */ template class SeqDriverInterface : public SeqClass { public: typedef D* (*create_driver_callback)(); SeqDriverInterface(const STD_string& driverlabel="unnamedSeqDriverInterface") : current_driver(0) { set_label(driverlabel); } virtual ~SeqDriverInterface(){ if(current_driver) delete current_driver; } SeqDriverInterface& operator = (const SeqDriverInterface& di) { SeqClass::operator = (di); if(current_driver) delete current_driver; current_driver=0; if(di.current_driver) current_driver=di.current_driver->clone_driver(); return *this; } D& operator * () {return *get_driver();} D* operator -> () {return get_driver();} private: // overwriting virtual functions from SeqClass bool prep() {return bool(get_driver());} // make sure correct driver is loaded D* get_driver() { odinPlatform current_pf=SeqPlatformProxy::get_current_platform(); if(!current_driver) allocate_driver(); else { odinPlatform driver_platform=current_driver->get_driverplatform(); if(driver_platform!=current_pf) { delete current_driver; allocate_driver(); } } if(!current_driver) { STD_cerr << "ERROR: " << get_label() << ": Driver missing for platform " << SeqPlatformProxy::get_platform_str(current_pf) << STD_endl; } if(current_driver->get_driverplatform()!=current_pf) { STD_string drvplat(SeqPlatformProxy::get_possible_platforms()[current_driver->get_driverplatform()]); STD_cerr << "ERROR: " << get_label() << ": Driver has wrong platform signature " << drvplat << ", but expected " << SeqPlatformProxy::get_platform_str(current_pf) << STD_endl; } return current_driver; } void allocate_driver() { current_driver=pfinterface->create_driver(current_driver); if(current_driver) current_driver->set_label(get_label()); } SeqPlatformProxy pfinterface; D* current_driver; }; #endif odin-1.8.5/odinseq/seqgradwave.cpp0000644000175000017500000001046011322062345014055 00000000000000#include "seqgradwave.h" SeqGradWave::SeqGradWave(const STD_string& object_label,direction gradchannel, double gradduration, float maxgradstrength,const fvector& waveform) : SeqGradChan(object_label,gradchannel,maxgradstrength,gradduration) { set_wave(waveform); } SeqGradWave::SeqGradWave(const SeqGradWave& sgw) { SeqGradWave::operator = (sgw); } SeqGradWave::SeqGradWave(const STD_string& object_label) : SeqGradChan(object_label) { } SeqGradWave& SeqGradWave::set_wave(const fvector& waveform) { Log odinlog(this,"set_wave"); wave=waveform; ODINLOG(odinlog,normalDebug) << "wave(" << wave.length() << ")" << STD_endl; return *this; } float SeqGradWave::get_integral(double tmin, double tmax) const { Log odinlog(this,"get_integral"); double dur=get_gradduration(); ODINLOG(odinlog,normalDebug) << "dur=" << dur << STD_endl; if(tmin<0.0) tmin=0.0; if(tmin>dur) tmin=dur; if(tmax<0.0) tmax=0.0; if(tmax>dur) tmax=dur; ODINLOG(odinlog,normalDebug) << "dur/tmin/tmax=" << dur << "/" << tmin << "/" << tmax << STD_endl; double len=double(wave.length()); unsigned int startindex=(unsigned int)(secureDivision(tmin,dur)*len+0.5); unsigned int endindex =(unsigned int)(secureDivision(tmax,dur)*len+0.5); ODINLOG(odinlog,normalDebug) << "len/startindex/endindex=" << len << "/" << startindex << "/" << endindex << STD_endl; float integral=wave.range(startindex,endindex).sum(); ODINLOG(odinlog,normalDebug) << "sum=" << integral << STD_endl; integral= secureDivision(integral * get_strength() * dur,len); ODINLOG(odinlog,normalDebug) << "integral=" << integral << STD_endl; return integral; } unsigned int SeqGradWave::get_npts() const { return wave.length(); } SeqGradWave& SeqGradWave::operator = (const SeqGradWave& sgw) { Log odinlog(this,"operator="); SeqGradChan::operator = (sgw); wave=sgw.wave; ODINLOG(odinlog,normalDebug) << "wave(" << wave.length() << ")" << STD_endl; return *this; } STD_string SeqGradWave::get_grdpart(float matrixfactor) const { return graddriver->get_wave_program(get_strength(),matrixfactor); } bool SeqGradWave::prep() { Log odinlog(this,"prep"); if(!SeqGradChan::prep()) return false; check_wave(); return graddriver->prep_wave(get_strength(),get_grdfactors_norot(),get_gradduration(),wave); } SeqGradChan& SeqGradWave::get_subchan(double starttime, double endtime) const { Log odinlog(this,"get_subchan"); double startindex_round=starttime/get_gradduration()*double(wave.length())*1000.0+0.5; double endindex_round= endtime/get_gradduration()*double(wave.length())*1000.0+0.5; unsigned int startindex=(unsigned int)(startindex_round)/1000; unsigned int endindex =(unsigned int)(endindex_round)/1000; ODINLOG(odinlog,normalDebug) << "startindex/endindex=" << startindex << "/" << endindex << STD_endl; JDXfloatArr subwave(wave.range(startindex,endindex)); if(!subwave.length()) { subwave.resize(1); if(wave.length()>startindex) subwave[0]=wave[startindex]; } ODINLOG(odinlog,normalDebug) << "starttime/endtime/length=" << starttime << "/" << endtime << "/" << subwave.length() << STD_endl; SeqGradWave* sgw= new SeqGradWave(STD_string(get_label())+"_("+ftos(starttime)+"-"+ftos(endtime)+")", get_channel(),endtime-starttime,get_strength(),subwave); sgw->prep(); // we have to call prep() manually here because prep_all() has already been executed sgw->set_temporary(); return *sgw; } int SeqGradWave::get_wavesize() const { Log odinlog(this,"get_wavesize"); ODINLOG(odinlog,normalDebug) << "wavesize=" << wave.length() << STD_endl; return wave.length(); } void SeqGradWave::resize(unsigned int newsize) { Log odinlog(this,"resize"); ODINLOG(odinlog,normalDebug) << "to " << newsize << STD_endl; wave.interpolate(newsize); check_wave(); graddriver->update_wave(wave); } void SeqGradWave::check_wave() { Log odinlog(this,"check_wave"); float max=0.0; for(unsigned int i=0; i 1.0) {if(fabs(wave[i])>max) max=fabs(wave[i]); wave[i]= 1.0;} if(wave[i]<-1.0) {if(fabs(wave[i])>max) max=fabs(wave[i]); wave[i]=-1.0;} } if(max>0.0) ODINLOG(odinlog,warningLog) << "Corrected SeqGradWave value of " << max << " to stay within [-1,1] limits" << STD_endl; } odin-1.8.5/odinseq/seqacqdeph.h0000644000175000017500000000565611322062345013342 00000000000000/*************************************************************************** seqacqdeph.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQACQDEPH_H #define SEQACQDEPH_H #include #include class SeqAcqInterface; // forward declaration /** * @addtogroup odinseq * @{ */ /** * This enum is used to specify the type of the pre-dephasing or post-rephasing gradient: * - FID: It will have opposite polarity * - spinEcho: It will have the same polarity * - rephase: Gradient pulse to rephase acquisition gradients */ enum dephaseMode {FID,spinEcho,rephase}; ////////////////////////////////////////////////////////////////////////// /** * \brief Pre-read dephasing * * This class provides a pre-dephasing or post-rephasing gradient pulse for acquisition objects */ class SeqAcqDeph : public SeqGradChanParallel { public: /** * Constructs a read dephase gradient pulse labeled 'object_label' with the following properties: * - acq: The acquisition object for which the dephasing should be performed * - polarity: Specifies whether the gradient will have balanced (FID) or * inverted polarity (spinEcho). */ SeqAcqDeph(const STD_string& object_label,const SeqAcqInterface& acq, dephaseMode mode = FID); /** * Constructs a copy of 'sad' */ SeqAcqDeph(const SeqAcqDeph& sad); /** * Construct an empty read dephase gradient pulse with the given label */ SeqAcqDeph(const STD_string& object_label = "unnamedSeqAcqDeph"); /** * Assignment operator that makes this object become a copy of 'sad' */ SeqAcqDeph& operator = (const SeqAcqDeph& sad); /** * returns vector to iterate through different segments in multi-shot EPI */ const SeqVector& get_epi_segment_vector() const; /** * returns vector to iterate through different GRAPPA interleaves in parallel-imaging EPI */ const SeqVector& get_epi_reduction_vector() const; private: void common_init(); SeqVector dummyvec; Handler segvec; }; /** @} */ #endif odin-1.8.5/odinseq/seqgradpulse.cpp0000644000175000017500000000463411322062345014251 00000000000000#include "seqgradpulse.h" SeqGradConstPulse::SeqGradConstPulse(const STD_string& object_label,direction gradchannel, float gradstrength, float gradduration) : SeqGradChanList(object_label), constgrad(object_label+"_grad",gradchannel,gradstrength,gradduration), offgrad(object_label+"_off",gradchannel,0.0){ SeqGradConstPulse::set_strength(gradstrength); // set duration of offgrad, do NOT call virtual functions in constructor (*this)+= constgrad + offgrad; } SeqGradConstPulse::SeqGradConstPulse(const SeqGradConstPulse& sgcp) { SeqGradConstPulse::operator = (sgcp); } SeqGradConstPulse::SeqGradConstPulse(const STD_string& object_label) : SeqGradChanList(object_label) {} SeqGradConstPulse& SeqGradConstPulse::operator = (const SeqGradConstPulse& sgcp) { SeqGradChanList::operator = (sgcp); constgrad=sgcp.constgrad; offgrad=sgcp.offgrad; clear(); (*this)+= constgrad + offgrad; return *this; } SeqGradInterface& SeqGradConstPulse::set_strength(float gradstrength) { constgrad.set_strength(gradstrength); offgrad.set_duration(systemInfo->get_grad_switch_time(constgrad.get_strength())); return *this; } ///////////////////////////////////////////////////////////////////////////////// SeqGradVectorPulse::SeqGradVectorPulse(const STD_string& object_label, direction gradchannel, float maxgradstrength, const fvector& trimarray, float gradduration) : SeqGradChanList(object_label), vectorgrad(object_label+"_grad",gradchannel,maxgradstrength,trimarray,gradduration), offgrad(object_label+"_off",gradchannel,0.0){ SeqGradVectorPulse::set_strength(maxgradstrength); // set duration of offgrad, do NOT call virtual functions in constructor (*this)+= vectorgrad + offgrad; } SeqGradVectorPulse::SeqGradVectorPulse(const SeqGradVectorPulse& sgvp) { SeqGradVectorPulse::operator = (sgvp); } SeqGradVectorPulse::SeqGradVectorPulse(const STD_string& object_label) : SeqGradChanList(object_label) { } SeqGradVectorPulse& SeqGradVectorPulse::operator = (const SeqGradVectorPulse& sgvp) { SeqGradChanList::operator = (sgvp); vectorgrad=sgvp.vectorgrad; offgrad=sgvp.offgrad; clear(); (*this)+= vectorgrad + offgrad; return *this; } SeqGradInterface& SeqGradVectorPulse::set_strength(float gradstrength) { vectorgrad.set_strength(gradstrength); offgrad.set_duration(systemInfo->get_grad_switch_time(vectorgrad.get_strength())); return *this; } odin-1.8.5/odinseq/seqcounter.h0000644000175000017500000001441611322062345013406 00000000000000/*************************************************************************** seqcounter.h - description ------------------- begin : Fri Jan 19 2007 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQCOUNTER_H #define SEQCOUNTER_H #include #include #include /** * @addtogroup odinseq_internals * @{ */ class SeqCounter; // forward declaration class SeqObjList; // forward declaration /** * The base class for platform specific drivers of counters objects to iterate over vectors */ class SeqCounterDriver : public SeqDriverBase { public: SeqCounterDriver() {} virtual ~SeqCounterDriver() {} /** * Will be called once during prepping the sequence */ virtual bool prep_driver() = 0; /** * Function to update driver internals which is called before * the driver is queried for actions, seqlist can be zero */ virtual void update_driver(const SeqCounter* counter, const SeqObjList* seqlist, const List* vectors) const = 0; /** * Duration the loop itself takes before iteration is started */ virtual double get_preduration () const = 0; /** * Duration the loop itself takes after its kernel is iterated */ virtual double get_postduration() const = 0; /** * Duration the loop itself takes before each iteration */ virtual double get_preduration_inloop() const = 0; /** * Duration the loop itself takes after each iteration */ virtual double get_postduration_inloop() const = 0; /** * Asks driver whether a program has to be created at all for the given context and loopkernel, * useful to avoid 'empty' loops in the program */ virtual bool create_program(programContext& context, const STD_string& loopkernel) const = 0; /** * Returns the head of the loop, i.e. code before the loop kernel */ virtual STD_string get_program_head(programContext& context, const STD_string& loopkernel, unsigned int times) const = 0; /** * Returns the tail of the loop, i.e. code after the loop kernel */ virtual STD_string get_program_tail(programContext& context, const STD_string& loopkernel, unsigned int times) const = 0; /** * Returns the head of the loop, i.e. code before the loop kernel if the loop is unrolled */ virtual STD_string get_program_head_unrolled(programContext& context, unsigned int index) const = 0; /** * Returns commands to iterate vectors manually */ virtual STD_string get_program_iterator(programContext& context) const = 0; /** * Will be called before vectors are prepped for the current iteration */ virtual void pre_vecprepevent (eventContext& context) const = 0; /** * Will be called after vectors are prepped for the current iteration * If repcounter>=0, the repetition display of the platform will be updated to 'repcounter' */ virtual void post_vecprepevent(eventContext& context, int repcounter) const = 0; /** * Will be called if any attribute of the counter was changed */ virtual void outdate_cache() const = 0; /** * Asks driver whether the loop should be unrolled i.e. whether each iteration will be * explicitely written to the program, seqlist can be zero */ virtual bool unroll_program(const SeqCounter* counter, const SeqObjList* seqlist, const List* vectors, programContext& context) const = 0; /** * Return an exact copy of this driver */ virtual SeqCounterDriver* clone_driver() const = 0; }; /////////////////////////////////////////////////////////////////////////////////// /** * The base class for objects iterating through vectors by incremental counting */ class SeqCounter : public Handled, public virtual SeqTreeObj { public: /** * Construct an empty counter object with the given label */ SeqCounter(const STD_string& object_label = "unnamedSeqCounter"); /** * Constructs a copy of 'sl' */ SeqCounter(const SeqCounter& sc); virtual ~SeqCounter() {} /** * Assignment operator */ SeqCounter& operator = (const SeqCounter& sc); /** * The number of iterations of this counter object */ virtual int get_times() const; /** * Adds a vector to this counter */ virtual void add_vector(const SeqVector& seqvector); // counter functions int get_counter() const {return counter;} // also used by SeqVector bool counter_is_active() const {return counter!=-1;} void init_counter(unsigned int start=0) const; void increment_counter() const {counter++;} void disable_counter() const {counter=-1;} // helper functions (also used by platform drivers) bool prep_veciterations() const; protected: // helpers to reduce template code mutable STD_list::const_iterator veciter; STD_list::const_iterator get_vecbegin() const {return vectors.get_const_begin();} STD_list::const_iterator get_vecend() const {return vectors.get_const_end();} unsigned int n_vectors() const {return vectors.size();} List vectors; void clear_vectorlist() {vectors.clear();} mutable SeqDriverInterface counterdriver; // overwriting virtual functions from SeqClass bool prep(); void clear_container(); private: friend class SeqVector; // helper functions (also used by SeqVector) virtual bool unroll_program(programContext& context) const {return true;} void set_vechandler_for_all() const; mutable int counter; }; /** @} */ #endif odin-1.8.5/odinseq/seqtrigg.h0000644000175000017500000001423011363773555013056 00000000000000/*************************************************************************** seqtrigg.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQTRIGG_H #define SEQTRIGG_H #include #include ////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The base class for platform specific drivers of external triggers */ class SeqTriggerDriver : public SeqDriverBase { public: SeqTriggerDriver() {} virtual ~SeqTriggerDriver() {} virtual double get_postduration() const = 0; virtual bool prep_exttrigger(double duration) = 0; virtual bool prep_halttrigger() = 0; virtual bool prep_snaptrigger(const STD_string& snapshot_fname) = 0; virtual bool prep_resettrigger() = 0; virtual void event(eventContext& context, double start) const = 0; virtual STD_string get_program(programContext& context) const = 0; virtual SeqTriggerDriver* clone_driver() const = 0; }; ////////////////////////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * * \brief Output trigger * * Insert triggers for external devices into the sequence. */ class SeqTrigger : public SeqObjBase { public: /** * Constructs a trigger labeled 'object_label' with the following properties: * - duration: The duration of the trigger pulse */ SeqTrigger(const STD_string& object_label, double duration); /** * Default Constructor */ SeqTrigger(const STD_string& object_label = "unnamedSeqTrigger"); /** * Constructs a trigger which is a copy of 'st' */ SeqTrigger(const SeqTrigger& st) {SeqTrigger::operator = (st);} /** * This assignment operator will make this object become an exact copy of 'st'. */ SeqTrigger& operator = (const SeqTrigger& st); // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; double get_duration() const; unsigned int event(eventContext& context) const; private: // overwriting virtual functions from SeqClass bool prep(); mutable SeqDriverInterface triggdriver; double triggdur; }; ////////////////////////////////////////////////////////////////////// /** * * \brief Input trigger * * Halt sequence until an input trigger is received (e.g. cardiac gating). */ class SeqHalt : public SeqObjBase { public: /** * Constructs a trigger labeled 'object_label' */ SeqHalt(const STD_string& object_label = "unnamedSeqHalt"); /** * Constructs a trigger which is a copy of 'sh' */ SeqHalt(const SeqHalt& sh) {SeqHalt::operator = (sh);} /** * This assignment operator will make this object become an exact copy of 'sh'. */ SeqHalt& operator = (const SeqHalt& sh); // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; double get_duration() const; unsigned int event(eventContext& context) const; private: // overwriting virtual functions from SeqClass bool prep(); mutable SeqDriverInterface triggdriver; }; ////////////////////////////////////////////////////////////////////// /** * * \brief Magnetization snapshot * * This class is used to trigger a snapshot of the current magnetization * during simulation of the sequence. */ class SeqSnapshot : public SeqObjBase { public: /** * Constructs a trigger labeled 'object_label' with the following properties: * - snapshot_fname: The file name where the magnetization will be stored consecutively in float format. */ SeqSnapshot(const STD_string& object_label, const STD_string& snapshot_fname); /** * Default Constructor */ SeqSnapshot(const STD_string& object_label = "unnamedSeqSnapshot"); /** * Constructs a snapshot trigger which is a copy of 'ss' */ SeqSnapshot(const SeqSnapshot& ss) {SeqSnapshot::operator = (ss);} /** * This assignment operator will make this object become an exact copy of 'ss'. */ SeqSnapshot& operator = (const SeqSnapshot& ss); // overloading virtual function from SeqTreeObj double get_duration() const {return 0.0;} unsigned int event(eventContext& context) const; private: // overwriting virtual functions from SeqClass bool prep(); STD_string magn_fname; mutable SeqDriverInterface triggdriver; }; ////////////////////////////////////////////////////////////////////// /** * * \brief Magnetization reset * * This class is used to reset the current magnetization to its initial equilibrium state * during simulation of the sequence. */ class SeqMagnReset : public SeqObjBase { public: /** * Constructs a trigger labeled 'object_label' */ SeqMagnReset(const STD_string& object_label = "unnamedSeqMagnReset"); /** * Constructs a snapshot trigger which is a copy of 'smr' */ SeqMagnReset(const SeqMagnReset& smr) {SeqMagnReset::operator = (smr);} /** * This assignment operator will make this object become an exact copy of 'smr'. */ SeqMagnReset& operator = (const SeqMagnReset& smr); // overloading virtual function from SeqTreeObj double get_duration() const {return 0.0;} unsigned int event(eventContext& context) const; private: // overwriting virtual functions from SeqClass bool prep(); mutable SeqDriverInterface triggdriver; }; /** @} */ #endif odin-1.8.5/odinseq/seqdriver_standalone.cpp0000644000175000017500000000241011322062345015754 00000000000000#ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif #ifdef STANDALONE_PLUGIN #include "../platforms/StandAlone/odinseq_standalone/seqplot_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqstandalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqacq_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqacqepi_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqcounter_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqdec_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqdelay_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqfreq_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqgradchan_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqgradtrapez_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqlist_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqparallel_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqphase_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqpuls_standalone.cpp" #include "../platforms/StandAlone/odinseq_standalone/seqtrigg_standalone.cpp" #endif odin-1.8.5/odinseq/seqfreq.h0000644000175000017500000002606711455553540012702 00000000000000/*************************************************************************** seqfreq.h - description ------------------- begin : Wed Aug 14 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQFREQ_H #define SEQFREQ_H #include #include #include #include /////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Abstract interfac class for all sequence objects that occupy a * transmitter/receiver channel, e.g. pulse objects or acquisition objects */ class SeqFreqChanInterface : public virtual SeqClass { public: /** * Specify the nucleus for this frequency channel */ virtual SeqFreqChanInterface& set_nucleus(const STD_string& nucleus) {if(marshall) marshall->set_nucleus(nucleus); else marshall_error(); return *this;} /** * Sets the freqlist for the object */ virtual SeqFreqChanInterface& set_freqlist(const dvector& freqlist) {if(marshall) marshall->set_freqlist(freqlist); else marshall_error(); return *this;} /** * Sets the phaselist for the object */ virtual SeqFreqChanInterface& set_phaselist(const dvector& phaselist) {if(marshall) marshall->set_phaselist(phaselist); else marshall_error(); return *this;} /** * Returns the frequency list vector (for loop insertion) */ virtual const SeqVector& get_freqlist_vector() const {if(marshall) return marshall->get_freqlist_vector(); else marshall_error(); return get_dummyvec();} /** * Returns the phaselist vector (for loop insertion) */ virtual const SeqVector& get_phaselist_vector() const {if(marshall) return marshall->get_phaselist_vector(); else marshall_error(); return get_dummyvec();} /** * Returns the frequency list vector (for loop insertion) */ operator const SeqVector& () const {return get_freqlist_vector();} /** * Sets the frequency encoding scheme */ virtual SeqFreqChanInterface& set_encoding_scheme(encodingScheme scheme) {if(marshall) marshall->get_mutable_freqlist_vector().set_encoding_scheme(scheme); else marshall_error(); return *this;} /** * Sets the reordering scheme for the frequency list */ virtual SeqFreqChanInterface& set_reorder_scheme(reorderScheme scheme, unsigned int nsegments=1) {if(marshall) marshall->get_mutable_freqlist_vector().set_reorder_scheme(scheme,nsegments); else marshall_error(); return *this;} /** * Returns the reordering vector of the frequency list (for loop insertion) */ virtual const SeqVector& get_reorder_vector() const {if(marshall) return marshall->get_freqlist_vector().get_reorder_vector(); else marshall_error(); return get_dummyvec();} /** * Sets the encoding scheme of the phase list */ virtual SeqFreqChanInterface& set_phaselist_encoding_scheme(encodingScheme scheme) {if(marshall) marshall->get_mutable_phaselist_vector().set_encoding_scheme(scheme); else marshall_error(); return *this;} /** * Sets the reordering scheme for the phase list */ virtual SeqFreqChanInterface& set_phaselist_reorder_scheme(reorderScheme scheme, unsigned int nsegments=1) {if(marshall) marshall->get_mutable_phaselist_vector().set_reorder_scheme(scheme,nsegments); else marshall_error(); return *this;} /** * Returns the reordering vector of the phase list (for loop insertion) */ virtual const SeqVector& get_phaselist_reorder_vector() const {if(marshall) return marshall->get_phaselist_vector().get_reorder_vector(); else marshall_error(); return get_dummyvec();} /** * Sets the frequency list to a single value 'freqoffset' */ SeqFreqChanInterface& set_freqoffset(double freqoffset); /** * Sets the phase list to a single value 'phaseval' */ SeqFreqChanInterface& set_phase(double phaseval); /** * Sets a phase list for RF spoiling of length 'size', multiplicator 'incr' and uniform 'offset'. * Defaults are recommended by the 'Handbook of MRI' */ SeqFreqChanInterface& set_phasespoiling(unsigned int size=80, double incr=117.0, double offset=0.0); protected: SeqFreqChanInterface() {} virtual ~SeqFreqChanInterface() {} void set_marshall(SeqFreqChanInterface* mymarshall) {marshall=mymarshall;} // to be used in constructor code private: friend class SeqAcqEPI; // to allow SeqAcqEPI full access to its driver SeqFreqChanInterface* marshall; // for marshalling member functions to a sub-object virtual SeqVector& get_mutable_freqlist_vector() {if(marshall) return marshall->get_mutable_freqlist_vector(); else marshall_error(); return get_dummyvec();} virtual SeqVector& get_mutable_phaselist_vector() {if(marshall) return marshall->get_mutable_phaselist_vector(); else marshall_error(); return get_dummyvec();} }; /////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The base class for platform specific drivers of transmit/receive channels */ class SeqFreqChanDriver : public SeqDriverBase { public: SeqFreqChanDriver() {} virtual ~SeqFreqChanDriver() {} virtual bool prep_driver(const STD_string& nucleus, const dvector& freqlist) = 0; virtual void prep_iteration(double current_frequency, double current_phase, double freqchan_duration) const = 0; virtual int get_channel() const = 0; virtual STD_string get_iteratorcommand(objCategory cat,int freqlistindex) const = 0; virtual svector get_freqvec_commands(const STD_string& iterator, const STD_string& instr) const = 0; virtual STD_string get_pre_program(programContext& context, objCategory cat, const STD_string& instr_label, double default_frequency, double default_phase) const = 0; virtual SeqFreqChanDriver* clone_driver() const = 0; virtual void pre_event (eventContext& context,double starttime) const = 0; virtual void post_event(eventContext& context,double starttime) const = 0; }; /////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * This is the base class for all sequence objects that occupy a * transmitter/receiver channel */ class SeqFreqChan : public SeqVector, public virtual SeqFreqChanInterface { public: /** * Constructs an empty frequency channel labeled 'object_label' */ SeqFreqChan(const STD_string& object_label="unnamedSeqFreqChan"); /** * Constructs a frequency channel labeled 'object_label' with the following properties: * - nucleus: The nucleus for which the frequency channel should be reserved. * The default is the protons resonance frequency. * - freqlist: This is an array of frequencies at which the transmit/receive signal will be * modulated/demodulated. * - phaselist: This is an array of phases at which the transmit/receive signal will be * modulated/demodulated. */ SeqFreqChan(const STD_string& object_label,const STD_string& nucleus, const dvector& freqlist=0,const dvector& phaselist=0); /** * Constructs a copy of 'sfc' */ SeqFreqChan(const SeqFreqChan& sfc); /** * Destructor */ virtual ~SeqFreqChan() {} /** * Assignment operator that makes this frequency channel become a copy of 'sfc' */ SeqFreqChan& operator = (const SeqFreqChan& sfc); /** * Return the assigned number of this frequency channel */ int get_channel() const {return freqdriver->get_channel();} /** * Returns the freqlist of the object */ dvector get_freqlist() const {return frequency_list;} /** * Returns the current phase (in rad !) */ double get_phase() const {return phaselistvec.get_phase();} /** * Returns the current frequency */ virtual double get_frequency() const; /** * Return the index for the phase list */ unsigned int get_phaselistindex() const {return phaselistvec.get_phaselistindex();} /** * Return the index for the frequency list */ virtual unsigned int get_freqlistindex() const {return 1;} /** * Returns the command to iterate through the frequency list */ STD_string get_iteratorcommand(objCategory cat) const; // overloaded virtual functions of SeqFreqChanInterface SeqFreqChanInterface& set_nucleus(const STD_string& nucleus); SeqFreqChanInterface& set_freqlist (const dvector& freqlist) {frequency_list=freqlist; return *this;} SeqFreqChanInterface& set_phaselist(const dvector& phaselist) {phaselistvec.set_phaselist(phaselist); return *this;} const SeqVector& get_freqlist_vector() const {return *this;} const SeqVector& get_phaselist_vector() const {return phaselistvec;} // overloaded virtual functions of SeqVector unsigned int get_vectorsize() const {return frequency_list.size();} bool prep_iteration() const; bool is_qualvector() const {return false;} svector get_vector_commands(const STD_string& iterator) const {return freqdriver->get_freqvec_commands(iterator,get_driver_instr_label());} // overloaded functions for SeqTreeObj SeqValList get_freqvallist(freqlistAction action) const; protected: STD_string get_pre_program(programContext& context, objCategory cat, const STD_string& instr_label) const; void pre_event (eventContext& context,double starttime) const {freqdriver->pre_event(context,starttime);} void post_event(eventContext& context,double starttime) const {freqdriver->post_event(context,starttime);} /** * Overload this function to return the duration of the object * while it effectively occupies the RF channel */ virtual double get_freqchan_duration() const {return 0.0;} // overwriting virtual functions from SeqClass bool prep(); private: friend class SeqPhaseListVector; // overloaded virtual functions of SeqFreqChanInterface SeqVector& get_mutable_freqlist_vector() {return *this;} SeqVector& get_mutable_phaselist_vector() {return phaselistvec;} double get_default_phase() const {return closest2zero(phaselistvec.get_phaselist());} double get_default_frequency() const {return closest2zero(frequency_list);} static double closest2zero(const dvector& v); // for EPIC virtual STD_string get_driver_instr_label() const {return "";} // the hardware driver mutable SeqDriverInterface freqdriver; // the nucleus of this freq/phase object STD_string nucleusName; // the frequency list to iterate through dvector frequency_list; // the phaselist associated with this freq/phase object SeqPhaseListVector phaselistvec; }; ///////////////////////////////////////////////////////////////////////// #endif odin-1.8.5/odinseq/seqacq.cpp0000644000175000017500000002020111455553540013024 00000000000000#include "seqacq.h" #include "seqdelay.h" #include "seqmeth.h" #include #include void SeqAcq::common_init() { sweep_width=0.0; npts=0; oversampl=1.0; rel_center=0.5; reflect_flag=false; readoutIndex=-1; trajIndex=-1; weightIndex=-1; dimvec=new Handler*[n_recoIndexDims]; for(int i=0; i; default_recoindex[i]=0; } } SeqAcq::~SeqAcq() { for(int i=0; i1.0) { unsigned int adcsize_os=(unsigned int)(oversampl*shape.size()+0.5); fvector newshape(shape); newshape.interpolate(adcsize_os); readoutIndex=recoInfo->append_readout_shape(newshape,dstsize); } else { readoutIndex=recoInfo->append_readout_shape(shape,dstsize); } return *this; } void SeqAcq::set_kspace_traj(const farray& kspaceTraj) { Log odinlog(this,"set_kspace_traj"); if(kspaceTraj.dim()!=3) { ODINLOG(odinlog,errorLog) << "Dimension of kspaceTraj != 3" << STD_endl; return; } if(kspaceTraj.size(2)!=3) { ODINLOG(odinlog,errorLog) << "Third dimension of kspaceTraj != 3" << STD_endl; return; } unsigned int trajsize=kspaceTraj.size(1); if(trajsize!=npts) ODINLOG(odinlog,warningLog) << "size mismatch : " << trajsize << "!=" << npts << STD_endl; trajIndex=recoInfo->append_kspace_traj(kspaceTraj); } void SeqAcq::set_weight_vec(const cvector& weightVec) { Log odinlog(this,"set_weight_vec"); unsigned int vecsize=weightVec.length(); if(vecsize!=npts) ODINLOG(odinlog,warningLog) << "size mismatch : " << vecsize << "!=" << npts << STD_endl; weightIndex=recoInfo->append_adc_weight_vec(weightVec); } double SeqAcq::get_acquisition_center() const { Log odinlog(this,"get_acquisition_center"); double centerpts=rel_center*double(npts); ODINLOG(odinlog,normalDebug) << "centerpts=" << centerpts << STD_endl; double result=get_acquisition_start()+secureDivision(centerpts,sweep_width); ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } SeqAcqInterface& SeqAcq::set_sweepwidth(double sw, float os_factor) { Log odinlog(this,"set_sweepwidth"); double possible_sw_os=acqdriver->adjust_sweepwidth(sw*os_factor); ODINLOG(odinlog,normalDebug) << "possible_sw_os/sw/os_factor=" << possible_sw_os << "/" << sw << "/" << os_factor << STD_endl; sweep_width=secureDivision(possible_sw_os,os_factor); oversampl=STD_max(float(1.0),os_factor); return *this; } SeqAcqInterface& SeqAcq::set_reco_vector(recoDim dim, const SeqVector& vec, const dvector& valvec) { Log odinlog(this,"set_reco_vector"); if(dimset_handled(&vec); ODINLOG(odinlog,normalDebug) << "valvec(" << recoDimLabel[dim] << ")=" << valvec.printbody() << STD_endl; recoInfo->set_DimValues(dim,valvec); } else { ODINLOG(odinlog,warningLog) << "dim=" << dim << " out of range" << STD_endl; } return *this; } SeqAcqInterface& SeqAcq::set_default_reco_index(recoDim dim, unsigned int index) { Log odinlog(this,"set_default_reco_index"); if(dim odinlog(this,"set_npts"); ODINLOG(odinlog,normalDebug) << "nAcqPoints=" << nAcqPoints << STD_endl; npts=nAcqPoints; if(!npts) ODINLOG(odinlog,warningLog) << "Zero sampling points" << STD_endl; return *this; } SeqAcq& SeqAcq::operator = (const SeqAcq& sa) { SeqObjBase::operator = (sa); SeqFreqChan::operator = (sa); sweep_width=sa.sweep_width; npts=sa.npts; oversampl=sa.oversampl; rel_center=sa.rel_center; reflect_flag=sa.reflect_flag; readoutIndex=sa.readoutIndex; trajIndex=sa.trajIndex; weightIndex=sa.weightIndex; for(int i=0; i odinlog(this,"prep"); if(!SeqFreqChan::prep()) return false; kcoord.oversampling=oversampl; kcoord.relcenter=rel_center; kcoord.adcSize=int(float(npts)*kcoord.oversampling+0.5); if(reflect_flag) kcoord.flags=kcoord.flags|recoReflectBit; kcoord.readoutIndex=readoutIndex; kcoord.trajIndex=trajIndex; kcoord.weightIndex=weightIndex; kcoord.dtIndex=recoInfo->append_dwell_time(secureInv(oversampl*sweep_width)); kcoord.channels=acqdriver->get_numof_channels(); // For slicetime functor in odinreco: // store slice order in DimValues of recoInfo according to vector in slice dimension const SeqVector* vec=dimvec[slice]->get_handled(); if(vec) { ivector ivec(vec->get_index_matrix()); dvector ivals(ivec.size()); for(unsigned int i=0; iset_DimValues(slice,ivals); } return acqdriver->prep_driver(kcoord, oversampl*sweep_width, (unsigned int)(oversampl*npts+0.5), get_acquisition_center(), get_channel()); } STD_string SeqAcq::get_program(programContext& context) const { STD_string result=SeqFreqChan::get_pre_program(context,acqObj,acqdriver->get_instr_label()); result+=acqdriver->get_program(context,get_phaselistindex()); return result; } double SeqAcq::get_duration() const { double result=acqdriver->get_predelay(); result+=get_freqchan_duration(); result+=acqdriver->get_postdelay(oversampl*sweep_width); return result; } SeqValList SeqAcq::get_freqvallist(freqlistAction action) const { Log odinlog(this,"get_freqvallist"); SeqValList result(get_label()); double newfreq=SeqFreqChan::get_frequency(); if(action==calcAcqList) { result.set_value(newfreq); ODINLOG(odinlog,normalDebug) << "freq=" << newfreq << STD_endl; } return result; } const kSpaceCoord& SeqAcq::get_kcoord() const { Log odinlog(this,"get_kcoord"); // fill reco index with values of the attached vectors for(int i=0; iget_handled(); if(vec) kcoord.index[i]=vec->get_acq_index(); else kcoord.index[i]=default_recoindex[i]; } return kcoord; } RecoValList SeqAcq::get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const { Log odinlog(this,"get_recovallist"); kSpaceCoord idx(get_kcoord()); idx.reps=reptimes; coords.append_coord(idx); RecoValList result(get_label()); result.set_value(idx.number); return result; } unsigned int SeqAcq::event(eventContext& context) const { Log odinlog(this,"event"); double startelapsed=context.elapsed; SeqTreeObj::event(context); if(context.action==seqRun) { SeqFreqChan::pre_event(context,startelapsed); ODINLOG(odinlog,normalDebug) << "startelapsed/get_acquisition_start()=" << startelapsed << "/" << get_acquisition_start() << STD_endl; acqdriver->event(context,startelapsed+get_acquisition_start()); SeqFreqChan::post_event(context,startelapsed+get_acquisition_start()+get_freqchan_duration()); } if(context.event_progmeter) context.event_progmeter->increase_counter(); return 1; } STD_string SeqAcq::get_properties() const { return "SweepWidth="+ftos(sweep_width)+", Samples="+itos(npts)+", OverSampling="+ftos(oversampl); } odin-1.8.5/odinseq/seqacqepi.h0000644000175000017500000003153111625224370013172 00000000000000/*************************************************************************** seqacqepi.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQACQEPI_H #define SEQACQEPI_H #include #include #include #include #include #include #include #include #include /** * @ingroup odinseq_internals * The base class for platform specific EPI drivers */ class SeqEpiDriver : public SeqDriverBase, public SeqObjList, public virtual SeqAcqInterface, public virtual SeqGradInterface { public: SeqEpiDriver() {} virtual ~SeqEpiDriver() {} virtual void init_driver(const STD_string& object_label,double sweepwidth, float kread_min, float kread_max, unsigned readntps, float kphase_min, float kphase_max, unsigned phasentps,int startindex_phase, bool ramp_sampling,rampType rampmode, float ramp_steepness, const STD_string& nucleus, const dvector& phaselist, const dvector& freqlist, unsigned int echo_pairs) = 0; virtual unsigned get_npts_read() const = 0; virtual unsigned int get_numof_gradechoes() const = 0; virtual double get_echoduration() const = 0; virtual double get_ramp_rastertime() const = 0; virtual float get_gradintegral2center_read() const = 0; virtual float get_gradintegral2center_phase() const = 0; virtual fvector get_readout_shape() const = 0; virtual const kSpaceCoord& get_kcoord_template(unsigned int& padded_zeroes) const = 0; virtual SeqEpiDriver* clone_driver() const = 0; unsigned int get_npts() const {return get_npts_read()*get_numof_gradechoes();} protected: SeqEpiDriver(const SeqEpiDriver& seda) : SeqObjList(seda) {SeqEpiDriver::operator = (seda);} SeqEpiDriver& operator = (const SeqEpiDriver& seda) { SeqObjList::operator =(seda); return *this; } }; ///////////////////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * The default EPI driver */ class SeqEpiDriverDefault : public SeqEpiDriver { // virtual functions of SeqFreqChanInterface are marhshalled to adc public: SeqEpiDriverDefault(); ~SeqEpiDriverDefault() {} SeqEpiDriverDefault(const SeqEpiDriverDefault& sedi); void init_driver(const STD_string& object_label,double sweepwidth, float kread_min, float kread_max, unsigned readntps, float kphase_min, float kphase_max, unsigned phasentps,int startindex_phase, bool ramp_sampling, rampType rampmode, float ramp_steepness, const STD_string& nucleus, const dvector& phaselist, const dvector& freqlist, unsigned int echo_pairs); // overloading virtual functions from SeqDriverBase odinPlatform get_driverplatform() const {return standalone;} // implemented virtual functions from SeqEpiDriver unsigned int get_npts_read() const {return adc.get_npts();} unsigned int get_numof_gradechoes() const; double get_echoduration() const {return posread.get_gradduration();} double get_ramp_rastertime() const {return posread.get_timestep();} float get_gradintegral2center_read() const {return gradint2center_read;} float get_gradintegral2center_phase() const {return gradint2center_phase;} fvector get_readout_shape() const {return readshape;} const kSpaceCoord& get_kcoord_template(unsigned int& padded_zeroes) const {padded_zeroes=0; return adc.get_kcoord();} SeqEpiDriver* clone_driver() const {return new SeqEpiDriverDefault(*this);} // marshalling virtual functions of SeqAcqInterface to adc, except: double get_acquisition_center() const; double get_acquisition_start() const; SeqAcqInterface& set_template_type(templateType type); // implementing virtual functions of SeqGradInterface SeqGradInterface& set_strength(float gradstrength) {return *this;} SeqGradInterface& invert_strength() {kernel.invert_strength(); return *this;} float get_strength() const {return kernel.get_strength();} fvector get_gradintegral() const; double get_gradduration() const {return kernel.get_gradduration();} SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix) {kernel.set_gradrotmatrix(matrix); return *this;} private: void build_seq(); SeqAcq adc; SeqDelay acqdelay_begin; SeqDelay acqdelay_middle; SeqDelay acqdelay_end; SeqGradTrapez posread; SeqGradTrapez negread; SeqGradTrapez phaseblip1st; SeqGradTrapez phaseblip2nd; SeqGradDelay phasezero1st; SeqGradDelay phasezero2nd; SeqGradDelay phasezero_lastblip; SeqGradChanParallel gradkernel; SeqGradChanParallel lastgradkernel; SeqObjList oneadckernel; SeqObjList adckernel; SeqObjList lastadckernel; SeqParallel kernel; SeqParallel lastkernel; SeqObjLoop loop; float gradint2center_read; float gradint2center_phase; int centerindex_phase; fvector readshape; templateType templtype; int echopairs; bool lastecho; }; ///////////////////////////////////////////////////////////////////////////////////// class SeqAcqEPIdephObjs; // forward declaration /** * @addtogroup odinseq * @{ */ /** * \brief Acquisition + echo-planar imaging readout * * This class represents an acquisition window with an EPI gradient. */ class SeqAcqEPI : public SeqObjBase, public virtual SeqAcqInterface, public virtual SeqGradInterface { public: /** * Constructs an acquisition window with an EPI gradient labeled 'object_label' with the * following properties: * - sweepwidth: The sampling frequency * - read_size: The number of sampling points per gradient echo, with ramp_sampling enabled, this is the number of points after regridding * - FOVread: The Field Of View in read direction * - phase_size: The final matrix size in phase direction without partial fourier undersampling * - FOVphase: The Field Of View in phase direction * - shots: Number of shots, a multi-shot (segmented) EPI readout will be created if 'shots' is larger than 1 * - reduction: Reduction factor (parallel imaging) * - os_factor: The oversampling factor, os_factor=1 means no oversampling * - nucleus: The nucleus to measure * - phaselist: Phase list for acquisition * - freqlist: Frequency list for acquisition * - rampmode: This parameter determines the shape of the ramp waveform * - ramp_sampling: The EPI readout performs data acquisition during the ramps if this parameter is set to 'true' * - ramp_steepness: This parameter in the range of ]0,1] determines the relative rising * speed of the gradient strength, i.e. with 1 the gradients are switched * as fast as possible * - fourier_factor: The amount of undersampling (0=no undersampling, 1=half fourier) * - echo_pairs: Number of interleaved acquired pairs of echoes for one phase-encodin step, 0 means only one echo */ SeqAcqEPI(const STD_string& object_label, double sweepwidth, unsigned int read_size, float FOVread, unsigned int phase_size, float FOVphase, unsigned int shots=1, unsigned int reduction=1, float os_factor=1.0, const STD_string& nucleus="", const dvector& phaselist=0, const dvector& freqlist=0, rampType rampmode = linear, bool ramp_sampling=false, float ramp_steepness=1.0, float fourier_factor=0.0, unsigned int echo_pairs=0, bool invert_partial_fourier=false); /** * Constructs an acquisition window with an EPI gradient which is a copy of 'sae' */ SeqAcqEPI(const SeqAcqEPI& sae); /** * Constructs an empty acquisition window with an EPI gradient with the given label. */ SeqAcqEPI(const STD_string& object_label="unnamedSeqAcqEPI"); /** * Destructor */ ~SeqAcqEPI(); /** * Returns the number of points that will be acquired during each read gradient period, * including the ramp points. */ unsigned int get_npts_read() const {return driver->get_npts_read();} /** * Returns the number of gradient echoes, i.e. the number of k-space lines that will * be sampled */ unsigned int get_numof_gradechoes() const {return driver->get_numof_gradechoes();} /** * Returns the readout gradient shape that is used for regridding */ fvector get_readout_shape() const {return driver->get_readout_shape();} /** * This assignment operator will make this object become an exact copy of 'sae'. */ SeqAcqEPI& operator = (const SeqAcqEPI& sae); // forwarding virtual functions of SeqAcqInterface to driver // we cannot use marshalling with a fixed pointer here because // driver may be changed when switching platform double get_acquisition_center() const {return driver->get_acquisition_center();} double get_acquisition_start() const {return driver->get_acquisition_start();} unsigned int get_npts() const {return driver->get_npts();} SeqAcqInterface& set_sweepwidth(double sw, float os_factor); // produce warning double get_sweepwidth() const {return driver->get_sweepwidth();} float get_oversampling() const {return os_factor_cache;} SeqAcqInterface& set_template_type(templateType type); SeqAcqInterface& set_reco_vector(recoDim dim, const SeqVector& vec, const dvector& valvec=dvector()) {driver->set_reco_vector(dim,vec,valvec); return *this;} SeqAcqInterface& set_default_reco_index(recoDim dim, unsigned int index) {driver->set_default_reco_index(dim,index); return *this;} // forwarding virtual functions of SeqFreqChanInterface to driver SeqFreqChanInterface& set_nucleus(const STD_string& nucleus) {driver->set_nucleus(nucleus); return *this;} SeqFreqChanInterface& set_freqlist(const dvector& freqlist) {driver->set_freqlist(freqlist); return *this;} SeqFreqChanInterface& set_phaselist(const dvector& phaselist) {driver->set_phaselist(phaselist); return *this;} const SeqVector& get_freqlist_vector() const {return driver->get_freqlist_vector();} const SeqVector& get_phaselist_vector() const {return driver->get_phaselist_vector();} // forwarding virtual functions of SeqGradInterface to driver SeqGradInterface& set_strength(float gradstrength) {driver->set_strength(gradstrength); return *this;} SeqGradInterface& invert_strength() {driver->invert_strength(); return *this;} float get_strength() const {return driver->get_strength();} fvector get_gradintegral() const {return driver->get_gradintegral();} double get_gradduration() const {return driver->get_gradduration();} SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix) {driver->set_gradrotmatrix(matrix); return *this;} // forwarding virtual functions of SeqTreeObj to driver STD_string get_program(programContext& context) const {return driver->get_program(context);} double get_duration() const {return driver->get_duration();} SeqValList get_freqvallist(freqlistAction action) const {return driver->get_freqvallist(action);} void query(queryContext& context) const {driver->query(context);} RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const; bool contains(const SeqTreeObj* sto) const {return driver->contains(sto);} void tree(SeqTreeCallbackAbstract* display) const {driver->tree(display);} unsigned int event(eventContext& context) const {return driver->event(context);} STD_string get_properties() const {return driver->get_properties();} private: SeqVector& get_mutable_freqlist_vector() {return driver->get_mutable_freqlist_vector();} SeqVector& get_mutable_phaselist_vector() {return driver->get_mutable_phaselist_vector();} // overloaded for SeqAcqDeph const SeqVector* get_dephgrad(SeqGradChanParallel& dephobj, bool rephase) const; // overwriting virtual functions from SeqClass bool prep(); void common_init(); void create_deph_and_reph(); unsigned int readsize_os_cache; float os_factor_cache; unsigned int phasesize_cache; unsigned int segments_cache; unsigned int reduction_cache; int echo_pairs_cache; float blipint_cache; templateType templtype_cache; rampType ramptype_cache; mutable SeqDriverInterface driver; SeqAcqEPIdephObjs* dephobjs; }; /** @} */ #endif odin-1.8.5/odinseq/seqobj.cpp0000644000175000017500000000057211322062345013032 00000000000000#include "seqobj.h" SeqObjBase::SeqObjBase(const STD_string& object_label) : SeqTreeObj() { Log odinlog(object_label.c_str(),"SeqObjBase()"); set_label(object_label); } SeqObjBase::SeqObjBase(const SeqObjBase& soa) { SeqObjBase::operator = (soa); } SeqObjBase& SeqObjBase::operator = (const SeqObjBase& soa) { SeqTreeObj::operator = (soa); return *this; } odin-1.8.5/odinseq/seqgrad.h0000644000175000017500000000501611322062345012640 00000000000000/*************************************************************************** seqgrad.h - description ------------------- begin : Wed Aug 8 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRAD_H #define SEQGRAD_H #include class RotMatrix; // forward declaration /** * @addtogroup odinseq_internals * @{ */ /** * This is the abstract base class for all objects that represent * gradient fields */ class SeqGradInterface : public virtual SeqClass { public: /** * Changes the strength of the gradient object */ virtual SeqGradInterface& set_strength(float gradstrength) = 0; /** * Changes the polarity of the gradient, i.e. inverts the sign of the gradient strength */ virtual SeqGradInterface& invert_strength() = 0; /** * Returns the strength of the gradient object */ virtual float get_strength() const = 0; /** * Returns the integral vector of the gradient course */ virtual fvector get_gradintegral() const = 0; /** * Returns the norm of the integral vector of the gradient course */ float get_gradintegral_norm() const; /** * Returns the duration of the gradient object. This function returns * only the effective duration during whichthe gradient is active, * any delays before and after the gradient are omitted. */ virtual double get_gradduration() const = 0; /** * This function can be used to specify a rotation of the gradient object * in the spatial domain, the rotation will be applied to this object only * rather than to the whole sequence. */ virtual SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix) = 0; protected: SeqGradInterface() {} virtual ~SeqGradInterface() {} }; /** @} */ #endif odin-1.8.5/odinseq/odinpulse.h0000644000175000017500000003021511322062345013213 00000000000000/*************************************************************************** odinpulse.h - description ------------------- begin : Tue Jun 4 2002 copyright : (C) 2002 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINPULSE_H #define ODINPULSE_H #include #include #include class SeqSimAbstract; // forward declaration class Sample; // forward declaration #define _BOUNDARY_VALUE_ 0.005 #define _SETREFGAIN_ADIABATIC_INTERVAL_ 0.01 #define _SETREFGAIN_ADIABATIC_INCR_FACTOR_ 1.1 #define _SETREFGAIN_ITERATIONS_ 3 // Parameter values of this optimization parameter must be in range [0,1] #define _TRAJ_OPTIMIZE_PARLABEL_ "FreeParameter" ////////////////////////////////////////////////// /** * @addtogroup odinseq_internals * @{ */ /** * * Wrapper class for trajectory functions. */ class JDXtrajectory : public JDXfunction, public StaticHandler { public: JDXtrajectory(const STD_string& jdxlabel="unnamedJDXtrajectory") : JDXfunction(trajFunc,jdxlabel) {} JDXtrajectory(const JDXtrajectory& jt) : JDXfunction(jt) {} JDXtrajectory& operator = (const JDXtrajectory& jt) {JDXfunction::operator = (jt); return *this;} void init_trajectory(OdinPulse* pls=0) {if(allocated_function) allocated_function->init_trajectory(pls);} const kspace_coord& calculate(float s) const; const traj_info& get_traj_info() const; static void init_static(); static void destroy_static(); }; ////////////////////////////////////////////////// /** * * Wrapper class for pulse shape functions. */ class JDXshape : public JDXfunction, public StaticHandler { public: JDXshape(const STD_string& jdxlabel="unnamedJDXshape") : JDXfunction(shapeFunc,jdxlabel) {} JDXshape(const JDXshape& js) : JDXfunction(js) {} JDXshape& operator = (const JDXshape& js) {JDXfunction::operator = (js); return *this;} void init_shape() {if(allocated_function) allocated_function->init_shape();} STD_complex calculate(const kspace_coord& coord ) const; STD_complex calculate(float s, float Tp) const; const shape_info& get_shape_info() const; farray get_excitation_mask(float fov, unsigned int size) const; static void init_static(); static void destroy_static(); }; ////////////////////////////////////////////////// struct OdinPulseData; // forward declaration /** @} */ ////////////////////////////////////////////////// /** * @addtogroup odinseq * @{ */ /** * \brief Advandced RF pulses * * * This class represents an advanced RF pulse. The RF and gradient * shape will be calculated according to a set of given parameters. */ class OdinPulse : public JcampDxBlock, public virtual SeqClass { public: /** * Constructs an OdinPulse with the given label. If 'interactive' is set to 'true', the RF, gradient shape and * pulse_gain will be recalculted each time a parameter has been changed */ OdinPulse(const STD_string& pulse_label="unnamedOdinPulse",bool interactive=false); /** * Constructs an OdinPulse which is a copy of 'pulse' */ OdinPulse(const OdinPulse& pulse); virtual ~OdinPulse(); /** * This assignment operator will make this OdinPulse become an exact copy of 'pulse'. */ OdinPulse& operator = (const OdinPulse& pulse); /** * * Sets the pulse mode (dimensionality) of the pulse */ OdinPulse& set_dim_mode(funcMode dmode); /** * * Returns the pulse mode (dimensionality) of the pulse */ funcMode get_dim_mode() const; /** * * Returns the number of data points */ unsigned int get_size() const; /** * * specifies number of data points */ OdinPulse& resize(unsigned int newsize); /** * * Sets the duration of the pulse */ OdinPulse& set_Tp(double duration); /** * * Returns the duration of the pulse */ double get_Tp() const; /** * * Specifies whether to consider maximum gradient strength and * slew-rate while calculating the trajectory. */ OdinPulse& set_consider_system_cond(bool flag); /** * * Returns whether to consider maximum gradient strength and * slew-rate while calculating the trajectory. */ bool get_consider_system_cond() const; /** * * Specifies whether to consider Nyquist-theorem while sampling along * the k-space trajectory. */ OdinPulse& set_consider_Nyquist_cond(bool flag); /** * * Returns whether to consider Nyquist-theorem while sampling along * the k-space trajectory. */ bool get_consider_Nyquist_cond() const; /** * * Sets the spatial resolution if the pulse is calculated according * to the small tip angle approximation, otherwise this has no effect. */ OdinPulse& set_spat_resolution(double sigma); /** * * Sets whether minimum spatial resolution is used. */ OdinPulse& use_min_spat_resolution(bool flag); /** * * Returns the spatial resolution */ double get_spat_resolution() const; /** * * Sets the field of excitation, i.e. the spatial area where no aliasing occurs */ OdinPulse& set_field_of_excitation(double fox); /** * * Returns the field of excitation */ double get_field_of_excitation() const; /** * * Sets the spatial offset in the given direction */ OdinPulse& set_spatial_offset(direction direction, double offset); /** * * Returns the spatial offset in the given direction */ double get_spatial_offset(direction direction) const; /** * * Sets the nucleus for the pulse */ OdinPulse& set_nucleus(const STD_string& nucleusname); /** * * Returns the nucleus for the pulse */ STD_string get_nucleus() const; /** * * Sets the type of the pulse, this is necessary for calculating the pulse gain of * adiabatic pulses and optimization of pulses. */ OdinPulse& set_pulse_type(pulseType type); /** * * Returns the type of the pulse */ pulseType get_pulse_type() const; /** * * Specifies the composite pulse to use. * A composite pulse can be specified by a string * of the form a1(x2) a2(x2) ... where a1,a2,... * are the flipangles in degree and x1,x2,... * are the axes, .e.g. X,-X,Y or -Y. */ OdinPulse& set_composite_pulse(const STD_string& cpstring); /** * * Returns a 2dim array with the first index indicating the pulse in the composite pulse * train and the second index selects the flipangle(=0) or pulse phase(=1) of the sub-pulse. */ farray get_composite_pulse_parameters() const; /** * * Returns 'true' if the pulse is a composite pulse */ bool is_composite_pulse() const; /** * * Returns the number of composite pulses */ unsigned int get_numof_composite_pulse() const; /** * * Returns whether the pulse shape is adiabatic */ bool is_adiabatic() const; /** * * Returns the relative center of the pulse, * i.e. the point where the center of k-space is passed. * The value will be in the range in the range [0,1]. */ float get_rel_center() const; /** * * Returns the pulse gain */ double get_pulse_gain() const; /** * * Returns the correction factor for the IDEA flipangle */ float get_flipangle_corr_factor() const; /** * * Sets the flip angle */ OdinPulse& set_flipangle(double angle); /** * * Returns the flip angle */ double get_flipangle() const; /** * * Generates the pulse */ OdinPulse& generate(); /** * * Calculates the pulse gain in comparison to a 90deg 1ms block-shaped pulse */ OdinPulse& set_pulse_gain(); /** * * Update all relations and recalculate pulse */ virtual OdinPulse& update(); /** * * Calculates the power deposition of the pulse */ float get_power_depos() const; /** * * Specifies the pulse shape and its parameters by a string where the first * element is the function name followed by the parameters in braces separated by commas */ OdinPulse& set_shape(const STD_string& shapeval); /** * * Specifies the pulse trajectory and its parameters by a string where the first * element is the function name followed by the parameters in braces separated by commas */ OdinPulse& set_trajectory(const STD_string& shapeval); /** * * Specifies the pulse filter and its parameters by a string where the first * element is the function name followed by the parameters in braces separated by commas */ OdinPulse& set_filter(const STD_string& shapeval); /** * * Sets the value of the pulse shape parameter which has the label 'parameter_label' to 'value' */ OdinPulse& set_shape_parameter(const STD_string& parameter_label, const STD_string& value); /** * * Sets the value of the pulse trajectory parameter which has the label 'parameter_label' to 'value' */ OdinPulse& set_trajectory_parameter(const STD_string& parameter_label, const STD_string& value); /** * * Sets the value of the pulse filter parameter which has the label 'parameter_label' to 'value' */ OdinPulse& set_filter_parameter(const STD_string& parameter_label, const STD_string& value); /** * * Returns the value of the pulse shape parameter which has the given label */ STD_string get_shape_parameter(const STD_string& parameter_label) const; /** * * Returns the value of the pulse trajectory parameter which has the given label */ STD_string get_trajectory_parameter(const STD_string& parameter_label) const; /** * * Returns the value of the pulse filter parameter which has the given label */ STD_string get_filter_parameter(const STD_string& parameter_label) const; /** * * Returns the label of the current pulse shape */ STD_string get_shape() const; /** * * Returns the label of the current pulse trajectory */ STD_string get_trajectory() const; /** * * Returns the label of the current pulse filter */ STD_string get_filter() const; /** * Returns the gradient waveform for the specified channel */ const fvector& get_Grad(direction channel) const; /** * * Returns the scaling factor for the gradient channels */ double get_G0() const; /** * Returns the complex RF waveform */ const cvector& get_B1() const; /** * * Returns the scaling factor for the RF channels */ double get_B10() const; /** * Simulates the effect of the pulse using simulator 'sim' * using virtual sample 'sample'. */ void simulate_pulse(SeqSimAbstract& sim, const Sample& sample) const; /** * * This function writes the RF waveform to file in the native (binary) * format of the current platform */ int write_rf_waveform (const STD_string& filename) const; /** * * This function loads the RF waveform from file in the native (binary) * format of the current platform */ int load_rf_waveform (const STD_string& filename); // overloading virtual functions of JcampDxBlock int load(const STD_string& filename); int write(const STD_string& filename) const; protected: virtual void update_B10andPower(); OdinPulse& recalc_pulse(); double get_Tp_1pulse() const; private: int append_all_members(); static float ensure_unit_range(float x); OdinPulse& make_composite_pulse(); static float gradient_system_max (const fvector& Gvec, float Gmax, float maxslew, float Tp); static float max_kspace_step(const fvector& Gz,float gamma,float Tp,float G0); static float max_kspace_step2(const fvector& Gx, const fvector& Gy, float gamma,float Tp,float G0); OdinPulse& resize_noupdate(unsigned int newsize); // this pointer holds all data of the pulse OdinPulseData* data; }; /** @} */ #endif odin-1.8.5/odinseq/seqfreq.cpp0000644000175000017500000000743011322062345013215 00000000000000#include "seqfreq.h" SeqFreqChanInterface& SeqFreqChanInterface::set_freqoffset(double freqoffset) { dvector flist(1); flist[0]=freqoffset; return set_freqlist(flist); } SeqFreqChanInterface& SeqFreqChanInterface::set_phase(double phaseval) { dvector plist(1); plist[0]=phaseval; return set_phaselist(plist); } SeqFreqChanInterface& SeqFreqChanInterface::set_phasespoiling(unsigned int size, double incr, double offset) { dvector plist(size); plist[0]=incr+offset; // recommended initialisation, handbook of MRI for(unsigned int iphase=1; iphase odinlog(this,"SeqFreqChan(...)"); set_label(object_label); // this is neccessary because SeqClass is a virtual base class phaselistvec.user=this; } SeqFreqChan::SeqFreqChan(const STD_string& object_label,const STD_string& nucleus, const dvector& freqlist,const dvector& phaselist) : SeqVector(object_label), freqdriver(object_label+"_freqdriver"), phaselistvec(object_label+"_phaselistvec") { Log odinlog(this,"SeqFreqChan(...)"); nucleusName=nucleus; frequency_list=freqlist; SeqFreqChan::set_phaselist (phaselist); // Do NOT call virtual function in constructor phaselistvec.user=this; } SeqFreqChan::SeqFreqChan(const SeqFreqChan& sfc) { SeqFreqChan::operator = (sfc); } SeqFreqChan& SeqFreqChan::operator = (const SeqFreqChan& sfc) { Log odinlog(this,"operator = (...)"); SeqVector::operator = (sfc); nucleusName=sfc.nucleusName; freqdriver=sfc.freqdriver; phaselistvec=sfc.phaselistvec; frequency_list=sfc.frequency_list; phaselistvec.user=this; // precaution return *this; } SeqFreqChanInterface& SeqFreqChan::set_nucleus(const STD_string& nucleus) { Log odinlog(this,"set_nucleus"); nucleusName=nucleus; return *this; } STD_string SeqFreqChan::get_iteratorcommand(objCategory cat) const { return freqdriver->get_iteratorcommand(cat,get_freqlistindex()); } SeqValList SeqFreqChan::get_freqvallist(freqlistAction action) const { Log odinlog(this,"get_freqvallist"); SeqValList result(get_label()); result.set_value(get_frequency()); return result; } STD_string SeqFreqChan::get_pre_program(programContext& context, objCategory cat, const STD_string& instr_label) const { return freqdriver->get_pre_program(context,cat,instr_label,get_default_frequency(),get_default_phase()); } double SeqFreqChan::get_frequency() const { if(frequency_list.size()) return frequency_list[get_current_index()]; else return 0.0; } bool SeqFreqChan::prep() { Log odinlog(this,"prep"); if(!SeqClass::prep()) return false; freqdriver->prep_driver(nucleusName,get_freqlist()); prep_iteration(); // to initialize constant frequency offset return true; } bool SeqFreqChan::prep_iteration() const { Log odinlog(this,"prep_iteration"); double phase=get_phase(); double freq=get_frequency(); ODINLOG(odinlog,normalDebug) << "freq/phase=" << freq << "/" << phase << STD_endl; freqdriver->prep_iteration(freq,phase,get_freqchan_duration()); return true; } double SeqFreqChan::closest2zero(const dvector& v) { Log odinlog("SeqFreqChan","closest2zero"); unsigned int n=v.length(); if(!n) return 0.0; double result=v[0]; double min=fabs(result); for(unsigned int i=0; i::staticdone=false; odin-1.8.5/odinseq/seqacqread.cpp0000644000175000017500000001322111455553540013664 00000000000000#include "seqacqread.h" #include "seqlist.h" void SeqAcqRead::common_init() { SeqAcqInterface::set_marshall(&acq); SeqFreqChanInterface::set_marshall(&acq); } SeqAcqRead::SeqAcqRead(const STD_string& object_label,double sweepwidth,unsigned int read_size, float fov, direction gradchannel,float os_factor, float partial_fourier, bool partial_fourier_at_end, const STD_string& nucleus,const dvector& phaselist,const dvector& freqlist, float timestep, rampType rampmode ) : SeqParallel(object_label), corrected_partfour(STD_max(0.0f,STD_min(1.0f,partial_fourier))), // check and correct range acq(object_label+"_acq",(1.0-0.5*corrected_partfour)*read_size+0.5,sweepwidth,os_factor,nucleus,phaselist,freqlist), read(object_label+"_read"), middelay(object_label+"_middelay",0.0), midgrad(object_label+"_midgrad",gradchannel,0.0), tozero(object_label+"_tozero",0.0) { Log odinlog(this,"SeqAcqRead"); common_init(); float gradstrength=secureDivision(2.0*PII*acq.get_sweepwidth(),systemInfo->get_gamma(nucleus)*fov); // Use adjusted sweepwidth double constgradduration=secureDivision(acq.get_npts(),acq.get_sweepwidth()); double rastertime=systemInfo->get_rastertime(gradObj); if(rastertime>0.0) { int nraster=(int)secureDivision(constgradduration,rastertime); if(rastertime*nraster!=constgradduration) nraster++; // always increase length of constant part constgradduration=nraster*rastertime; } read=SeqGradTrapez(object_label+"_read",gradchannel, gradstrength, constgradduration, timestep, rampmode); tozero=SeqDelay(object_label+"_tozero",read.get_offramp_duration()+systemInfo->get_inter_grad_delay()); float rel_center=secureDivision(0.5*(1.0-corrected_partfour),1.0-0.5*corrected_partfour); ODINLOG(odinlog,normalDebug) << "rel_center=" << rel_center << STD_endl; if(partial_fourier_at_end) rel_center=1.0-rel_center; acq.set_rel_center(rel_center); float dephintegral=-(read.get_onramp_integral()+rel_center*read.get_constgrad_integral()); float rephintegral=-(read.get_offramp_integral()+(1.0-rel_center)*read.get_constgrad_integral()); // Initialze once so that consecutive calls to get_dephgrad return always the same objects // readdephgrad=SeqGradTrapez(object_label+"_readdephgrad", // dephintegral, // gradchannel,0.5 *read.get_constgrad_duration(), // timestep,rampmode); readdephgrad=SeqGradTrapez(object_label+"_readdephgrad",dephintegral,gradstrength,gradchannel,timestep,rampmode); // readrephgrad=SeqGradTrapez(object_label+"_readrephgrad", // rephintegral, // gradchannel,0.5 *read.get_constgrad_duration(), // timestep,rampmode); readrephgrad=SeqGradTrapez(object_label+"_readrephgrad",rephintegral,gradstrength,gradchannel,timestep,rampmode); build_seq(); } SeqAcqRead::SeqAcqRead(const STD_string& object_label) : SeqParallel(object_label) { common_init(); } SeqAcqRead::SeqAcqRead(const SeqAcqRead& sar) { common_init(); SeqAcqRead::operator = (sar); } double SeqAcqRead::get_acquisition_center() const { double result=0.0; result+=SeqParallel::get_pulprogduration(); result+=middelay.get_duration(); result+=acq.get_acquisition_center(); return result; } double SeqAcqRead::get_acquisition_start() const { double result=0.0; result+=SeqParallel::get_pulprogduration(); result+=middelay.get_duration(); result+=acq.get_acquisition_start(); return result; } SeqAcqInterface& SeqAcqRead::set_sweepwidth(double sw, float os_factor) { Log odinlog(this,"set_sweepwidth"); ODINLOG(odinlog,warningLog) << "Ignoring request to change sweepwidth after construction" << STD_endl; return *this; } SeqAcqRead& SeqAcqRead::operator = (const SeqAcqRead& sar) { SeqParallel::operator = (sar); acq=sar.acq; read=sar.read; middelay=sar.middelay; midgrad=sar.midgrad; tozero=sar.tozero; readdephgrad=sar.readdephgrad; readrephgrad=sar.readrephgrad; build_seq(); return *this; } void SeqAcqRead::build_seq() { Log odinlog(this,"build_seq"); bool seqset=false; double ppgdur=SeqParallel::get_pulprogduration(); double gradstart=systemInfo->get_grad_shift_delay()+read.get_onramp_duration(); double acqstart=ppgdur+acq.get_acquisition_start(); double shift=gradstart-acqstart; ODINLOG(odinlog,normalDebug) << "ppgdur/gradstart/acqstart/shift=" << ppgdur << "/" << gradstart << "/" << acqstart << "/" << shift << STD_endl; if(shift>=systemInfo->get_min_duration(delayObj)) { ODINLOG(odinlog,normalDebug) << "acq is played out later, because gradient switching is delayed" << STD_endl; middelay.set_duration(shift); SeqParallel::operator = ( read / ( middelay + acq + tozero ) ); seqset=true; } if((-shift)>=systemInfo->get_min_duration(gradObj)) { ODINLOG(odinlog,normalDebug) << "gradients are played out later, because acq is delayed" << STD_endl; midgrad.set_duration(-shift); SeqParallel::operator = ( (midgrad+read) / ( acq + tozero ) ); seqset=true; } if(!seqset) { ODINLOG(odinlog,normalDebug) << "acq and gradients are played out simultaneously" << STD_endl; SeqParallel::operator = ( read / ( acq + tozero ) ); } } const SeqVector* SeqAcqRead::get_dephgrad(SeqGradChanParallel& dephobj, bool rephase) const { SeqGradTrapez* sgt; if(rephase) sgt=new SeqGradTrapez(readrephgrad); // Create deep copy so user can modify SeqAcqDeph safely else sgt=new SeqGradTrapez(readdephgrad); // Create deep copy so user can modify SeqAcqDeph safely sgt->set_temporary(); dephobj+=(*sgt); return 0; } odin-1.8.5/odinseq/seqplatform.cpp0000644000175000017500000000676511322062345014116 00000000000000#include "seqplatform.h" #include "seqdriver.h" #include ///////////////////////////////////////////////////////////////////////////////// void SeqPlatformProxy::set_current_platform(odinPlatform pF) { if(platforms) platforms->set_current(pF); } odinPlatform SeqPlatformProxy::get_current_platform() { if(platforms) return platforms->get_current_platform_id(); else return SeqPlatformInstances::pf_during_platform_construction; } int SeqPlatformProxy::load_systemInfo(const STD_string& filename) { Log odinlog("SeqPlatformProxy","load_systemInfo"); SeqPlatformProxy(); // create platform instances JDXstring pfdummy("","Platform",true,notBroken); // determine the platform first pfdummy.load(filename); if(STD_string(pfdummy)=="") return -1; ODINLOG(odinlog,normalDebug) << "pfdummy=" << STD_string(pfdummy) << STD_endl; odinPlatform pF=odinPlatform(0); svector poss(get_possible_platforms()); for(unsigned int i=0; i odinlog("SeqPlatformProxy","get_possible_platforms"); SeqPlatformProxy(); // create platform instances svector result; result.resize(numof_platforms); for(unsigned int i=0; iinstance[i]) { result+=STD_string(platforms->instance[i]->get_label())+" ACTIONS:\n\n"; result+=SeqCmdLine::format_actions(platforms->instance[i]->get_actions_usage()); } } #endif return result; } int SeqPlatformProxy::get_platform_for_action(const STD_string& action) { #ifndef NO_CMDLINE Log odinlog("SeqPlatformProxy","get_platform_for_action"); SeqPlatformProxy(); // create platform instances for(unsigned int ipf=0; ipfinstance[ipf]) { SeqCmdlineActionList actions=platforms->instance[ipf]->get_actions_usage(); ODINLOG(odinlog,normalDebug) << "platform/actions.size()=" << ipf << "/" << actions.size() << STD_endl; for(STD_list::const_iterator it=actions.begin(); it!=actions.end(); ++it) { STD_string pfact=it->action; ODINLOG(odinlog,normalDebug) << "pfact=" << pfact << STD_endl; if(pfact==action) return ipf; } } } #endif return -1; } SeqPlatform* SeqPlatformProxy::get_platform_ptr() {return platforms->get_current();} void SeqPlatformProxy::init_static() { Log odinlog("SeqClass","init_static"); platforms.init("platforms"); } void SeqPlatformProxy::destroy_static() { Log odinlog("SeqPlatformProxy","destroy_static"); platforms.destroy(); } template class SingletonHandler; SingletonHandler SeqPlatformProxy::platforms; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/odinseq/seqmakefile.cpp0000644000175000017500000002132311363773555014053 00000000000000#include "seqmakefile.h" #include "seqplatform.h" #include "seqdriver.h" #ifndef NO_CMDLINE STD_string SeqMakefile::get_exe_postfix() { STD_string result; #ifdef USING_WIN32 result=".exe"; #endif return result; } STD_string SeqMakefile::get_so_postfix() { STD_string result=".so"; #ifdef MACOS result=".dylib"; #endif #ifdef USING_WIN32 result=".dll"; #endif return result; } STD_string SeqMakefile::get_obj_postfix() { STD_string result=".o"; #ifdef USING_WIN32 #ifndef USING_GCC result=".obj"; #endif #endif return result; } SeqMakefile::SeqMakefile(const STD_string& methlabel, const STD_string& odin_install_prefix, const STD_string& compiler, const STD_string& compiler_flags, const STD_string& linker, const STD_string& extra_includes, const STD_string& extra_libs) : inst_prefix(odin_install_prefix), cxx(compiler), cxxflags(compiler_flags), ld(linker), add_includes(extra_includes), add_libs(extra_libs) { set_label(methlabel); // SeqPlatformCreator(); // create platform instances/drivers } STD_string SeqMakefile::get_Makefile(const STD_string& methroot) const { STD_string result; unsigned int i; result+="all: "+get_methlabel()+get_exe_postfix()+" "; /*if(pf!=paravision)*/ result+=get_methlabel()+get_so_postfix(); result+="\n\n"; // code for shared object svector cmd_chain(get_method_compile_chain(false,true)); if(cmd_chain.size()<3) return result; result+=get_methlabel()+get_obj_postfix()+": "+get_methlabel()+".cpp\n"; result+=" "+cmd_chain[0]+"\n"; // stuff for unique id result+=" "+cmd_chain[1]+"\n"; // compilation of object result+="\n\n"; result+=get_methlabel()+get_so_postfix()+": "+get_methlabel()+get_obj_postfix()+"\n"; for(i=2; i='a' && c<='z') result=true; if(c>='A' && c<='Z') result=true; if(!firstchar && c>='0' && c<='9') result=true; return result; } STD_string valid_c_label(const STD_string& label) { STD_string clabel(label); if(!clabel.length()) { clabel="Label"; } else { if(!valid_c_char(clabel[0],true)) clabel="_"+clabel; for(unsigned int i=0; i unique_id"; ichain++; result[ichain]=compiler+" -c "+get_methlabel()+".cpp "+includes+cxxflags+" -fPIC "+defines; ichain++; if(executable) { STD_string exeflags; #ifdef MACOS exeflags="-Wl,-bind_at_load "; // avoids lots of warnings #endif result[ichain]=linker+" "+exeflags+cxxflags+" -o "+get_methlabel()+" "+get_methlabel()+get_obj_postfix()+" -lc "+libdir+LDFLAGS+" "+odin_libs; ichain++; } if(shared_object) { result[ichain] ="rm -f *"+get_so_postfix()+" so_locations"; ichain++; STD_string soflags; #ifdef MACOS soflags=" -dynamiclib "; // the MacOS way of shared objects #else soflags=" -shared -Wl,-soname,`cat unique_id`"+get_so_postfix()+" "; #endif soflags+=" -o `cat unique_id`"+get_so_postfix()+" "; result[ichain]=linker+soflags+get_methlabel()+get_obj_postfix()+" -lc "+libdir+LDFLAGS+" "+odin_libs; ichain++; } #endif return result; } STD_string SeqMakefile::get_method_clean() const { return "rm -f unique_id *"+get_so_postfix()+" *"+get_obj_postfix()+" "+get_methlabel()+" odin_parx* "+get_methlabel()+"_sequencePars* odinpls* "+get_methlabel()+".ppg "+get_methlabel()+".r odin_versionInfo "+get_methlabel()+"_description "+get_methlabel()+"_messages"; } STD_string SeqMakefile::get_method_install(const STD_string& methdir) const { return "./"+get_methlabel()+" write_code -s "+methdir; } svector SeqMakefile::get_odin4idea_method_compile_chain(const STD_string& in_dir, const STD_string& odindir, const STD_string& vxworks_path, const STD_string& vxworks_cxx, const STD_string& vxworks_flags, const STD_string& win_cxx, const STD_string& hostd_flags, const STD_string& host_flags) const { STD_string defines=get_methdefines(get_methlabel()+"_main",valid_c_label(get_methlabel())); /* This will be done in cxxwrapper #ifdef USING_WIN32 // add path for ppc-compiler binaries JDXfileName ppc_path(vxworks_path); // normalize file name STD_string oldpath=secure_getenv("PATH"); // remove blanks which make ccppc fail while(oldpath.find("; ")!=STD_string::npos) oldpath=replaceStr(oldpath,"; ",";"); while(oldpath.find(" ;")!=STD_string::npos) oldpath=replaceStr(oldpath," ;",";"); if(oldpath.find(ppc_path) == STD_string::npos) { STD_string path="PATH="+oldpath+";"+ppc_path; _putenv(path.c_str()); } #endif */ JDXfileName methdir(in_dir); // normalize filename STD_string method_bname=methdir+SEPARATOR_STR+get_methlabel(); STD_string method_bname_slash=replaceStr(method_bname,"\\","/"); // use forward slashes for vxworks STD_string includes; svector result; result.resize(3); includes=STD_string(" -I")+odindir+SEPARATOR_STR+"vxworks"+SEPARATOR_STR+"include"; result[0]=JDXfileName(vxworks_cxx)+" "+method_bname_slash+".cpp -c "+includes+" "+defines+" "+vxworks_flags+" -o "+method_bname_slash+".o"; // srccode must be 1st for ccpentium includes=STD_string(" -I")+odindir+SEPARATOR_STR+"host"+SEPARATOR_STR+"include"; result[1]=JDXfileName(win_cxx)+" "+method_bname+".cpp -c "+includes+" "+defines+" "+host_flags+" -Fo"+method_bname+".obj"; includes=STD_string(" -I")+odindir+SEPARATOR_STR+"hostd"+SEPARATOR_STR+"include"; result[2]=JDXfileName(win_cxx)+" "+method_bname+".cpp -c "+includes+" "+defines+" "+hostd_flags+" -Fo"+method_bname+"d.obj"; return result; } #endif odin-1.8.5/odinseq/seqvec.cpp0000644000175000017500000002645411322062345013044 00000000000000#include "seqvec.h" #include "seqloop.h" #include #include void SeqVector::common_int() { reordvec=0; nr_cache_up2date=false; } SeqVector::SeqVector(const STD_string& object_label) { common_int(); set_label(object_label); } SeqVector::SeqVector(const STD_string& object_label, unsigned int nindices, int slope, int offset ) { common_int(); set_label(object_label); ivector ivec(nindices); for(unsigned int i=0; i odinlog(this,"~SeqVector()"); if(reordvec) delete reordvec; } SeqVector& SeqVector::operator = (const SeqVector& sv) { SeqClass::operator = (sv); indexvec=sv.indexvec; if(reordvec) delete reordvec; reordvec=0; if(sv.reordvec) reordvec=new SeqReorderVector(this,sv.reordvec); return *this; } unsigned int SeqVector::get_numof_iterations() const { Log odinlog(this,"get_numof_iterations"); unsigned int result=get_vectorsize(); if(reordvec) { result=reordvec->get_reordered_size(result); } ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } int SeqVector::get_current_index() const { Log odinlog(this,"get_current_index"); int result=0; const SeqVector* sim=simhandler.get_handled(); if(sim) { result=sim->get_current_index(); ODINLOG(odinlog,normalDebug) << "result(sim)=" << result << STD_endl; } else { if(loopcounter_is_active()) { result=get_loopcounter(); ODINLOG(odinlog,normalDebug) << "result(loopcounter)=" << result << STD_endl; } } if(reordvec) { result=reordvec->get_reordered_index(result); ODINLOG(odinlog,normalDebug) << "result(reordvec)=" << result << STD_endl; } return result; } int SeqVector::get_acq_index() const { Log odinlog(this,"get_acq_index"); int result=get_current_index(); if(result>=0 && resultnr_cache_up2date==false) nr_cache_up2date=false; if(nr_cache_up2date) return nr_cache; nr_cache=noRelation; if(vechandler.get_handled()) { ODINLOG(odinlog,normalDebug) << "has vechandler" << STD_endl; if(reordvec && reordvec->vechandler.get_handled()) { ODINLOG(odinlog,normalDebug) << "has reorder vector" << STD_endl; if(vechandler.get_handled()->contains(reordvec->vechandler.get_handled())) nr_cache=reorderInner; if(reordvec->vechandler.get_handled()->contains(vechandler.get_handled())) nr_cache=vecInner; } else ODINLOG(odinlog,normalDebug) << "has NO reorder vector" << STD_endl; } else ODINLOG(odinlog,normalDebug) << "has NO vechandler" << STD_endl; programContext gpgcontext; gpgcontext.mode=brukerGpg; if(reordvec && nr_cache!=noRelation) { if(reordvec->vechandler.get_handled()->unroll_program(gpgcontext) || vechandler.get_handled()->unroll_program(gpgcontext)) nr_cache=unrolledLoop; } if(nr_cache==noRelation) ODINLOG(odinlog,normalDebug) << "noRelation" << STD_endl; if(nr_cache==reorderInner) ODINLOG(odinlog,normalDebug) << "reorderInner" << STD_endl; if(nr_cache==vecInner) ODINLOG(odinlog,normalDebug) << "vecInner" << STD_endl; if(nr_cache==unrolledLoop) ODINLOG(odinlog,normalDebug) << "unrolledLoop" << STD_endl; nr_cache_up2date=true; if(reordvec) reordvec->nr_cache_up2date=true; return nr_cache; } iarray SeqVector::get_index_matrix() const { unsigned int ncols=get_numof_iterations(); unsigned int nrows=1; if(reordvec) nrows=reordvec->get_numof_iterations(); iarray result(nrows,ncols); unsigned int icol,irow; if(reordvec) { for(irow=0; irowget_reordered_index(icol,irow); } } } else { for(icol=0; icolget_current_index(); return result; } STD_string SeqVector::get_reord_iterator(const STD_string& iterator) const { STD_string result(iterator); if(reordvec) result=reordvec->get_reordered_iterator(iterator); return result; } const SeqVector& SeqVector::set_vechandler(const SeqCounter *sc) const { Log odinlog(this,"set_vechandler"); ODINLOG(odinlog,normalDebug) << "counter=" << sc->get_label() << STD_endl; vechandler.set_handled(sc); return *this; } bool SeqVector::loopcounter_is_active() const { Log odinlog(this,"loopcounter_is_active"); bool result=false; const SeqCounter* sc=vechandler.get_handled(); ODINLOG(odinlog,normalDebug) << "sc=" << (void*)sc << STD_endl; if(sc) { result=sc->counter_is_active(); ODINLOG(odinlog,normalDebug) << "loop " << vechandler.get_handled()->get_label() << " says " << result << STD_endl; } return result; } int SeqVector::get_loopcounter() const { Log odinlog(this,"get_loopcounter"); unsigned int result=0; const SeqCounter* sc=vechandler.get_handled(); if(sc) { result=sc->get_counter(); ODINLOG(odinlog,normalDebug) << "result(" << sc->get_label() << ")=" << result << STD_endl; } if(result>=get_numof_iterations()) result=0; return result; } bool SeqVector::is_qualvector() const { if(indexvec.size()) return false; // assume simple index vector return true; } bool SeqVector::is_acq_vector() const { if(simhandler.get_handled()) return simhandler.get_handled()->is_acq_vector(); return Handled::is_handled(); } /////////////////////////////////////////////////////////////////////////////// // template instantiations, collect them here to include tjutils/tjhandler_code.h only once template class Handler; template class Handled; /////////////////////////////////////////////////////////////////////////////// SeqReorderVector::SeqReorderVector(const SeqVector* user, const SeqReorderVector* copy_templ) : reord_scheme(noReorder), n_reord_segments(1), encoding_scheme(linearEncoding), reorder_user(user) { set_label(STD_string(user->get_label())+"_reordvec"); if(copy_templ) { reord_scheme=copy_templ->reord_scheme; n_reord_segments=copy_templ->n_reord_segments; encoding_scheme=copy_templ->encoding_scheme; } } unsigned int SeqReorderVector::get_reordered_size(unsigned int vecsize) const { Log odinlog(this,"get_reordered_size"); unsigned int result=vecsize; if( reord_scheme==blockedSegmented || reord_scheme==interleavedSegmented) { result=vecsize/n_reord_segments; ODINLOG(odinlog,normalDebug) << "vecsize/n_reord_segments/result=" << vecsize << "/" << n_reord_segments << "/" << result << STD_endl; } return result; } svector SeqReorderVector::get_vector_commands(const STD_string& iterator) const { reord_iterator_cache=iterator; // cache for later use by get_reordered_iterator() return reorder_user->get_reord_vector_commands(iterator); } int SeqReorderVector::get_reordered_index(int counter, int reord_iteration) const { Log odinlog(this,"get_reordered_index"); int nvals_per_segment =reorder_user->get_numof_iterations(); ODINLOG(odinlog,normalDebug) << "counter/reord_iteration/nvals_per_segment/n_reord_segments=" << counter << "/" << reord_iteration << "/" << nvals_per_segment << "/" << n_reord_segments << STD_endl; int peindex=counter; if(reord_scheme==rotateReorder) { ODINLOG(odinlog,normalDebug) << "using rotateReorder" << STD_endl; peindex=counter+reord_iteration; if(peindex>=nvals_per_segment) peindex-=nvals_per_segment; } if( reord_scheme==blockedSegmented ) { ODINLOG(odinlog,normalDebug) << "using blockedSegmented" << STD_endl; peindex=reord_iteration*nvals_per_segment+counter; } if( reord_scheme==interleavedSegmented ) { ODINLOG(odinlog,normalDebug) << "using interleavedSegmented" << STD_endl; peindex=counter*n_reord_segments+reord_iteration; } // phase-encoding scheme int result=peindex; //default if(encoding_scheme==reverseEncoding) { result=reorder_user->get_vectorsize()-1-peindex; } if(encoding_scheme==centerOutEncoding || encoding_scheme==centerInEncoding) { int sign=int(pow(-1,peindex)); int n=reorder_user->get_vectorsize(); int cent=n/2; int index=peindex; if(encoding_scheme==centerInEncoding) index=n-1-peindex; result=cent+sign*int((index+1)/2); ODINLOG(odinlog,normalDebug) << "sign/cent=" << sign << "/" << cent<< STD_endl; } if(encoding_scheme==maxDistEncoding) { result = peindex%2 * (reorder_user->get_vectorsize()+1)/2 + peindex/2; } ODINLOG(odinlog,normalDebug) << "peindex/result" << peindex << "/" << result << STD_endl; return result; } STD_string SeqReorderVector::get_reordered_iterator(const STD_string& iterator) const { STD_string result(iterator); STD_string nvals_per_segment =itos(reorder_user->get_numof_iterations()); if(reord_scheme==rotateReorder) { result= "("+iterator+"+"+reord_iterator_cache+")%"+nvals_per_segment; } if( reord_scheme==blockedSegmented ) { result= reord_iterator_cache+"*"+nvals_per_segment+"+"+iterator; } if( reord_scheme==interleavedSegmented ) { result= iterator+"*"+itos(n_reord_segments)+"+"+reord_iterator_cache; } // phase-encoding scheme STD_string vectorsize =itos(reorder_user->get_vectorsize()); if(encoding_scheme==reverseEncoding) { result = vectorsize +"-1-(" + result + ")"; } if(encoding_scheme==centerOutEncoding || encoding_scheme==centerInEncoding) { STD_string sign="(int)(pow(-1,"+result+"))"; STD_string cent=vectorsize+"/2"; STD_string indexstr=result; if(encoding_scheme==centerInEncoding) indexstr="("+vectorsize+"-1-"+result+")"; result=cent+"+"+sign+"*(int)(("+indexstr+"+1)/2)"; } if(encoding_scheme==maxDistEncoding) { result = result + "%2 * (" +vectorsize + "+1)/2 + "+result+"/2"; } return result; } unsigned int SeqReorderVector::get_vectorsize() const { unsigned int result=1; if(reord_scheme==rotateReorder) result=reorder_user->get_vectorsize(); if( blockedSegmented <= reord_scheme && reord_scheme <= interleavedSegmented ) { result=n_reord_segments; } return result; } // Template instantiations template class ListItem; template class List; template class Handler; template class Handled; odin-1.8.5/odinseq/seqlist.h0000644000175000017500000001324411322062345012700 00000000000000/*************************************************************************** seqlist.h - description ------------------- begin : Wed Aug 14 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQLIST_H #define SEQLIST_H #include #include #include #include #define _MIN_PPG_CMDSIZE_ 25 #define _MIN_GP_CMDSIZE_ 50 /** * @addtogroup odinseq_internals * @{ */ /** * The base class for platform specific drivers of lists of sequence objects */ class SeqListDriver : public SeqDriverBase { public: SeqListDriver() {} virtual ~SeqListDriver() {} virtual STD_string pre_program (programContext& context, const SeqRotMatrixVector* rotmats) const = 0; virtual STD_string post_program(programContext& context, const SeqRotMatrixVector* rotmats) const = 0; virtual STD_string get_itemprogram(const SeqTreeObj* item, programContext& context) const = 0; virtual void pre_event (eventContext& context, const RotMatrix* rotmatrix) const = 0; virtual void post_event(eventContext& context, const RotMatrix* rotmatrix) const = 0; virtual void pre_itemevent (const SeqTreeObj* item, eventContext& context) const = 0; virtual void post_itemevent(const SeqTreeObj* item, eventContext& context) const = 0; virtual bool prep_driver() = 0; virtual SeqListDriver* clone_driver() const = 0; }; /** @} */ ////////////////////////////////////////////////////////////////////// class SeqObjLoop; // forward declaration class SeqDecoupling; // forward declaration class SeqGradObjInterface; // forward declaration class SeqGradChan; // forward declaration class SeqGradChanList; // forward declaration /** * @ingroup odinseq * * \brief Container for sequence objects * * This is a container class for other sequence objects. */ class SeqObjList : public SeqObjBase, public List { public: /** * Construct an empty sequence container with the given label */ SeqObjList(const STD_string& object_label="unnamedSeqObjList"); /** * Constructs a copy of 'so' */ SeqObjList(const SeqObjList& so); ~SeqObjList(); /** * Assignment operator that makes this sequence container become a copy of 'so' */ SeqObjList& operator = (const SeqObjList& so); /** * Special assignment for loops */ SeqObjList& operator = (const SeqObjLoop& sl); /** * Special assignment for decoupling */ SeqObjList& operator = (const SeqDecoupling& sd); /** * Special treatment for single non-container sequence objects */ SeqObjList& operator = (const SeqObjBase& soa); /** * Special treatment for assignment from gradient objects */ SeqObjList& operator = (SeqGradObjInterface& sgoa) {clear(); return (*this)+=sgoa;} /** * Special treatment for assignment from gradient objects */ SeqObjList& operator = (SeqGradChan& sgc) {clear(); return (*this)+=sgc;} /** * Special treatment for assignment from gradient objects */ SeqObjList& operator = (SeqGradChanList& sgcl) {clear(); return (*this)+=sgcl;} /** * Special treatment for appending sequence objects */ SeqObjList& operator += (const SeqObjBase& soa); /** * Special treatment for appending gradient objects */ SeqObjList& operator += (SeqGradObjInterface& sgoa); /** * Special treatment for appending gradient objects */ SeqObjList& operator += (SeqGradChan& sgc); /** * Special treatment for appending gradient objects */ SeqObjList& operator += (SeqGradChanList& sgcl); /** * Specifies an extra vector of rotatition matrices to be used with this container. * The part held by this container will be executed with the current rotation matrix. * The sequence vector 'matrixVec' can then be attached to a loop to iterate over the different matrices. */ SeqObjList& set_gradrotmatrixvector(const SeqRotMatrixVector& matrixVec) {gradrotmatrixvec.set_handled(&matrixVec); return *this;} // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; unsigned int event(eventContext& context) const; double get_duration() const; STD_string get_properties() const; void query(queryContext& context) const; RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const; SeqValList get_freqvallist(freqlistAction action) const; SeqValList get_delayvallist() const; double get_rf_energy() const; protected: // overloading virtual function from SeqClass void clear_container() {clear();} bool prep(); private: friend class SeqGradChan; friend class SeqOperator; // overloading virtual function from SeqObjBase bool contains_list() const {return true;} mutable SeqDriverInterface listdriver; Handler gradrotmatrixvec; static Handler current_gradrotmatrixvec; }; #endif odin-1.8.5/odinseq/odinpulse_shapes.cpp0000644000175000017500000003351311625224370015121 00000000000000#include "odinpulse.h" #include "seqplatform.h" #ifndef __DBL_EPSILON__ #define __DBL_EPSILON__ 1.e-38 #endif //////////////////////////////////////////////////// // adiabatic shapes: /** * * Sech Pulse */ class Sech : public JDXfunctionPlugIn { JDXdouble trunc; JDXdouble bw; public: Sech() : JDXfunctionPlugIn ( "Sech" ) { set_description ( "Adiabatic hyperbolic secant pulse." ); trunc=0.01; trunc.set_minmaxval ( 0.001,0.5 ).set_description ( "Relative amplitude at the edges of the pulse" ); append_member ( trunc,"TruncationLevel" ); bw=10.0; bw.set_minmaxval ( 0.001,100.0 ).set_description ( "Inversion width" ).set_unit ( ODIN_FREQ_UNIT ); append_member ( bw,"BandWidth" ); } STD_complex calculate_shape ( float s, float Tp ) const { double beta=2.0*acosh ( secureInv ( trunc ) ); double my=secureDivision ( PII*Tp*bw,beta ); double x=beta* ( s-0.5 ); double sech= ( 1/cosh ( x ) ); double amplitude=100*sech; double phase=my*log ( sech ); return STD_complex ( amplitude*cos ( phase ),amplitude*sin ( phase ) ); } const shape_info& get_shape_properties() const { shape_info_retval.adiabatic=true; return shape_info_retval; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Sech;} }; //////////////////////////////////////////////////// /** * * Wurst Pulse */ class Wurst : public JDXfunctionPlugIn { JDXdouble ncycles; JDXdouble truncpar; public: Wurst() : JDXfunctionPlugIn ( "Wurst" ) { set_description ( "Adiabatic WURST pulse (Kupce and Freeman 1995, JMR A 117:246)" ); ncycles=10.0; ncycles.set_minmaxval ( 1.0,50.0 ).set_description ( "Number of phase cycles" ); append_member ( ncycles,"NumOfCycles" ); truncpar=10.0; truncpar.set_minmaxval ( 1.0,50.0 ).set_description ( "Truncation Parameter" ); append_member ( truncpar,"Truncation" ); } STD_complex calculate_shape ( float s, float Tp ) const { float beta_t,phi,amplitude,ss; ss=s-0.5; phi=4.0* ( 2.0*PII*ncycles ) *ss*ss; beta_t=ss*PII; amplitude=1.0-pow ( double ( fabs ( sin ( beta_t ) ) ),double ( truncpar ) ); return STD_complex ( amplitude*cos ( phi ),amplitude*sin ( phi ) ); } const shape_info& get_shape_properties() const { shape_info_retval.adiabatic=true; return shape_info_retval; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Wurst;} }; //////////////////////////////////////////////////// /** * * Wurst Pulse */ class Fermi : public JDXfunctionPlugIn { JDXdouble width; JDXdouble slope; public: Fermi() : JDXfunctionPlugIn ( "Fermi" ) { set_description ( "Fermi pulse for MT and B1 mapping with Bloch-Siegert shift" ); width=0.75; width.set_minmaxval ( 0, 1 ).set_description ( "Distance of Fermi Function turning points (not FWHM)" ); append_member ( width,"width" ); slope=80; slope.set_minmaxval ( 0,150 ).set_description ( "Exponential factor in Fermi function: influences the slope of the ramps" ); append_member ( slope,"slope" ); } STD_complex calculate_shape ( float s, float Tp ) const { STD_complex result ( exp ( -width / 2 * slope ) / ( exp ( ( fabs ( s - 0.5 ) - width / 2 ) * slope ) + 1 ), 0 ); if ( s < __DBL_EPSILON__ || s > 1 - __DBL_EPSILON__ ) result = STD_complex ( 0,0 ); return result; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Fermi;} }; //////////////////////////////////////////////////// /** * * Const Pulse */ class ConstPulse : public JDXfunctionPlugIn { public: ConstPulse() : JDXfunctionPlugIn ( "Const" ) { set_description ( "Constant-amplitude pulse" ); } STD_complex calculate_shape ( float,float ) const { return STD_complex ( 1.0 ); } STD_complex calculate_shape ( const kspace_coord& ) const { return STD_complex ( 1.0 ); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new ConstPulse;} }; //////////////////////////////////////////////////// /** * * Sinc Pulse */ class Sinc : public JDXfunctionPlugIn { public: JDXdouble thick; Sinc() : JDXfunctionPlugIn ( "Sinc" ) { set_description ( "Pulse with a box-car shaped excitation profile" ); thick=5.0; thick.set_minmaxval ( 0.01,200.0 ).set_description ( "Slice thickness" ).set_unit ( ODIN_SPAT_UNIT ); append_member ( thick,"SliceThickness" ); } STD_complex calculate_shape ( const kspace_coord& tdep ) const { return STD_complex ( sinc ( 0.5*tdep.kz*thick ) ); } const shape_info& get_shape_properties() const { shape_info_retval.spatial_extent=thick; return shape_info_retval; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Sinc;} }; //////////////////////////////////////////////////// /** * * Import ASCII */ class ImportASCII : public JDXfunctionPlugIn { public: JDXfileName fname; JDXcomplexArr shape; ImportASCII() : JDXfunctionPlugIn ( "ImportASCII" ) { set_description ( "Import pulse from ASCII file which must have the format 'amplitude phase amplitude phase ...'. The phase is taken as rad." ); fname.set_description ( "ASCII file name" ); append_member ( fname,"FileName" ); } void init_shape() { if ( fname=="" ) return; STD_string sF; ::load ( sF,fname ); svector posstring=tokens ( sF ); unsigned int numpoints=posstring.size() /2; shape.redim ( numpoints ); for ( unsigned int i=0; iregister_function ( shapeFunc,zeroDeeMode ).register_function ( shapeFunc,oneDeeMode ).register_function ( shapeFunc,twoDeeMode ); ( new ImportASCII )->register_function ( shapeFunc,zeroDeeMode ).register_function ( shapeFunc,oneDeeMode ).register_function ( shapeFunc,twoDeeMode ); ( new ImportBruker )->register_function ( shapeFunc,zeroDeeMode ).register_function ( shapeFunc,oneDeeMode ).register_function ( shapeFunc,twoDeeMode ); ( new Sinc )->register_function ( shapeFunc,oneDeeMode ); ( new Sech )->register_function ( shapeFunc,zeroDeeMode ); ( new Wurst )->register_function ( shapeFunc,zeroDeeMode ); ( new Fermi )->register_function ( shapeFunc,zeroDeeMode ); ( new Rect )->register_function ( shapeFunc,twoDeeMode ); ( new Disk )->register_function ( shapeFunc,twoDeeMode ); ( new NPeaks )->register_function ( shapeFunc,twoDeeMode ); } void JDXshape::destroy_static() { // pulgins will be deleted by JDXfunction } EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/odinseq/seqdelay.cpp0000644000175000017500000000165611322062345013362 00000000000000#include "seqdelay.h" SeqDelay::SeqDelay(const STD_string& object_label,float delayduration, const STD_string& command,const STD_string& durationVariable) : SeqObjBase(object_label),SeqDur(object_label,delayduration), delaydriver(object_label) { cmd=command; durcmd=durationVariable; } SeqDelay::SeqDelay(const SeqDelay& sd) : delaydriver(sd.get_label()) { SeqDelay::operator = (sd); } SeqDelay& SeqDelay::set_command(const STD_string& command) { cmd=command; return *this; } SeqDelay& SeqDelay::operator = (const SeqDelay& sd) { SeqObjBase::operator = (sd); SeqDur::operator = (sd); delaydriver=sd.delaydriver; cmd=sd.cmd; durcmd=sd.durcmd; return *this; } SeqDelay& SeqDelay::operator = (float dur) { set_duration(dur); return *this; } STD_string SeqDelay::get_program(programContext& context) const { return delaydriver->get_program(context,get_duration(),cmd,durcmd); } odin-1.8.5/odinseq/seqgradobj.h0000644000175000017500000000403311322062345013331 00000000000000/*************************************************************************** seqgradobj.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADOBJ_H #define SEQGRADOBJ_H #include #include #include #include class SeqObjList; // forward declaration class SeqRotMatrixVector; // forward declaration /** * @addtogroup odinseq_internals * @{ */ /** * This is the abstract base class for all gradient objects that can be part of a sequence */ class SeqGradObjInterface : public virtual SeqGradInterface, public virtual SeqTreeObj, public Handled, public Handled { public: // overloading virtual functions from SeqTreeObj double get_duration() const; double get_pulprogduration() const; // Do we still need this? virtual bool need_gp_terminator() const {return false;} protected: SeqGradObjInterface(const STD_string& object_label="unnamedSeqGradObjInterface"); SeqGradObjInterface(const SeqGradObjInterface& sgoa); SeqGradObjInterface& operator = (const SeqGradObjInterface& sgoa); }; /** @} */ #endif odin-1.8.5/odinseq/seqloop.h0000644000175000017500000001121511455553540012703 00000000000000/*************************************************************************** seqloop.h - description ------------------- begin : Mon Aug 13 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQLOOP_H #define SEQLOOP_H #include #include #include /** * @addtogroup odinseq * @{ */ /** * \brief Sequence Loop * * This class represents a loop which is used to enclose other sequence objects * so that they are repeatedely played out in the sequence */ class SeqObjLoop : public SeqCounter, public SeqObjList, public Embed { public: /** * Construct an empty loop object with the given label */ SeqObjLoop(const STD_string& object_label = "unnamedSeqObjLoop"); /** * Constructs a copy of 'sl' */ SeqObjLoop(const SeqObjLoop& sl); ~SeqObjLoop() {} /** * Assignment operator that makes this loop object become a copy of 'sl' */ SeqObjLoop& operator = (const SeqObjLoop& sl); /** * Duration the loop itself takes before iteration is started */ double get_preduration () const; /** * Duration the loop itself takes after its kernel is iterated */ double get_postduration() const; /** * Sets the inner part of loop, only useful for explicit setup of loops, i.e. in SeqEpiDriverDefault */ SeqObjLoop& set_body(const SeqObjBase& so); /** * Specify the number of times the body of the loop will be repeated, only useful for explicit setup of loops, i.e. in SeqEpiDriverDefault */ SeqObjLoop& set_times(unsigned int t); /** * Generates and returns a new loop object that is a copy of this. The new loop will * loop over 'embeddedBody'. */ SeqObjLoop& operator () (const SeqObjBase& embeddedBody); /** * This operator will append 'seqvector' to the list of vectors the loop will iterate through */ SeqObjLoop& operator [] (const SeqVector& seqvector); /** * This operator specifies the number of times the body of the loop will be repeated */ SeqObjLoop& operator [] (unsigned int t); // overwriting virtual functions from SeqCounter int get_times() const; // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const; double get_duration() const; unsigned int event(eventContext& context) const; SeqValList get_freqvallist(freqlistAction action) const; SeqValList get_delayvallist() const; double get_rf_energy() const; void query(queryContext& context) const; RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const; STD_string get_properties() const; private: // overwriting virtual functions from SeqClass bool prep(); void clear_container(); // overwriting virtual functions from SeqCounter void add_vector(const SeqVector& seqvector); bool unroll_program(programContext& context) const; /** * Returns 'true' if the loop only repeats its contents and does not change its objects while looping. * If 'only_qualvectors' is set to true, all vectors that do not influence the timing or RF power * deposition will be considered as repetitions. */ bool is_repetition_loop(bool only_qualvectors=false) const; /** * Returns 'true' if the loop only repeats the acquisition ordering. */ bool is_acq_repetition_loop() const; /** * Returns 'true' if the loop repeats its kernel by altering values of the vectors therein * (gradient strength, frequency, phase) but without changing the order of the sequence objects. */ bool is_obj_repetition_loop() const; /** * Returns 'true' if the subtree of the loop contains an iterator which changes reco indices. */ bool contains_acq_iter() const; float get_single_duration() const; unsigned int times; unsigned int get_numof_acq() const; mutable unsigned int numof_acq_cache; mutable bool is_toplevel_reploop; }; /** @} */ #endif odin-1.8.5/odinseq/seqmeth.h0000644000175000017500000003114211322062345012657 00000000000000/*************************************************************************** seqmeth.h - description ------------------- begin : Thu Aug 9 2001 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQMETH_H #define SEQMETH_H #include #include #include #include #include ////////////////////////////////////////////////////////////////////// // forward declarations class SeqMethod; class SeqPulsar; ////////////////////////////////////////////////////////////////////// /** * @ingroup odinseq_internals * Proxy class to deal with different ODIN methods at once */ class SeqMethodProxy : public StaticHandler { public: SeqMethodProxy() { Log odinlog("SeqMethodProxy","SeqMethodProxy()"); } static void set_current_method(unsigned int index); static SeqMethod* get_current_method(); static unsigned int get_numof_methods(); static unsigned int delete_methods(); static const char* get_method_label(); static const char* get_status_string(); // pointer-like syntax to access current method SeqMethod* operator -> () {return get_current_method();} SeqMethod& operator [] (unsigned int index); static bool load_method_so(const STD_string& so_filename); // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); protected: // called by derivedmethod classes to register themselves static void register_method(SeqMethod* meth); private: // struct to store references to all registered methods struct MethodList : public STD_list, public Labeled {}; static SingletonHandler registered_methods; // struct to store references to the current method struct MethodPtr : public Labeled { SeqMethod* ptr; }; static SingletonHandler current_method; static SeqMethod* empty_method; }; ////////////////////////////////////////////////////////////////////// /* State diagram for SeqMethod, i.e. for all NMR sequences: Possible transitions between states are indicated by the corresponding member functions that perform the transition. empty <--------\ | | | clear() | init() | | | V | | initialised ---| | | | | build() | | | V | | built ---------| | | | | prepare() | | | V | | prepared ------' */ /** * @ingroup odinseq * * \brief Base class for methods (sequences) * * The base class for all NMR sequences. * To create a new sequence, write a new class which is derived * from SeqMethod and overload the following virtual functions * with the specified functionality: * - void method_pars_init(): Initialize sequence parameters (set default values, * append to the list of registered parameters of the method) * - void method_seq_init(): Create the internal layout of the sequence, i.e. * the sequence tree * - void method_rels(): Calculate timings of the sequence * - void method_pars_set(): Finalize the sequence * * To get an idea what has to be done in each function, please take a * look at the example sequences. */ class SeqMethod : protected SeqMethodProxy, public SeqObjList, public virtual JDXeditCaller, public StateMachine { public: /** * Constructs a method with the given label. */ SeqMethod(const STD_string& method_label); /** * Destructor */ virtual ~SeqMethod(); // public interface to obtain the different states: /** * Performs state transition to 'empty' */ bool clear() {return empty.obtain_state();} /** * Performs state transition to 'initialised' */ bool init() {return initialised.obtain_state();} /** * Performs state transition to 'built' */ bool build() {return built.obtain_state();} /** * Performs state transition to 'prepared' */ bool prepare() {return prepared.obtain_state();} /** * Updates the timing of the sequence (TR, TE) without changing its structure. * If the sequence is not yet in the 'built' state, this state will * be obtained first. */ bool update_timings(); /** * Prepares the acquisition parameters, i.e. recoInfo structure * and performs platform specific preparation (generating pulse program, etc.). * This function will be called by the current frontend (ODIN GUI, odin2idea, ...) * prior to the measurement. */ bool prep_acquisition() const; /** * Returns the description of the method */ const char* get_description() const {return description.c_str();} /** * This function is used in the ODINMAIN function to hand over control to the SeqMethod object. */ int process(int argc, char *argv[]); /** * Loads the sequence protocol (systemInfo, geometryInfo, sequencePars) from file 'filename' */ int load_protocol(const STD_string& filename); /** * Writes the sequence protocol (systemInfo, geometryInfo, sequencePars) to file 'filename' */ int write_protocol(const STD_string& filename) const {create_protcache(); return protcache->write(filename);} /** * Returns the method-specific parameters */ JcampDxBlock& get_methodPars() {return *methodPars;} /** * Loads the sequence parameters (commonPars & methodPars) from file */ int load_sequencePars(const STD_string& filename); /** * Writes the sequence parameters (commonPars & methodPars) to file */ int write_sequencePars(const STD_string& filename) const; /** * Sets the value of the sequence parameter 'parameter_label' to 'value'. * Returns true if successful. */ bool set_sequenceParameter(const STD_string& parameter_label, const STD_string& value); /** * Sets the current set of common sequence parameters */ SeqMethod& set_commonPars(const SeqPars& pars); /** * Returns the current set of common sequence parameters */ SeqPars& get_commonPars() {return (*commonPars);} /** * Sets the current geometry to 'geo' */ SeqMethod& set_geometry(const Geometry& geo) {geometryInfo->operator = (geo); return *this;} /** * Returns the current geometry */ Geometry& get_geometry() {return *(geometryInfo.unlocked_ptr());} /** * Loads the current geometry from disk */ int load_geometry(const STD_string& filename) {return geometryInfo->load(filename);} /** * Writes the current geometry to disk */ int write_geometry(const STD_string& filename) const {return geometryInfo->write(filename);} /** * Returns reference to the current study info */ Study& get_studyInfo() {return *(studyInfo.unlocked_ptr());} /** * Writes the systemInfo to disk */ int write_systemInfo(const STD_string& filename) const {return systemInfo->write(filename);} /** * Loads the systemInfo from disk */ int load_systemInfo(const STD_string& filename); /** * Initialises the method with the given system-specific stuff */ SeqMethod& init_systemInfo(double basicfreq,double maxgrad,double slewrate); /** * Writes the recoInfo to disk */ int write_recoInfo(const STD_string& filename) const; /** * Writes all files which describe the measurement, uses the given filename-prefix */ int write_meas_contex(const STD_string& prefix) const; /** * Returns the scan duration for this method */ double get_totalDuration() const; /** * Returns the current main nucleus of the sequence, i.e. the nucleus for which both, excitation and acquisition, will be performed */ STD_string get_main_nucleus() const {return systemInfo->get_main_nucleus();} /** * Returns the total number of acquisition windows in the sequence. */ unsigned int get_numof_acquisitions() const; /** * Returns a list of Pulsar pulses which are currently * active. */ STD_list get_active_pulsar_pulses() const; // overloaded virtual functions from SeqTreeObj unsigned int event(eventContext& context) const; // leave this public for idea_emulation void set_current_testcase(unsigned int index) {if(index empty; bool reset(); State initialised; bool empty2initialised(); State built; bool initialised2built(); State prepared; bool built2prepared(); }; ////////////////////////////////////////////////////////////////////// // Macro to include in every sequence file to create an entry point // Double-stage macros to stringize METHOD_LABEL, see http://c-faq.com/ansi/stringize.html #define ODINMETHOD_STRINGIZE_MACRO(x) #x #define ODINMETHOD_STRINGIZE(x) ODINMETHOD_STRINGIZE_MACRO(x) #ifdef NO_CMDLINE #define ODINMETHOD_ENTRY_POINT \ int ODINMAIN(int argc, char *argv[]) {\ return (new METHOD_CLASS(ODINMETHOD_STRINGIZE(METHOD_LABEL)))->process(argc,argv); \ } #else #define ODINMETHOD_ENTRY_POINT \ int ODINMAIN(int argc, char *argv[]) {\ if(LogBase::set_log_levels(argc,argv,false)) return 0; \ return (new METHOD_CLASS(ODINMETHOD_STRINGIZE(METHOD_LABEL)))->process(argc,argv); \ } #endif #endif odin-1.8.5/odinseq/seqgradvec.h0000644000175000017500000000664311322062345013345 00000000000000/*************************************************************************** seqgradvec.h - description ------------------- begin : Tue Aug 13 2002 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQGRADVEC_H #define SEQGRADVEC_H #include #include /** * @addtogroup odinseq * @{ */ /** * \brief Vector of constant gradients * * This class represents a gradient object with a constant gradient * shape with the the strength taken from a vector. This object * can be attached to a SeqLoop to iterate over the values in the * vector. */ class SeqGradVector : public SeqGradChan, public SeqVector { public: /** * Constructs a gradient vector labeled 'object_label' with the following properties: * - gradchannel: The channel this object should be played out * - maxgradstrength: The maximum gradient strength for this object * - trimarray: The vector of gradient strength values * - gradduration: The duration of this gradient object */ SeqGradVector(const STD_string& object_label,direction gradchannel, float maxgradstrength,const fvector& trimarray, double gradduration); /** * Constructs a copy of 'sgv' */ SeqGradVector(const SeqGradVector& sgv); /** * Construct an empty gradient object with the given label */ SeqGradVector(const STD_string& object_label = "unnamedSeqGradVector"); /** * Specifies the trim values that will be used */ SeqGradVector& set_trims(const fvector& trims); /** * Returns the trim values that will be used */ fvector get_trims() const {return trimvals;} /** * Assignment operator that makes this gradient channel object become a copy of 'sgv' */ SeqGradVector& operator = (const SeqGradVector& sgv); private: friend class SeqGradSubVector; friend class SeqGradVectorPulse; // overwriting virtual functions from SeqClass bool prep(); // overwriting virtual functions from SeqGradChan SeqGradChan& get_subchan(double starttime, double endtime) const; STD_string get_grdpart(float matrixfactor) const; float get_integral() const {return get_current_strength()*get_gradduration();} // overwriting virtual functions from SeqVector svector get_vector_commands(const STD_string& iterator) const; unsigned int get_vectorsize() const; bool prep_iteration() const; bool is_qualvector() const {return false;} svector get_reord_vector_commands(const STD_string& iterator) const; float get_current_strength() const; const SeqGradVector* parent; fvector trimvals; }; /** @} */ ///////////////////////////////////////////////////////////////// #endif odin-1.8.5/odinseq/seqparallel.h0000644000175000017500000001150511322062345013517 00000000000000/*************************************************************************** seqparallel.h - description ------------------- begin : Fri Apr 16 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPARALLEL_H #define SEQPARALLEL_H #include #include #include #include /** * @addtogroup odinseq_internals * @{ */ /** * The base class for platform specific drivers of parallel RF/gradient handling */ class SeqParallelDriver : public SeqDriverBase { public: SeqParallelDriver() {} virtual ~SeqParallelDriver() {} virtual STD_string get_program(programContext& context, const SeqObjBase* soa, const SeqGradObjInterface* sgoa) const = 0; virtual double get_duration (const SeqObjBase* soa, const SeqGradObjInterface* sgoa) const = 0; virtual double get_predelay (const SeqObjBase* soa, const SeqGradObjInterface* sgoa) const = 0; virtual SeqParallelDriver* clone_driver() const = 0; }; ///////////////////////////////////////////////////////////////////////////////////////// /** * This container class is used to play out a sequence object (RF pulse, acquisition) * and a gradient object in parallel */ class SeqParallel : public SeqObjBase, public virtual SeqGradInterface { public: /** * Construct an empty gradient channel list with the given label */ SeqParallel(const STD_string& object_label="unnamedSeqParallel"); /** * Constructs a copy of 'sgp' */ SeqParallel(const SeqParallel& sgp); /** * Assignment operator */ SeqParallel& operator = (const SeqParallel& sgp); /** * Makes 'sgc' become the gradient part */ SeqParallel& operator /= (SeqGradChan& sgc); /** * Makes 'sgcl' become the gradient part */ SeqParallel& operator /= (SeqGradChanList& sgcl); /** * Makes 'sgcp' become the gradient part */ SeqParallel& operator /= (SeqGradChanParallel& sgcp); /** * Makes 'sgoa' become the gradient part */ SeqParallel& operator /= (SeqGradObjInterface& sgoa); /** * Makes 'soa' become the RF part */ SeqParallel& operator /= (const SeqObjBase& soa); // overloading virtual function from SeqTreeObj STD_string get_program(programContext& context) const {return pardriver->get_program(context,get_pulsptr(),get_const_gradptr());} double get_duration() const; STD_string get_properties() const; unsigned int event(eventContext& context) const; SeqValList get_freqvallist(freqlistAction action) const; SeqValList get_delayvallist() const; void query(queryContext& context) const; RecoValList get_recovallist(unsigned int reptimes, JDXkSpaceCoords& coords) const; double get_rf_energy() const; // overloading virtual function from SeqGradInterface SeqGradInterface& set_strength(float gradstrength); SeqGradInterface& invert_strength(); float get_strength() const; fvector get_gradintegral() const; double get_gradduration() const; SeqGradInterface& set_gradrotmatrix(const RotMatrix& matrix); /** * Returns the duration for the gradient commands in the pulse programm */ double get_pulprogduration() const; /** * Clears the RF anf gradient part */ void clear(); protected: SeqParallel& set_pulsptr(const SeqObjBase* pptr); const SeqObjBase* get_pulsptr() const; SeqParallel& set_gradptr(SeqGradObjInterface* gptr); SeqParallel& set_gradptr(const SeqGradObjInterface* gptr); SeqParallel& clear_gradptr(); SeqGradObjInterface* get_gradptr() const; const SeqGradObjInterface* get_const_gradptr() const; private: friend class SeqOperator; friend class SeqObjList; friend class SeqObjVector; friend class SeqGradObjInterface; friend class SeqGradChanList; friend class SeqEpiDriverParavision; // overloading virtual function from SeqClass void clear_container() {clear();} mutable SeqDriverInterface pardriver; Handler pulsptr; Handler gradptr; Handler const_gradptr; }; /** @} */ #endif odin-1.8.5/odinseq/seqgradchanlist.cpp0000644000175000017500000001607111322062345014724 00000000000000#include "seqgradchanlist.h" #include "seqparallel.h" #include "seqgradchanparallel.h" #include void bad_serial(const Labeled& s1, const Labeled& s2) { Log odinlog("","bad_serial"); ODINLOG(odinlog,errorLog) << s1.get_label() << "+=" << s2.get_label() << ": different channels"; } SeqGradChanList::SeqGradChanList(const STD_string& object_label) { set_label(object_label); } SeqGradChanList::SeqGradChanList(const SeqGradChanList& sgcl) { Log odinlog(this,"SeqGradChanList"); SeqGradChanList::operator = (sgcl); } SeqGradChanList::~SeqGradChanList() { clear(); } SeqGradChanList& SeqGradChanList::operator = (const SeqGradChanList& sgcl) { Log odinlog(this,"operator = (...)"); SeqTreeObj::operator = (sgcl); clear(); for(constiter it=sgcl.get_const_begin();it!=sgcl.get_const_end();++it) { append(**it); } return *this; } double SeqGradChanList::get_duration() const { Log odinlog(this,"SeqGradChanList::get_duration"); SeqGradChanList dummylist(*this); SeqGradChanParallel dummypar; dummypar+=dummylist; SeqParallel dummy; dummy.set_gradptr((SeqGradObjInterface*)&dummypar); // will use SeqParallel to calculate duration ODINLOG(odinlog,normalDebug) << "duration=" << dummy.get_duration() << STD_endl; return dummy.get_duration(); } direction SeqGradChanList::get_channel() const { Log odinlog(this,"get_channel"); if(size()) return (*get_const_begin())->get_channel(); else return readDirection; } fvector SeqGradChanList::get_gradintegral() const { fvector result(3); for(constiter it=get_const_begin();it!=get_const_end();++it) { result=result+(*it)->get_gradintegral(); } return result; } SeqGradInterface& SeqGradChanList::set_strength(float gradstrength) { Log odinlog(this,"set_strength"); for(iter it=get_begin();it!=get_end();++it) { (*it)->set_strength(gradstrength); } return *this; } SeqGradInterface& SeqGradChanList::invert_strength() { Log odinlog(this,"invert_strength"); for(iter it=get_begin();it!=get_end();++it) { (*it)->invert_strength(); } return *this; } float SeqGradChanList::get_strength() const { Log odinlog(this,"get_strength"); float result=0.0; for(constiter it=get_const_begin();it!=get_const_end();++it) { float tmp=(*it)->get_strength(); if(fabs(tmp)>fabs(result)) result=tmp; } return result; } double SeqGradChanList::get_gradduration() const { Log odinlog(this,"SeqGradChanList::get_gradduration"); double result=0.0; ODINLOG(odinlog,normalDebug) << "size()=" << size() << STD_endl; for(constiter it=get_const_begin();it!=get_const_end();++it) { ODINLOG(odinlog,normalDebug) << "dur[" << (*it)->get_label() << "]=" << (*it)->get_gradduration() << STD_endl; result+=(*it)->get_gradduration(); } return result; } SeqGradInterface& SeqGradChanList::set_gradrotmatrix(const RotMatrix& matrix) { Log odinlog(this,"set_gradrotmatrix"); for(iter it=get_begin();it!=get_end();++it) (*it)->set_gradrotmatrix(matrix); return *this; } SeqGradChanList& SeqGradChanList::operator += (SeqGradChanList& sgcl) { Log odinlog(this,"SeqGradChanList::operator += (SeqGradChanList)"); if(size() && sgcl.size()) { if(get_channel()!=sgcl.get_channel()) { bad_serial(*this,sgcl); return *this; } } constiter it; // avoid redefenition error with VC6 SeqGradChanList chanlistbuff; // use buffer to avoid deadlocks for(it=sgcl.get_const_begin();it!=sgcl.get_const_end();++it) { ODINLOG(odinlog,normalDebug) << "appending >" << (*it)->get_label() << "<" << STD_endl; chanlistbuff+=(**it); } for(it=chanlistbuff.get_const_begin();it!=chanlistbuff.get_const_end();++it) { ODINLOG(odinlog,normalDebug) << "appending >" << (*it)->get_label() << "<" << STD_endl; (*this)+=(**it); } return *this; } SeqGradChanList& SeqGradChanList::operator += (SeqGradChan& sgc) { Log odinlog(this,"SeqGradChanList::operator += (SeqGradChan)"); ODINLOG(odinlog,normalDebug) << "appending >" << sgc.get_label() << "<" << STD_endl; if(size()) { if(get_channel()!=sgc.get_channel()) { bad_serial(*this,sgc); return *this; } } append(sgc); return *this; } void SeqGradChanList::clear_container() {clear();} unsigned int SeqGradChanList::event(eventContext& context) const { unsigned int result=0; for(constiter it=get_const_begin();it!=get_const_end();++it) { result+=(*it)->event(context); } return result; } void SeqGradChanList::query(queryContext& context) const { SeqTreeObj::query(context); // defaults if(context.action==count_acqs) return; // nothing to do context.treelevel++; for(constiter it=get_const_begin();it!=get_const_end();++it) { context.parentnode=this; // reset to this because it might changed by last query (*it)->query(context); } context.treelevel--; } STD_string SeqGradChanList::get_properties() const { return "NumOfChanObjs="+itos(size()); } fvector SeqGradChanList::get_switchpoints() const { Log odinlog(this,"get_switchpoints"); fvector result(size()); double elapsed_sp=0.0; unsigned int index=0; for(constiter it=get_const_begin();it!=get_const_end();++it) { elapsed_sp+=(*it)->get_gradduration(); result[index]=elapsed_sp; ODINLOG(odinlog,normalDebug) << "switchpoint(" << (*it)->get_label() << ")=" << elapsed_sp << STD_endl; index++; } return result; } SeqGradChanList& SeqGradChanList::get_chanlist4gp(const fvector& switchpoints) { Log odinlog(this,"get_chanlist4gp"); ODINLOG(odinlog,normalDebug) << "switchpoints=" << (1000.0*switchpoints).printbody() << STD_endl; SeqGradChanList *retso=new SeqGradChanList(STD_string(get_label())+"_4gp"); retso->set_temporary(); double elapsed_sp=0.0; for(unsigned int isp=0; ispget_gradduration()*1000.0+0.5)==graddur) retso->append(*chanptr); else { SeqGradChan& chanseg=chanptr->get_subchan(startelapsed-chanstart,elapsed_sp-chanstart); chanseg.set_gradrotmatrix(chanptr->gradrotmatrix); retso->append(chanseg); } } } return *retso; } SeqGradChan* SeqGradChanList::get_chan(double& chanstart, double midtime) { Log odinlog(this,"get_chan"); SeqGradChan* result=0; double elapsed_sp=0.0; for(constiter it=get_const_begin();it!=get_const_end();++it) { double startelapsed=elapsed_sp; elapsed_sp+=(*it)->get_gradduration(); if( (midtime>startelapsed) && (midtime; odin-1.8.5/odinseq/seqgradobj.cpp0000644000175000017500000000160711322062345013670 00000000000000#include "seqgradobj.h" #include "seqparallel.h" SeqGradObjInterface::SeqGradObjInterface(const STD_string& object_label) : SeqTreeObj() { set_label(object_label); } SeqGradObjInterface::SeqGradObjInterface(const SeqGradObjInterface& sgoa) { SeqGradObjInterface::operator = (sgoa); } SeqGradObjInterface& SeqGradObjInterface::operator = (const SeqGradObjInterface& sgoa) { SeqTreeObj::operator = (sgoa); return *this; } double SeqGradObjInterface::get_duration() const { Log odinlog(this,"SeqGradObjInterface::get_duration()"); SeqParallel dummy; dummy.set_gradptr(this); // will use SeqParallel to calculate duration ODINLOG(odinlog,normalDebug) << "duration=" << dummy.get_duration() << STD_endl; return dummy.get_duration(); } double SeqGradObjInterface::get_pulprogduration() const { SeqParallel dummy; return dummy.SeqParallel::get_pulprogduration(); } odin-1.8.5/odinseq/seqgradconst.cpp0000644000175000017500000000465011322062345014245 00000000000000#include "seqgradconst.h" SeqGradConst::SeqGradConst(const STD_string& object_label,direction gradchannel, float gradstrength, double gradduration) : SeqGradChan(object_label,gradchannel,gradstrength,gradduration) {} SeqGradConst::SeqGradConst(const SeqGradConst& sgc) { SeqGradConst::operator = (sgc); } SeqGradConst::SeqGradConst(const STD_string& object_label) : SeqGradChan(object_label) {} STD_string SeqGradConst::get_grdpart(float matrixfactor) const { return graddriver->get_const_program(get_strength(),matrixfactor); } SeqGradConst& SeqGradConst::operator = (const SeqGradConst& sgc) { SeqGradChan::operator = (sgc); return *this; } SeqGradChan& SeqGradConst::get_subchan(double starttime, double endtime) const { SeqGradConst* sgc= new SeqGradConst(STD_string(get_label())+"_("+ftos(starttime)+"-"+ftos(endtime)+")",get_channel(),get_strength(),endtime-starttime); sgc->set_temporary(); return *sgc; } bool SeqGradConst::prep() { Log odinlog(this,"prep"); if(!SeqGradChan::prep()) return false; double dur=get_gradduration(); float str=get_strength(); float possible_maxgrad=dur*systemInfo->get_max_slew_rate(); if(fabs(str)>possible_maxgrad) { ODINLOG(odinlog,errorLog) << "Duration=" << dur << " too short to ramp up to strength=" << str << STD_endl; return false; } return graddriver->prep_const(str,get_grdfactors_norot(),dur); } /////////////////////////////////////////////////////////////////////////////////////////// SeqGradDelay::SeqGradDelay(const STD_string& object_label,direction gradchannel, double gradduration) : SeqGradChan(object_label,gradchannel,0.0,gradduration) { } SeqGradDelay::SeqGradDelay(const SeqGradDelay& sgd) { SeqGradDelay::operator = (sgd); } SeqGradDelay::SeqGradDelay(const STD_string& object_label) : SeqGradChan(object_label) { } STD_string SeqGradDelay::get_grdpart(float matrixfactor) const { return graddriver->get_delay_program(get_strength(),matrixfactor); } SeqGradDelay& SeqGradDelay::operator = (const SeqGradDelay& sgd) { SeqGradChan::operator = (sgd); return *this; } SeqGradChan& SeqGradDelay::get_subchan(double starttime, double endtime) const { SeqGradDelay* sgd= new SeqGradDelay(STD_string(get_label())+"_("+ftos(starttime)+"-"+ftos(endtime)+")",get_channel(),endtime-starttime); sgd->set_temporary(); return *sgd; } odin-1.8.5/odinseq/seqblsiegprep.cpp0000755000175000017500000000776111625224370014432 00000000000000/* Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ #include "seqblsiegprep.h" SeqBlSiegPrep::SeqBlSiegPrep ( const STD_string& object_label, float dur, float fa, float off, float wd, float sl ) : SeqPulsar ( object_label ) { set_shape ( "Fermi" ); set_dim_mode ( zeroDeeMode ); set_filter ( "NoFilter" ); width = wd; width.set_description ( "Distance of turning points of Fermi shaped pulse" ).set_label ( "FermiWidth" ); width.set_minmaxval ( 0,1 ); pars.append ( width ); slope = sl; slope.set_description ( "Slope of Fermi shaped pulse" ).set_label ( "FermiSlope" ); slope.set_minmaxval ( 0,150 ); pars.append ( slope ); duration = dur; duration.set_description ( "Duration of the Fermi pulse" ).set_label ( "Duration" ); duration.set_minmaxval ( 0,100 ); pars.append ( duration ); angle = fa; angle.set_description ( "Flipangle of Fermi pulse [ deg ]" ).set_label ( "Flipangle" ); angle.set_minmaxval ( 0,1000 ); pars.append ( angle ); offset = off; offset.set_description ( "Frequency offset of Fermi pulse [ Hz ]" ).set_label ( "Offset" ); offset.set_minmaxval ( -100000,100000 ); pars.append ( offset ); // set information parameters amplitude.set_description ( "Pulse Amplitude [ uT ]" ).set_label ( "PulseAmplitude" ); amplitude.set_parmode ( noedit ); info.append ( amplitude ); weighting.set_description ( "Weighting factor (Info) in [rad / uT^2]" ).set_label ( "Weighting" ); weighting.set_parmode ( noedit ); info.append ( weighting ); info.set_description ( "Infos about Bloch-Siegert preparation" ).set_label ( "Info" ); pars.append ( info ); pars.set_description ( "Parameters for the Bloch-Siegert preparation for B1-Mapping (see Sacolick et al. MRM(65)2010: 1315-1322)" ); prep(); } SeqBlSiegPrep::SeqBlSiegPrep ( const SeqBlSiegPrep& sbsp ) { SeqBlSiegPrep::operator=(sbsp); } bool SeqBlSiegPrep::prep() { Log odinlog ( this,"prep" ); set_shape ( "Fermi" ); set_shape_parameter ( "slope",ftos ( slope ) ); set_shape_parameter ( "width",ftos ( width ) ); set_pulsduration ( duration ); set_flipangle ( angle ); set_freqoffset ( offset ); // calculate the info parameters cvector rfWave = get_B1(); weighting=0; for ( int i = 0; i< rfWave.size(); i++ ) { weighting += ( abs ( rfWave[i] ) *abs ( rfWave[i] ) ); ODINLOG ( odinlog,verboseDebug ) << "abs(rfWave[" << i << "]) = " << abs ( rfWave[i] ) << STD_endl; } weighting *= duration/ rfWave.size() * // [ ms ] pow ( get_systemInfo().get_gamma ( "1H" ),2 ) / // [ ( rad * MHz / T ) ^ 2 ] ( 2 * offset ) * // [ 1 / Hz / rad ] 0.001 ; // --> final unit : [ rad / (uT ^ 2) ] amplitude = get_B10() *1000; // [ uT ] return true; } SeqBlSiegPrep& SeqBlSiegPrep::operator= ( const SeqBlSiegPrep& sbsp ) { ( *this ).SeqPulsar::operator= ( sbsp ); ( *this ).pars = sbsp.pars; ( *this ).info = sbsp.info; return *this; } odin-1.8.5/pulsar/0000755000175000017500000000000011735135551010773 500000000000000odin-1.8.5/pulsar/pulsar.10000644000175000017500000000124311734623145012303 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH PULSAR "1" "March 2012" "pulsar 1.8.5" "User Commands" .SH NAME pulsar \- Pulse editor of ODIN .SH SYNOPSIS .B pulsar [\fIoptions\fR] [\fI\fR] .SH DESCRIPTION pulsar: Pulse editor of ODIN .SH OPTIONS .HP \fB\-noedit\fR : View\-only mode .HP \fB\-s\fR : Load system defaults .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information odin-1.8.5/pulsar/pulsar.h0000644000175000017500000000331511322062353012363 00000000000000/*************************************************************************** pulsar.h - description ------------------- begin : Fri Jul 7 13:38:24 /etc/localtime 2000 copyright : (C) 2000 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef PULSAR_H #define PULSAR_H #include "pulsarview.h" #define IDS_PULSAR_ABOUT "Pulsar user interface\nVersion " VERSION \ "\n(w) 2000-2005 by Thies Jochimsen\n\n" class PulsarMain : public QObject, public GuiMainWindow { Q_OBJECT public: PulsarMain(); public slots: void slotFileDone(); void slotFileQuit(); void slotHelpAbout(); void changeCaption(const char* text); private: void initMenuBar(); bool queryExit(); PulsarView *view; GuiPopupMenu* fileMenu; GuiPopupMenu* importMenu; GuiPopupMenu* exportMenu; GuiPopupMenu* viewMenu; GuiPopupMenu* settingsMenu; GuiPopupMenu* helpMenu; }; #endif odin-1.8.5/pulsar/pulsarview.h0000644000175000017500000000536211322062353013262 00000000000000/*************************************************************************** pulsarview.h - description ------------------- begin : Thu Jun 20 19:02:26 CEST 2002 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef PULSARVIEW_H #define PULSARVIEW_H #include #include #include #include //////////////////////////////////////// // for debugging Pulsar component class PulsarComp { public: static const char* get_compName(); }; //////////////////////////////////////// struct PulsarCancel {}; // exception //////////////////////////////////////// class PulsarView : public QWidget, public virtual JDXeditWidget { Q_OBJECT public: PulsarView(QWidget *parent=0); ~PulsarView(); void initPulsarView(); static void usage(); signals: void done(); void newCaption(const char* text); public slots: void slotFileNew(); void slotFileOpen(); void slotFileSave(); void slotFileSaveAs(); // void swapSliderTracking(bool); void writeBrukerRf(); void exportRfampASCII(); void exportRfphaASCII(); void exportGxASCII(); void exportGyASCII(); void exportGzASCII(); void exportMampASCII(); void exportMphaASCII(); void exportMzASCII(); void exportPulseJDX(); void exportMagJDX(); void edit_systemInfo(); private slots: void updatePulse(); void updateMagnetization(); void emitDone(); private: // Implemented function of JDXeditWidget void updateWidget(); void vriteArray(const STD_string& filename, const fvector& data); void exportASCIIpulse(const fvector& data); void exportASCIImag(const fvector& data); OdinPulse* pulse; Sample* sample; SeqSimMagsi* mag; funcMode old_mode; STD_string fileName; GuiGridLayout *grid; JDXwidget* pulseWidget[n_dimModes]; JDXwidget* sampleWidget[n_dimModes]; JDXwidget* magnWidget[n_dimModes]; GuiProgressDialog* progress; int progcount; }; #endif odin-1.8.5/pulsar/main.cpp0000644000175000017500000000055611322062353012340 00000000000000#include "pulsar.h" int main(int argc, char *argv[]) { // do this here so we do not have to query X server in order to get usage for manual if(hasHelpOption(argc, argv)) {PulsarView::usage();exit(0);} GuiApplication a(argc, argv); // debug handler will be initialized here PulsarMain *pulsar=new PulsarMain(); return a.start(pulsar->get_widget()); } odin-1.8.5/pulsar/Makefile.am0000644000175000017500000000126711322062353012744 00000000000000 if GUI_ENABLED INCLUDES = $(all_includes) # Auto-generate any needed moc files %_moc.cpp: %.h $(MOC) -o $@ $< bin_PROGRAMS = pulsar pulsar_SOURCES = \ main.cpp \ pulsar.cpp pulsar.h pulsar_moc.cpp \ pulsarview.cpp pulsarview.h pulsarview_moc.cpp pulsar_LDADD = ../odinseq/libodinseq.la ../odinqt/libodinqt.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la # Auto-generate manual pages, only if not in srcdir %.1: % if test ! -f $(srcdir)/$@ ; 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then $(HELP2MAN) --name="$$(./$< --help | grep $<: | sed s/'$<: '//)" ./$< > $@ ; fi @GUI_ENABLED_TRUE@dist-hook: @GUI_ENABLED_TRUE@ -rm -rf $(distdir)/*_moc.cpp clean-local: -rm -f *_moc.cpp # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/pulsar/pulsarview.cpp0000644000175000017500000002343611363773560013635 00000000000000#include "pulsarview.h" #include #include const char* PulsarComp::get_compName() {return "Pulsar";} LOGGROUNDWORK(PulsarComp) void PulsarView::usage() { STD_cout << "pulsar: Pulse editor of ODIN" << STD_endl; STD_cout << "Usage: pulsar [options] []" << STD_endl; STD_cout << "Options:" << STD_endl; STD_cout << "\t-noedit : View-only mode" << STD_endl; STD_cout << "\t -s : Load system defaults" << STD_endl; STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; } PulsarView::PulsarView(QWidget *parent) : QWidget(parent) { Log odinlog("PulsarView","PulsarView(...)"); char buff[ODIN_MAXCHAR]; pulse=new OdinPulse("Pulse",true); ODINLOG(odinlog,normalDebug) << "generation pars initialised" << STD_endl; sample=new Sample("Sample",true,true); ODINLOG(odinlog,normalDebug) << "sample pars initialised" << STD_endl; mag=new SeqSimMagsi("Magnetization"); ODINLOG(odinlog,normalDebug) << "simulation pars initialised" << STD_endl; if(isCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-noedit")) { pulse->set_parmode(noedit); } if(getCommandlineOption(GuiApplication::argc(),GuiApplication::argv(),"-s",buff,ODIN_MAXCHAR)) { SeqPlatformProxy::load_systemInfo(buff); ODINLOG(odinlog,normalDebug) << "systemInfo file >" << buff << "< loaded" << STD_endl; } if(getLastArgument(GuiApplication::argc(),GuiApplication::argv(),buff,ODIN_MAXCHAR)) { if(STD_string(buff)!="") { pulse->load(buff); fileName=buff; ODINLOG(odinlog,normalDebug) << "pulsar file >" << buff << "< loaded" << STD_endl; } } grid=new GuiGridLayout( this, 2, 2); ODINLOG(odinlog,normalDebug) << "layout created" << STD_endl; /*------------- general pulse parameters ------------------------*/ old_mode=n_dimModes; unsigned int i; for(i=0; i odinlog("PulsarView","updateWidget()"); if(!progress) { progress=new GuiProgressDialog(this, false,0); progress->set_text("Calculating Pulse"); progress->show(); progcount=0; } else { progress->set_progress(progcount); progcount++; } if(progress->was_cancelled()) throw PulsarCancel(); pulseWidget[old_mode]->updateWidget(); updateMagnetization(); GuiApplication::process_events(); // Must be called manually because Qt event handler is blocked in optimization loop } void PulsarView::updatePulse() { Log odinlog("PulsarView","updatePulse()"); ODINLOG(odinlog,normalDebug) << "calling pulse->update() ..." << STD_endl; progress=0; try { pulse->update(); } catch(PulsarCancel) { ODINLOG(odinlog,normalDebug) << " cancelled" << STD_endl; } if(progress) delete progress; progress=0; ODINLOG(odinlog,normalDebug) << "done" << STD_endl; funcMode mode=pulse->get_dim_mode(); ODINLOG(odinlog,normalDebug) << "old_mode/mode=" << old_mode << "/" << mode << STD_endl; if(old_mode!=mode) { if(old_mode!=n_dimModes) { ODINLOG(odinlog,normalDebug) << "Hiding old JDXwidget" << STD_endl; pulseWidget[old_mode]->deleteDialogs(); pulseWidget[old_mode]->hide(); } ODINLOG(odinlog,normalDebug) << "Allocating JDXwidget" << STD_endl; if(pulseWidget[mode]==0) pulseWidget[mode]=new JDXwidget(*pulse,2,this,true); ODINLOG(odinlog,normalDebug) << "Showing JDXwidget" << STD_endl; pulseWidget[mode]->show(); grid->add_widget(pulseWidget[mode], 0, 0, GuiGridLayout::Default, 2, 1); connect(pulseWidget[mode],SIGNAL(valueChanged()),this,SLOT(updatePulse())); connect(pulseWidget[mode],SIGNAL(doneButtonPressed()),this,SLOT(emitDone())); } ODINLOG(odinlog,normalDebug) << "calling pulseWidget[" << mode << "]->updateWidget() ..." << STD_endl; pulseWidget[mode]->updateWidget(); ODINLOG(odinlog,normalDebug) << "done" << STD_endl; updateMagnetization(); old_mode=mode; } void PulsarView::updateMagnetization() { Log odinlog("PulsarView","updateMagnetization"); funcMode mode=pulse->get_dim_mode(); ODINLOG(odinlog,normalDebug) << "mode=" << mode << STD_endl; if(old_mode!=mode) { ODINLOG(odinlog,normalDebug) << "Changing mode" << STD_endl; bool onlineflag=true; unsigned int xsize=1; unsigned int ysize=1; unsigned int zsize=1; unsigned int freqsize=1; if(mode==zeroDeeMode) { freqsize=255; } if(mode==oneDeeMode) { zsize=255; } if(mode>=twoDeeMode) {xsize=31; ysize=31; onlineflag=false;} ODINLOG(odinlog,normalDebug) << "xsize/ysize/zsize/freqsize=" << xsize << "/" << ysize << "/" << zsize << "/" << freqsize << STD_endl; sample->resize(1,freqsize,zsize,ysize,xsize); mag->set_online_simulation(onlineflag); sample->update(); mag->update(); mag->prepare_simulation(*sample); // call once to resize mag pulse->simulate_pulse(*mag,*sample); // simulate once to get gray scale in 2D mode if(old_mode!=n_dimModes) { ODINLOG(odinlog,normalDebug) << "Deleting old widgets ..." << STD_endl; sampleWidget[old_mode]->deleteDialogs(); sampleWidget[old_mode]->hide(); magnWidget[old_mode]->deleteDialogs(); magnWidget[old_mode]->hide(); ODINLOG(odinlog,normalDebug) << "Deleting old widgets done" << STD_endl; } if(sampleWidget[mode]==0) { ODINLOG(odinlog,normalDebug) << "Creating new sampleWidget ..." << STD_endl; sampleWidget[mode]=new JDXwidget(*sample,1,this); sampleWidget[mode]->show(); grid->add_widget(sampleWidget[mode], 0, 1); connect(sampleWidget[mode],SIGNAL(valueChanged()),this,SLOT(updateMagnetization())); ODINLOG(odinlog,normalDebug) << "Creating new sampleWidget done" << STD_endl; } if(magnWidget[mode]==0) { ODINLOG(odinlog,normalDebug) << "Creating new magnWidget ..." << STD_endl; magnWidget[mode]=new JDXwidget(*mag,1,this); magnWidget[mode]->show(); grid->add_widget(magnWidget[mode], 1, 1); connect(magnWidget[mode],SIGNAL(valueChanged()),this,SLOT(updateMagnetization())); ODINLOG(odinlog,normalDebug) << "Creating new magnWidget done" << STD_endl; } sampleWidget[mode]->show(); magnWidget[mode]->show(); } sample->update(); mag->update(); if(mag->do_simulation()) pulse->simulate_pulse(*mag,*sample); sampleWidget[mode]->updateWidget(); magnWidget[mode]->updateWidget(); } void PulsarView::emitDone() {emit done();} void PulsarView::slotFileNew() { if(message_question("Resetting to defaults will delete the current values.\n" "Do you really want a fresh pulse ?", "New Pulse", this, true)) { (*pulse)=OdinPulse("Pulse",true); updatePulse(); } } void PulsarView::slotFileOpen() { STD_string newfile=get_open_filename("Open Pulse", fileName.c_str(), "", this); if (newfile!="") { fileName=newfile; emit newCaption(fileName.c_str()); pulse->load(fileName); updatePulse(); } } void PulsarView::slotFileSave() { if (fileName!="") { pulse->write(fileName); } else slotFileSaveAs(); } void PulsarView::slotFileSaveAs() { fileName=get_save_filename("Save Pulse", fileName.c_str(), "", this); if (fileName!="") { pulse->write(fileName); } } void PulsarView::writeBrukerRf() { STD_string fname=get_save_filename("Export Bruker Pulse", "", "", this); if (fname!="") { SeqPlatformProxy::set_current_platform(paravision); pulse->write_rf_waveform(fname); SeqPlatformProxy::set_current_platform(standalone); } } void PulsarView::vriteArray(const STD_string& filename, const fvector& data) { STD_string filestr; for(unsigned int i=0; iget_B1()));} void PulsarView::exportRfphaASCII() {exportASCIIpulse(phase(pulse->get_B1()));} void PulsarView::exportGxASCII() {exportASCIIpulse(pulse->get_Grad(readDirection));} void PulsarView::exportGyASCII() {exportASCIIpulse(pulse->get_Grad(phaseDirection));} void PulsarView::exportGzASCII() {exportASCIIpulse(pulse->get_Grad(sliceDirection));} void PulsarView::exportMampASCII() {exportASCIImag(mag->get_Mamp());} void PulsarView::exportMphaASCII() {exportASCIImag(mag->get_Mpha());} void PulsarView::exportMzASCII() {exportASCIImag(mag->get_Mz());} void PulsarView::exportPulseJDX() { STD_string fname=get_save_filename("Export JCAMP-DX Pulse", "", "", this); if(fname!="") { OdinPulse sd(*pulse); sd.set_filemode(include); sd.write(fname); } } void PulsarView::exportMagJDX() { STD_string fname=get_save_filename("Export JCAMP-DX Magnetization", "", "", this); if(fname!="") { SeqSimMagsi sm(*mag); sm.set_filemode(include); sm.write(fname); } } void PulsarView::edit_systemInfo() { JDXwidgetDialog* dlg=new JDXwidgetDialog(pulse->get_systemInfo(),1,this); connect(dlg,SIGNAL(valueChanged()),this,SLOT(updatePulse())); } odin-1.8.5/pulsar/pulsar.cpp0000644000175000017500000000642311322062353012721 00000000000000#include "pulsar.h" PulsarMain::PulsarMain() { Log odinlog("PulsarMain","PulsarMain(...)"); view=new PulsarView(GuiMainWindow::get_widget()); connect(view,SIGNAL(done()),this,SLOT(slotFileDone())); connect(view,SIGNAL(newCaption(const char*)),this,SLOT(changeCaption(const char*))); view->initPulsarView(); ODINLOG(odinlog,normalDebug) << "initView() done" << STD_endl; initMenuBar(); ODINLOG(odinlog,normalDebug) << "initMenuBar() done" << STD_endl; GuiMainWindow::show(view); } void PulsarMain::initMenuBar() { Log odinlog("PulsarMain","initMenuBar"); fileMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); fileMenu->insert_item("&New", view, SLOT(slotFileNew()), Qt::CTRL+Qt::Key_N); fileMenu->insert_item("&Open...", view, SLOT(slotFileOpen()), Qt::CTRL+Qt::Key_O); fileMenu->insert_separator(); fileMenu->insert_item("&Save", view, SLOT(slotFileSave()), Qt::CTRL+Qt::Key_S); fileMenu->insert_item("Save as...", view, SLOT(slotFileSaveAs()), 0); fileMenu->insert_separator(); fileMenu->insert_item("&Quit", this, SLOT(slotFileQuit()), Qt::CTRL+Qt::Key_Q); exportMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); exportMenu->insert_item("Export Bruker RF-Pulse", view, SLOT(writeBrukerRf())); exportMenu->insert_separator(); exportMenu->insert_item("Export ASCII RF-Amplitude", view, SLOT(exportRfampASCII())); exportMenu->insert_item("Export ASCII RF-Phase", view, SLOT(exportRfphaASCII())); exportMenu->insert_item("Export ASCII Gx", view, SLOT(exportGxASCII())); exportMenu->insert_item("Export ASCII Gy", view, SLOT(exportGyASCII())); exportMenu->insert_item("Export ASCII Gz", view, SLOT(exportGzASCII())); exportMenu->insert_separator(); exportMenu->insert_item("Export ASCII Magnetization Amplitide", view, SLOT(exportMampASCII())); exportMenu->insert_item("Export ASCII Magnetization Phase", view, SLOT(exportMphaASCII())); exportMenu->insert_item("Export ASCII z-Magnetization", view, SLOT(exportMzASCII())); exportMenu->insert_separator(); exportMenu->insert_item("Export JCAMP-DX Pulse", view, SLOT(exportPulseJDX())); exportMenu->insert_item("Export JCAMP-DX Magnetization", view, SLOT(exportMagJDX())); settingsMenu = new GuiPopupMenu(GuiMainWindow::get_widget()); settingsMenu->insert_item("&System Configuration ...", view, SLOT(edit_systemInfo()),0); helpMenu=new GuiPopupMenu(GuiMainWindow::get_widget()); helpMenu->insert_item("About...", this, SLOT(slotHelpAbout()), 0); GuiMainWindow::insert_menu("&File", fileMenu); GuiMainWindow::insert_menu("Ex&port", exportMenu); GuiMainWindow::insert_menu("&Settings", settingsMenu); GuiMainWindow::insert_menu_separator(); GuiMainWindow::insert_menu("&Help", helpMenu); } bool PulsarMain::queryExit() { return(message_question("Do your really want to quit?", "Quit...", GuiMainWindow::get_widget(), true)); } void PulsarMain::slotFileDone() { view->slotFileSave(); GuiApplication::quit(); } void PulsarMain::slotFileQuit() { if(queryExit()) { GuiApplication::quit(); } } void PulsarMain::slotHelpAbout() { message_question(IDS_PULSAR_ABOUT, "About...", GuiMainWindow::get_widget()); } void PulsarMain::changeCaption(const char* text) { GuiMainWindow::set_caption((STD_string("Pulsar " VERSION) + " - " + text).c_str()); } odin-1.8.5/AUTHORS0000644000175000017500000000107511322062355010451 00000000000000Thies Jochimsen : Project founder, main developer Michael v. Mengershausen : Data evaluation, vtk support Andreas Schaefer : EPI and MQC method, ICE program, bug reports Markus Koerber : Pinwheel pulse trajectories, more bug reports Robert Trampel : Simulation with relaxation Enrico Reimer : FileIO module, Converter, Filter framework Dirk Mueller : RF spoiling, filters, even more bug reports Torsten Schlumm. Christian Ros : ICE reconstruction to store raw data Martin Kraemer : BLADE reconstruction odin-1.8.5/odin.doxygen0000644000175000017500000016455211322062355011743 00000000000000# Doxyfile 1.5.6 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project # # All text after a hash (#) is considered a comment and will be ignored # The format is: # TAG = value [value, ...] # For lists items can also be appended using: # TAG += value [value, ...] # Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- # This tag specifies the encoding used for all characters in the config file # that follow. The default is UTF-8 which is also the encoding used for all # text before the first occurrence of this tag. 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STRIP_FROM_INC_PATH = # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter # (but less readable) file names. This can be useful is your file systems # doesn't support long names like on DOS, Mac, or CD-ROM. SHORT_NAMES = NO # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen # will interpret the first line (until the first dot) of a JavaDoc-style # comment as the brief description. If set to NO, the JavaDoc # comments will behave just like regular Qt-style comments # (thus requiring an explicit @brief command for a brief description.) JAVADOC_AUTOBRIEF = NO # If the QT_AUTOBRIEF tag is set to YES then Doxygen will # interpret the first line (until the first dot) of a Qt-style # comment as the brief description. If set to NO, the comments # will behave just like regular Qt-style comments (thus requiring # an explicit \brief command for a brief description.) QT_AUTOBRIEF = NO # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen # treat a multi-line C++ special comment block (i.e. a block of //! or /// # comments) as a brief description. This used to be the default behaviour. # The new default is to treat a multi-line C++ comment block as a detailed # description. Set this tag to YES if you prefer the old behaviour instead. MULTILINE_CPP_IS_BRIEF = NO # If the DETAILS_AT_TOP tag is set to YES then Doxygen # will output the detailed description near the top, like JavaDoc. # If set to NO, the detailed description appears after the member # documentation. DETAILS_AT_TOP = NO # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented # member inherits the documentation from any documented member that it # re-implements. INHERIT_DOCS = YES # If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce # a new page for each member. If set to NO, the documentation of a member will # be part of the file/class/namespace that contains it. SEPARATE_MEMBER_PAGES = NO # The TAB_SIZE tag can be used to set the number of spaces in a tab. # Doxygen uses this value to replace tabs by spaces in code fragments. TAB_SIZE = 4 # This tag can be used to specify a number of aliases that acts # as commands in the documentation. An alias has the form "name=value". # For example adding "sideeffect=\par Side Effects:\n" will allow you to # put the command \sideeffect (or @sideeffect) in the documentation, which # will result in a user-defined paragraph with heading "Side Effects:". # You can put \n's in the value part of an alias to insert newlines. ALIASES = # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C # sources only. Doxygen will then generate output that is more tailored for C. # For instance, some of the names that are used will be different. The list # of all members will be omitted, etc. OPTIMIZE_OUTPUT_FOR_C = NO # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java # sources only. Doxygen will then generate output that is more tailored for # Java. For instance, namespaces will be presented as packages, qualified # scopes will look different, etc. OPTIMIZE_OUTPUT_JAVA = NO # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran # sources only. Doxygen will then generate output that is more tailored for # Fortran. OPTIMIZE_FOR_FORTRAN = NO # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL # sources. Doxygen will then generate output that is tailored for # VHDL. OPTIMIZE_OUTPUT_VHDL = NO # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want # to include (a tag file for) the STL sources as input, then you should # set this tag to YES in order to let doxygen match functions declarations and # definitions whose arguments contain STL classes (e.g. func(std::string); v.s. # func(std::string) {}). This also make the inheritance and collaboration # diagrams that involve STL classes more complete and accurate. BUILTIN_STL_SUPPORT = NO # If you use Microsoft's C++/CLI language, you should set this option to YES to # enable parsing support. CPP_CLI_SUPPORT = NO # Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. # Doxygen will parse them like normal C++ but will assume all classes use public # instead of private inheritance when no explicit protection keyword is present. SIP_SUPPORT = NO # For Microsoft's IDL there are propget and propput attributes to indicate getter # and setter methods for a property. Setting this option to YES (the default) # will make doxygen to replace the get and set methods by a property in the # documentation. This will only work if the methods are indeed getting or # setting a simple type. If this is not the case, or you want to show the # methods anyway, you should set this option to NO. IDL_PROPERTY_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC # tag is set to YES, then doxygen will reuse the documentation of the first # member in the group (if any) for the other members of the group. By default # all members of a group must be documented explicitly. DISTRIBUTE_GROUP_DOC = NO # Set the SUBGROUPING tag to YES (the default) to allow class member groups of # the same type (for instance a group of public functions) to be put as a # subgroup of that type (e.g. under the Public Functions section). Set it to # NO to prevent subgrouping. Alternatively, this can be done per class using # the \nosubgrouping command. SUBGROUPING = YES # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum # is documented as struct, union, or enum with the name of the typedef. So # typedef struct TypeS {} TypeT, will appear in the documentation as a struct # with name TypeT. When disabled the typedef will appear as a member of a file, # namespace, or class. And the struct will be named TypeS. This can typically # be useful for C code in case the coding convention dictates that all compound # types are typedef'ed and only the typedef is referenced, never the tag name. TYPEDEF_HIDES_STRUCT = NO #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in # documentation are documented, even if no documentation was available. # Private class members and static file members will be hidden unless # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES EXTRACT_ALL = NO # If the EXTRACT_PRIVATE tag is set to YES all private members of a class # will be included in the documentation. EXTRACT_PRIVATE = NO # If the EXTRACT_STATIC tag is set to YES all static members of a file # will be included in the documentation. EXTRACT_STATIC = NO # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) # defined locally in source files will be included in the documentation. # If set to NO only classes defined in header files are included. EXTRACT_LOCAL_CLASSES = YES # This flag is only useful for Objective-C code. When set to YES local # methods, which are defined in the implementation section but not in # the interface are included in the documentation. # If set to NO (the default) only methods in the interface are included. EXTRACT_LOCAL_METHODS = NO # If this flag is set to YES, the members of anonymous namespaces will be # extracted and appear in the documentation as a namespace called # 'anonymous_namespace{file}', where file will be replaced with the base # name of the file that contains the anonymous namespace. By default # anonymous namespace are hidden. EXTRACT_ANON_NSPACES = NO # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all # undocumented members of documented classes, files or namespaces. # If set to NO (the default) these members will be included in the # various overviews, but no documentation section is generated. # This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_MEMBERS = YES # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all # undocumented classes that are normally visible in the class hierarchy. # If set to NO (the default) these classes will be included in the various # overviews. This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_CLASSES = YES # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all # friend (class|struct|union) declarations. # If set to NO (the default) these declarations will be included in the # documentation. HIDE_FRIEND_COMPOUNDS = NO # If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any # documentation blocks found inside the body of a function. # If set to NO (the default) these blocks will be appended to the # function's detailed documentation block. HIDE_IN_BODY_DOCS = NO # The INTERNAL_DOCS tag determines if documentation # that is typed after a \internal command is included. If the tag is set # to NO (the default) then the documentation will be excluded. # Set it to YES to include the internal documentation. INTERNAL_DOCS = NO # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate # file names in lower-case letters. If set to YES upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows # and Mac users are advised to set this option to NO. CASE_SENSE_NAMES = YES # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen # will show members with their full class and namespace scopes in the # documentation. If set to YES the scope will be hidden. HIDE_SCOPE_NAMES = NO # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen # will put a list of the files that are included by a file in the documentation # of that file. SHOW_INCLUDE_FILES = YES # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] # is inserted in the documentation for inline members. INLINE_INFO = YES # If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen # will sort the (detailed) documentation of file and class members # alphabetically by member name. If set to NO the members will appear in # declaration order. SORT_MEMBER_DOCS = YES # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the # brief documentation of file, namespace and class members alphabetically # by member name. If set to NO (the default) the members will appear in # declaration order. SORT_BRIEF_DOCS = NO # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the # hierarchy of group names into alphabetical order. If set to NO (the default) # the group names will appear in their defined order. SORT_GROUP_NAMES = NO # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be # sorted by fully-qualified names, including namespaces. If set to # NO (the default), the class list will be sorted only by class name, # not including the namespace part. # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. # Note: This option applies only to the class list, not to the # alphabetical list. SORT_BY_SCOPE_NAME = NO # The GENERATE_TODOLIST tag can be used to enable (YES) or # disable (NO) the todo list. This list is created by putting \todo # commands in the documentation. GENERATE_TODOLIST = YES # The GENERATE_TESTLIST tag can be used to enable (YES) or # disable (NO) the test list. This list is created by putting \test # commands in the documentation. GENERATE_TESTLIST = YES # The GENERATE_BUGLIST tag can be used to enable (YES) or # disable (NO) the bug list. This list is created by putting \bug # commands in the documentation. GENERATE_BUGLIST = YES # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or # disable (NO) the deprecated list. This list is created by putting # \deprecated commands in the documentation. GENERATE_DEPRECATEDLIST= YES # The ENABLED_SECTIONS tag can be used to enable conditional # documentation sections, marked by \if sectionname ... \endif. ENABLED_SECTIONS = # The MAX_INITIALIZER_LINES tag determines the maximum number of lines # the initial value of a variable or define consists of for it to appear in # the documentation. If the initializer consists of more lines than specified # here it will be hidden. Use a value of 0 to hide initializers completely. # The appearance of the initializer of individual variables and defines in the # documentation can be controlled using \showinitializer or \hideinitializer # command in the documentation regardless of this setting. MAX_INITIALIZER_LINES = 30 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated # at the bottom of the documentation of classes and structs. If set to YES the # list will mention the files that were used to generate the documentation. SHOW_USED_FILES = YES # If the sources in your project are distributed over multiple directories # then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy # in the documentation. The default is NO. SHOW_DIRECTORIES = NO # Set the SHOW_FILES tag to NO to disable the generation of the Files page. # This will remove the Files entry from the Quick Index and from the # Folder Tree View (if specified). The default is YES. SHOW_FILES = YES # Set the SHOW_NAMESPACES tag to NO to disable the generation of the # Namespaces page. This will remove the Namespaces entry from the Quick Index # and from the Folder Tree View (if specified). The default is YES. SHOW_NAMESPACES = YES # The FILE_VERSION_FILTER tag can be used to specify a program or script that # doxygen should invoke to get the current version for each file (typically from # the version control system). Doxygen will invoke the program by executing (via # popen()) the command , where is the value of # the FILE_VERSION_FILTER tag, and is the name of an input file # provided by doxygen. Whatever the program writes to standard output # is used as the file version. See the manual for examples. FILE_VERSION_FILTER = #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- # The QUIET tag can be used to turn on/off the messages that are generated # by doxygen. Possible values are YES and NO. If left blank NO is used. QUIET = YES # The WARNINGS tag can be used to turn on/off the warning messages that are # generated by doxygen. Possible values are YES and NO. If left blank # NO is used. WARNINGS = YES # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings # for undocumented members. If EXTRACT_ALL is set to YES then this flag will # automatically be disabled. WARN_IF_UNDOCUMENTED = NO # If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for # potential errors in the documentation, such as not documenting some # parameters in a documented function, or documenting parameters that # don't exist or using markup commands wrongly. WARN_IF_DOC_ERROR = YES # This WARN_NO_PARAMDOC option can be abled to get warnings for # functions that are documented, but have no documentation for their parameters # or return value. If set to NO (the default) doxygen will only warn about # wrong or incomplete parameter documentation, but not about the absence of # documentation. WARN_NO_PARAMDOC = NO # The WARN_FORMAT tag determines the format of the warning messages that # doxygen can produce. The string should contain the $file, $line, and $text # tags, which will be replaced by the file and line number from which the # warning originated and the warning text. Optionally the format may contain # $version, which will be replaced by the version of the file (if it could # be obtained via FILE_VERSION_FILTER) WARN_FORMAT = # The WARN_LOGFILE tag can be used to specify a file to which warning # and error messages should be written. If left blank the output is written # to stderr. WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- # The INPUT tag can be used to specify the files and/or directories that contain # documented source files. You may enter file names like "myfile.cpp" or # directories like "/usr/src/myproject". Separate the files or directories # with spaces. INPUT = ./ # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is # also the default input encoding. Doxygen uses libiconv (or the iconv built # into libc) for the transcoding. See http://www.gnu.org/software/libiconv for # the list of possible encodings. INPUT_ENCODING = UTF-8 # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank the following patterns are tested: # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90 FILE_PATTERNS = *.h \ gencoil.cpp \ genmakefile.cpp \ gensample.cpp \ micalc.cpp \ miconv.cpp \ swab.cpp # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. # If left blank NO is used. RECURSIVE = YES # The EXCLUDE tag can be used to specify files and/or directories that should # excluded from the INPUT source files. This way you can easily exclude a # subdirectory from a directory tree whose root is specified with the INPUT tag. EXCLUDE = platforms \ sequences \ replacements \ docs # The EXCLUDE_SYMLINKS tag can be used select whether or not files or # directories that are symbolic links (a Unix filesystem feature) are excluded # from the input. EXCLUDE_SYMLINKS = NO # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. Note that the wildcards are matched # against the file with absolute path, so to exclude all test directories # for example use the pattern */test/* EXCLUDE_PATTERNS = *CVS* \ *.svn* \ *_moc.cpp # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the # output. The symbol name can be a fully qualified name, a word, or if the # wildcard * is used, a substring. Examples: ANamespace, AClass, # AClass::ANamespace, ANamespace::*Test EXCLUDE_SYMBOLS = # The EXAMPLE_PATH tag can be used to specify one or more files or # directories that contain example code fragments that are included (see # the \include command). EXAMPLE_PATH = . # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank all files are included. EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude # commands irrespective of the value of the RECURSIVE tag. # Possible values are YES and NO. If left blank NO is used. EXAMPLE_RECURSIVE = NO # The IMAGE_PATH tag can be used to specify one or more files or # directories that contain image that are included in the documentation (see # the \image command). IMAGE_PATH = # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command , where # is the value of the INPUT_FILTER tag, and is the name of an # input file. Doxygen will then use the output that the filter program writes # to standard output. If FILTER_PATTERNS is specified, this tag will be # ignored. INPUT_FILTER = # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern # basis. Doxygen will compare the file name with each pattern and apply the # filter if there is a match. The filters are a list of the form: # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further # info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER # is applied to all files. FILTER_PATTERNS = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using # INPUT_FILTER) will be used to filter the input files when producing source # files to browse (i.e. when SOURCE_BROWSER is set to YES). FILTER_SOURCE_FILES = NO #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- # If the SOURCE_BROWSER tag is set to YES then a list of source files will # be generated. Documented entities will be cross-referenced with these sources. # Note: To get rid of all source code in the generated output, make sure also # VERBATIM_HEADERS is set to NO. SOURCE_BROWSER = YES # Setting the INLINE_SOURCES tag to YES will include the body # of functions and classes directly in the documentation. INLINE_SOURCES = NO # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct # doxygen to hide any special comment blocks from generated source code # fragments. Normal C and C++ comments will always remain visible. STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES # then for each documented function all documented # functions referencing it will be listed. REFERENCED_BY_RELATION = NO # If the REFERENCES_RELATION tag is set to YES # then for each documented function all documented entities # called/used by that function will be listed. REFERENCES_RELATION = NO # If the REFERENCES_LINK_SOURCE tag is set to YES (the default) # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will # link to the source code. Otherwise they will link to the documentstion. REFERENCES_LINK_SOURCE = YES # If the USE_HTAGS tag is set to YES then the references to source code # will point to the HTML generated by the htags(1) tool instead of doxygen # built-in source browser. The htags tool is part of GNU's global source # tagging system (see http://www.gnu.org/software/global/global.html). You # will need version 4.8.6 or higher. USE_HTAGS = NO # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen # will generate a verbatim copy of the header file for each class for # which an include is specified. Set to NO to disable this. VERBATIM_HEADERS = YES #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index # of all compounds will be generated. Enable this if the project # contains a lot of classes, structs, unions or interfaces. ALPHABETICAL_INDEX = YES # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns # in which this list will be split (can be a number in the range [1..20]) COLS_IN_ALPHA_INDEX = 5 # In case all classes in a project start with a common prefix, all # classes will be put under the same header in the alphabetical index. # The IGNORE_PREFIX tag can be used to specify one or more prefixes that # should be ignored while generating the index headers. IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- # If the GENERATE_HTML tag is set to YES (the default) Doxygen will # generate HTML output. GENERATE_HTML = YES # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `html' will be used as the default path. HTML_OUTPUT = # The HTML_FILE_EXTENSION tag can be used to specify the file extension for # each generated HTML page (for example: .htm,.php,.asp). If it is left blank # doxygen will generate files with .html extension. HTML_FILE_EXTENSION = .html # The HTML_HEADER tag can be used to specify a personal HTML header for # each generated HTML page. If it is left blank doxygen will generate a # standard header. HTML_HEADER = # The HTML_FOOTER tag can be used to specify a personal HTML footer for # each generated HTML page. If it is left blank doxygen will generate a # standard footer. HTML_FOOTER = # The HTML_STYLESHEET tag can be used to specify a user-defined cascading # style sheet that is used by each HTML page. It can be used to # fine-tune the look of the HTML output. If the tag is left blank doxygen # will generate a default style sheet. Note that doxygen will try to copy # the style sheet file to the HTML output directory, so don't put your own # stylesheet in the HTML output directory as well, or it will be erased! HTML_STYLESHEET = # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, # files or namespaces will be aligned in HTML using tables. If set to # NO a bullet list will be used. HTML_ALIGN_MEMBERS = YES # If the GENERATE_HTMLHELP tag is set to YES, additional index files # will be generated that can be used as input for tools like the # Microsoft HTML help workshop to generate a compiled HTML help file (.chm) # of the generated HTML documentation. GENERATE_HTMLHELP = NO # If the GENERATE_DOCSET tag is set to YES, additional index files # will be generated that can be used as input for Apple's Xcode 3 # integrated development environment, introduced with OSX 10.5 (Leopard). # To create a documentation set, doxygen will generate a Makefile in the # HTML output directory. Running make will produce the docset in that # directory and running "make install" will install the docset in # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find # it at startup. GENERATE_DOCSET = NO # When GENERATE_DOCSET tag is set to YES, this tag determines the name of the # feed. A documentation feed provides an umbrella under which multiple # documentation sets from a single provider (such as a company or product suite) # can be grouped. DOCSET_FEEDNAME = "Doxygen generated docs" # When GENERATE_DOCSET tag is set to YES, this tag specifies a string that # should uniquely identify the documentation set bundle. This should be a # reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen # will append .docset to the name. DOCSET_BUNDLE_ID = org.doxygen.Project # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML # documentation will contain sections that can be hidden and shown after the # page has loaded. For this to work a browser that supports # JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox # Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari). HTML_DYNAMIC_SECTIONS = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can # be used to specify the file name of the resulting .chm file. You # can add a path in front of the file if the result should not be # written to the html output directory. CHM_FILE = # If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can # be used to specify the location (absolute path including file name) of # the HTML help compiler (hhc.exe). If non-empty doxygen will try to run # the HTML help compiler on the generated index.hhp. HHC_LOCATION = # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag # controls if a separate .chi index file is generated (YES) or that # it should be included in the master .chm file (NO). GENERATE_CHI = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING # is used to encode HtmlHelp index (hhk), content (hhc) and project file # content. CHM_INDEX_ENCODING = # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag # controls whether a binary table of contents is generated (YES) or a # normal table of contents (NO) in the .chm file. BINARY_TOC = NO # The TOC_EXPAND flag can be set to YES to add extra items for group members # to the contents of the HTML help documentation and to the tree view. TOC_EXPAND = NO # The DISABLE_INDEX tag can be used to turn on/off the condensed index at # top of each HTML page. The value NO (the default) enables the index and # the value YES disables it. DISABLE_INDEX = NO # This tag can be used to set the number of enum values (range [1..20]) # that doxygen will group on one line in the generated HTML documentation. ENUM_VALUES_PER_LINE = 4 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index # structure should be generated to display hierarchical information. # If the tag value is set to FRAME, a side panel will be generated # containing a tree-like index structure (just like the one that # is generated for HTML Help). For this to work a browser that supports # JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, # Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are # probably better off using the HTML help feature. Other possible values # for this tag are: HIERARCHIES, which will generate the Groups, Directories, # and Class Hiererachy pages using a tree view instead of an ordered list; # ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which # disables this behavior completely. For backwards compatibility with previous # releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE # respectively. GENERATE_TREEVIEW = NO # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be # used to set the initial width (in pixels) of the frame in which the tree # is shown. TREEVIEW_WIDTH = 250 # Use this tag to change the font size of Latex formulas included # as images in the HTML documentation. The default is 10. Note that # when you change the font size after a successful doxygen run you need # to manually remove any form_*.png images from the HTML output directory # to force them to be regenerated. FORMULA_FONTSIZE = 10 #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will # generate Latex output. GENERATE_LATEX = NO # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `latex' will be used as the default path. LATEX_OUTPUT = # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be # invoked. If left blank `latex' will be used as the default command name. LATEX_CMD_NAME = latex # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to # generate index for LaTeX. If left blank `makeindex' will be used as the # default command name. MAKEINDEX_CMD_NAME = makeindex # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact # LaTeX documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_LATEX = NO # The PAPER_TYPE tag can be used to set the paper type that is used # by the printer. Possible values are: a4, a4wide, letter, legal and # executive. If left blank a4wide will be used. PAPER_TYPE = a4wide # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX # packages that should be included in the LaTeX output. EXTRA_PACKAGES = # The LATEX_HEADER tag can be used to specify a personal LaTeX header for # the generated latex document. The header should contain everything until # the first chapter. If it is left blank doxygen will generate a # standard header. Notice: only use this tag if you know what you are doing! LATEX_HEADER = # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated # is prepared for conversion to pdf (using ps2pdf). The pdf file will # contain links (just like the HTML output) instead of page references # This makes the output suitable for online browsing using a pdf viewer. PDF_HYPERLINKS = NO # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of # plain latex in the generated Makefile. Set this option to YES to get a # higher quality PDF documentation. USE_PDFLATEX = NO # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. # command to the generated LaTeX files. This will instruct LaTeX to keep # running if errors occur, instead of asking the user for help. # This option is also used when generating formulas in HTML. LATEX_BATCHMODE = NO # If LATEX_HIDE_INDICES is set to YES then doxygen will not # include the index chapters (such as File Index, Compound Index, etc.) # in the output. LATEX_HIDE_INDICES = NO #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output # The RTF output is optimized for Word 97 and may not look very pretty with # other RTF readers or editors. GENERATE_RTF = NO # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `rtf' will be used as the default path. RTF_OUTPUT = # If the COMPACT_RTF tag is set to YES Doxygen generates more compact # RTF documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_RTF = NO # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated # will contain hyperlink fields. The RTF file will # contain links (just like the HTML output) instead of page references. # This makes the output suitable for online browsing using WORD or other # programs which support those fields. # Note: wordpad (write) and others do not support links. RTF_HYPERLINKS = NO # Load stylesheet definitions from file. Syntax is similar to doxygen's # config file, i.e. a series of assignments. You only have to provide # replacements, missing definitions are set to their default value. RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an rtf document. # Syntax is similar to doxygen's config file. RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- # If the GENERATE_MAN tag is set to YES (the default) Doxygen will # generate man pages GENERATE_MAN = NO # The MAN_OUTPUT tag is used to specify where the man pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `man' will be used as the default path. MAN_OUTPUT = # The MAN_EXTENSION tag determines the extension that is added to # the generated man pages (default is the subroutine's section .3) MAN_EXTENSION = # If the MAN_LINKS tag is set to YES and Doxygen generates man output, # then it will generate one additional man file for each entity # documented in the real man page(s). These additional files # only source the real man page, but without them the man command # would be unable to find the correct page. The default is NO. MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- # If the GENERATE_XML tag is set to YES Doxygen will # generate an XML file that captures the structure of # the code including all documentation. GENERATE_XML = NO # The XML_OUTPUT tag is used to specify where the XML pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `xml' will be used as the default path. XML_OUTPUT = xml # The XML_SCHEMA tag can be used to specify an XML schema, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_SCHEMA = # The XML_DTD tag can be used to specify an XML DTD, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_DTD = # If the XML_PROGRAMLISTING tag is set to YES Doxygen will # dump the program listings (including syntax highlighting # and cross-referencing information) to the XML output. Note that # enabling this will significantly increase the size of the XML output. XML_PROGRAMLISTING = YES #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will # generate an AutoGen Definitions (see autogen.sf.net) file # that captures the structure of the code including all # documentation. Note that this feature is still experimental # and incomplete at the moment. GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- # If the GENERATE_PERLMOD tag is set to YES Doxygen will # generate a Perl module file that captures the structure of # the code including all documentation. Note that this # feature is still experimental and incomplete at the # moment. GENERATE_PERLMOD = NO # If the PERLMOD_LATEX tag is set to YES Doxygen will generate # the necessary Makefile rules, Perl scripts and LaTeX code to be able # to generate PDF and DVI output from the Perl module output. PERLMOD_LATEX = NO # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be # nicely formatted so it can be parsed by a human reader. This is useful # if you want to understand what is going on. On the other hand, if this # tag is set to NO the size of the Perl module output will be much smaller # and Perl will parse it just the same. PERLMOD_PRETTY = YES # The names of the make variables in the generated doxyrules.make file # are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. # This is useful so different doxyrules.make files included by the same # Makefile don't overwrite each other's variables. PERLMOD_MAKEVAR_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will # evaluate all C-preprocessor directives found in the sources and include # files. ENABLE_PREPROCESSING = YES # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro # names in the source code. If set to NO (the default) only conditional # compilation will be performed. Macro expansion can be done in a controlled # way by setting EXPAND_ONLY_PREDEF to YES. MACRO_EXPANSION = NO # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES # then the macro expansion is limited to the macros specified with the # PREDEFINED and EXPAND_AS_DEFINED tags. EXPAND_ONLY_PREDEF = NO # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files # in the INCLUDE_PATH (see below) will be search if a #include is found. SEARCH_INCLUDES = YES # The INCLUDE_PATH tag can be used to specify one or more directories that # contain include files that are not input files but should be processed by # the preprocessor. INCLUDE_PATH = # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard # patterns (like *.h and *.hpp) to filter out the header-files in the # directories. If left blank, the patterns specified with FILE_PATTERNS will # be used. INCLUDE_FILE_PATTERNS = # The PREDEFINED tag can be used to specify one or more macro names that # are defined before the preprocessor is started (similar to the -D option of # gcc). The argument of the tag is a list of macros of the form: name # or name=definition (no spaces). If the definition and the = are # omitted =1 is assumed. To prevent a macro definition from being # undefined via #undef or recursively expanded use the := operator # instead of the = operator. PREDEFINED = # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then # this tag can be used to specify a list of macro names that should be expanded. # The macro definition that is found in the sources will be used. # Use the PREDEFINED tag if you want to use a different macro definition. EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then # doxygen's preprocessor will remove all function-like macros that are alone # on a line, have an all uppercase name, and do not end with a semicolon. Such # function macros are typically used for boiler-plate code, and will confuse # the parser if not removed. SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- # The TAGFILES option can be used to specify one or more tagfiles. # Optionally an initial location of the external documentation # can be added for each tagfile. The format of a tag file without # this location is as follows: # TAGFILES = file1 file2 ... # Adding location for the tag files is done as follows: # TAGFILES = file1=loc1 "file2 = loc2" ... # where "loc1" and "loc2" can be relative or absolute paths or # URLs. If a location is present for each tag, the installdox tool # does not have to be run to correct the links. # Note that each tag file must have a unique name # (where the name does NOT include the path) # If a tag file is not located in the directory in which doxygen # is run, you must also specify the path to the tagfile here. TAGFILES = # When a file name is specified after GENERATE_TAGFILE, doxygen will create # a tag file that is based on the input files it reads. GENERATE_TAGFILE = # If the ALLEXTERNALS tag is set to YES all external classes will be listed # in the class index. If set to NO only the inherited external classes # will be listed. ALLEXTERNALS = NO # If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed # in the modules index. If set to NO, only the current project's groups will # be listed. EXTERNAL_GROUPS = YES # The PERL_PATH should be the absolute path and name of the perl script # interpreter (i.e. the result of `which perl'). PERL_PATH = #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will # generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base # or super classes. Setting the tag to NO turns the diagrams off. Note that # this option is superseded by the HAVE_DOT option below. This is only a # fallback. It is recommended to install and use dot, since it yields more # powerful graphs. CLASS_DIAGRAMS = YES # You can define message sequence charts within doxygen comments using the \msc # command. Doxygen will then run the mscgen tool (see # http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the # documentation. The MSCGEN_PATH tag allows you to specify the directory where # the mscgen tool resides. If left empty the tool is assumed to be found in the # default search path. MSCGEN_PATH = # If set to YES, the inheritance and collaboration graphs will hide # inheritance and usage relations if the target is undocumented # or is not a class. HIDE_UNDOC_RELATIONS = YES # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is # available from the path. This tool is part of Graphviz, a graph visualization # toolkit from AT&T and Lucent Bell Labs. The other options in this section # have no effect if this option is set to NO (the default) HAVE_DOT = YES # By default doxygen will write a font called FreeSans.ttf to the output # directory and reference it in all dot files that doxygen generates. This # font does not include all possible unicode characters however, so when you need # these (or just want a differently looking font) you can specify the font name # using DOT_FONTNAME. You need need to make sure dot is able to find the font, # which can be done by putting it in a standard location or by setting the # DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory # containing the font. DOT_FONTNAME = FreeSans # By default doxygen will tell dot to use the output directory to look for the # FreeSans.ttf font (which doxygen will put there itself). If you specify a # different font using DOT_FONTNAME you can set the path where dot # can find it using this tag. DOT_FONTPATH = # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect inheritance relations. Setting this tag to YES will force the # the CLASS_DIAGRAMS tag to NO. CLASS_GRAPH = YES # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect implementation dependencies (inheritance, containment, and # class references variables) of the class with other documented classes. COLLABORATION_GRAPH = NO # If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen # will generate a graph for groups, showing the direct groups dependencies GROUP_GRAPHS = YES # If the UML_LOOK tag is set to YES doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling # Language. UML_LOOK = NO # If set to YES, the inheritance and collaboration graphs will show the # relations between templates and their instances. TEMPLATE_RELATIONS = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT # tags are set to YES then doxygen will generate a graph for each documented # file showing the direct and indirect include dependencies of the file with # other documented files. INCLUDE_GRAPH = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and # HAVE_DOT tags are set to YES then doxygen will generate a graph for each # documented header file showing the documented files that directly or # indirectly include this file. INCLUDED_BY_GRAPH = YES # If the CALL_GRAPH and HAVE_DOT options are set to YES then # doxygen will generate a call dependency graph for every global function # or class method. Note that enabling this option will significantly increase # the time of a run. So in most cases it will be better to enable call graphs # for selected functions only using the \callgraph command. CALL_GRAPH = NO # If the CALLER_GRAPH and HAVE_DOT tags are set to YES then # doxygen will generate a caller dependency graph for every global function # or class method. Note that enabling this option will significantly increase # the time of a run. So in most cases it will be better to enable caller # graphs for selected functions only using the \callergraph command. CALLER_GRAPH = NO # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen # will graphical hierarchy of all classes instead of a textual one. GRAPHICAL_HIERARCHY = YES # If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES # then doxygen will show the dependencies a directory has on other directories # in a graphical way. The dependency relations are determined by the #include # relations between the files in the directories. DIRECTORY_GRAPH = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images # generated by dot. Possible values are png, jpg, or gif # If left blank png will be used. DOT_IMAGE_FORMAT = png # The tag DOT_PATH can be used to specify the path where the dot tool can be # found. If left blank, it is assumed the dot tool can be found in the path. DOT_PATH = # The DOTFILE_DIRS tag can be used to specify one or more directories that # contain dot files that are included in the documentation (see the # \dotfile command). DOTFILE_DIRS = # The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of # nodes that will be shown in the graph. If the number of nodes in a graph # becomes larger than this value, doxygen will truncate the graph, which is # visualized by representing a node as a red box. Note that doxygen if the # number of direct children of the root node in a graph is already larger than # DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note # that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. DOT_GRAPH_MAX_NODES = 50 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the # graphs generated by dot. A depth value of 3 means that only nodes reachable # from the root by following a path via at most 3 edges will be shown. Nodes # that lay further from the root node will be omitted. Note that setting this # option to 1 or 2 may greatly reduce the computation time needed for large # code bases. Also note that the size of a graph can be further restricted by # DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. MAX_DOT_GRAPH_DEPTH = 0 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent # background. This is enabled by default, which results in a transparent # background. Warning: Depending on the platform used, enabling this option # may lead to badly anti-aliased labels on the edges of a graph (i.e. they # become hard to read). DOT_TRANSPARENT = YES # Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output # files in one run (i.e. multiple -o and -T options on the command line). This # makes dot run faster, but since only newer versions of dot (>1.8.10) # support this, this feature is disabled by default. DOT_MULTI_TARGETS = NO # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will # generate a legend page explaining the meaning of the various boxes and # arrows in the dot generated graphs. GENERATE_LEGEND = YES # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will # remove the intermediate dot files that are used to generate # the various graphs. DOT_CLEANUP = YES #--------------------------------------------------------------------------- # Configuration::additions related to the search engine #--------------------------------------------------------------------------- # The SEARCHENGINE tag specifies whether or not a search engine should be # used. If set to NO the values of all tags below this one will be ignored. SEARCHENGINE = NO odin-1.8.5/INSTALL0000644000175000017500000004055511735132611010441 00000000000000 ============= BUILD ODIN FROM SCRATCH ON WINDOWS =================== Please note that the following instructions are for building ODIN from scratch on Windows using MinGW and to create a binary distribution of ODIN. If you just want to use ODIN on Windows, possibly in combination with IDEA, I strongly recommend that you download and install the binary distribution from the ODIN Download page, since the installation described here is pretty tedious. Uninstall any ODIN binary distributions before continuing. To get the GNU tools and compiler, download the MINGW and MSYS packages/installers from http://www.mingw.org/download.shtml. At the time of writing, these were the files MinGW-5.1.3.exe and MSYS-1.0.10.exe. Specify the location of MinGW during install of MSYS. Apply the patch posted here for Vista: http://lists-archives.org/mingw-users/06921-vista-gcc-cc1plus-bug.html Download and install the Qt open source distribution, e.g. qt-win-opensource-4.5.0-mingw.exe from http://www.qtsoftware.com/downloads/windows-cpp. It seems to be save to ignore the warning during install that the current MinGW is not compatible. Set the environment variables QTDIR and PATH manually, i.e. set QTDIR to the install directory and append %QTDIR%\bin to PATH. Create a directory (e.g. c:\MR-Software) to put all the ODIN-related stuff. Use the MSYS shell to install all further stuff. Please note: A drive letter X: in this shell can be used usin /X/, e.g. c: is /c/ in the MSYS shell. Download recent GSL source code, unpack and do a ./configure --prefix=/c/MR-Software --disable-shared --enable-static make make install Compile and install Blitz++ from source: ./configure --prefix=/c/MR-Software && make lib && make install Unpack qwt5. In qwtconfig.pri, comment out the line #CONFIG += QwtDll to build a static qwt (compiling of DLL fails). Do a qmake mingw32-make After compiling of qwt_designer_plugin.dll fails, install qwt manually: cp lib/libqwt.a /c/MR-Software/lib mkdir /c/MR-Software/include/qwt cp src/*.h /c/MR-Software/include/qwt Compile dcmtk source: 1) ./configure --prefix=/c/MR-Software 2) First 'make' (for libofstd) 3) create a built-in dictionary by going into dcmdata/libsrc and do a 'make builtindict'. Fix 'mkdictbi.cc:getUserName' if necessaray. 4) Compile and install the libraries by 'make && make install-lib' For LAPACK support: Get the g77 version of the AMD Core Math Library from http://developer.amd.com/acml.jsp and install it. Use a short installation path without dots, e.g. c:/acml, otherwise configure fails. Use the -a option of install.win (see below) to specify the location of libacml.a. For NIfTI/zlib support: 1) Download zlib from http://www.zlib.net and install with ./configure --prefix=/c/MR-Software && make install 2) Download nifticlib from http://niftilib.sourceforge.net/ Hack Makefile: Add -Ic:/MR-Software/include to ZLIB_INC and -Lc:/MR-Software/lib to ZLIB_PATH Use mingw32-make to compile, ignore errors in utils Install manually: cp lib/*.a /c/MR-Software/lib/ cp include/*.h /c/MR-Software/include/ Download the notepad2 editor from http://www.flos-freeware.ch/notepad2.html and copy Notepad2.exe to /c/MR-Software/bin Download and copy doxygen.exe to c:/Programme/Doxygen/ Download graphviz from http://www.graphviz.org/pub/graphviz/ARCHIVE/ and install it under Programme/ATT. Download and install NSIS with default settings to c:/Programme/NSIS/ Compile and pack ODIN using the script 'install.win' ============= INSTALLING ODIN ON LINUX/UNIX ======================= Prerequisites: ============== The following programs and libraries are required to compile ODIN for Linux/UNIX (In parenthesis are the version numbers of the packages with which ODIN has been tested successfully): * Qt library (3.0.* or later) * Qwt library (4.2.0 or later) * Blitz++ template library (0.8 or later) * GNU Scientific Library (0.9.3 or later) * optional: Vista/Lipsia library (http://www.cbs.mpg.de/institute/software/lipsia/download.html or vista-2.2.0 from ODIN download page), use configure option --enable-vistasupport to activate Vista support in ODIN * optional: NIFTI library (http://nifti.nimh.nih.gov), use configure option --enable-niftisupport to activate NIFTI support in ODIN * optional: vtk library (4.2.5, 4.4.2), use configure option --enable-vtksupport to activate VTK support in ODIN * optional: dcmtk library (3.5.4, 3.6.0), use configure option --enable-dcmtksupport to activate DICOM support in ODIN * optional: PNG library (1.2.27, 1.5.9), use configure option --enable-pngsupport to activate PNG support in ODIN * optional: gdb debugger and xterm terminal to attach debugger to running ODIN process * optional: oil library (0.3) for fast type conversion * optional: LAPACK for fast linear algebra. Since the NetLib implementation is currently not thread safe, we recommend using the thread-safe ACML (http://developer.amd.com/cpu/Libraries/acml/). Download the GFORTRAN version, and use --with-lapack-libname=acml during configure. A note for GRAPPA users: If no LAPACK is found during configure, Odin will fall back to using GSL for linear algebra. However, the GSL implementation is very slow (several orders of magnitude compared to LAPACK) which makes GRAPPA reconstruction impractical. So, please: MAKE SURE TO USE LAPACK FOR GRAPPA RECONSTRUCTION. At the best, use a thread-safe LAPACK implementation, like ACML. The actual library name can be given by --with-lapack-libname. A short HOWTO (for the impatient): ================================== After you've unpacked the archive go into the directory where this file resides and issue: ./configure && make After compilation log in as root and type make install After that you should be able to start Odin by odin on the command line. To configure/compile ODIN with other settings, enter ./configure --help to get a list of options. Platform Specific Notes: ======================== * Debian 4.0 (etch): To compile the tar.gz from the ODIN download page, the following packages are required: 'libqt3-mt-dev, libqwt-dev, libgsl0-dev'. Qt4 packages must be de-installed. Optionally, install libniftiio0-dev for NIFTI support, libdcmtk1-dev for DICOM support, liboil0.3-dev for fast type conversion, and atlas3-base for fast linear algebra. If you check out ODIN via SVN, you will need the additional packages 'autoconf automake libtool'. Blitz++ must be installed manually and configured with '--enable-shared' because of a known bug in the Debian package, see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=369753 for details. Fortunately, this bug gets fixed with the next release of Debian. * Debian 5.0 (lenny): Create and install a Debian package with 'make deb' ! * Red Hat Enterprise Linux 3 (hosting Brukers Paravision 3) ODIN was successfully installed with the following libraries and configure options: gsl-1.6: ./configure --enable-shared=yes --enable-static=no blitz-0.8: ./configure --enable-shared=yes --enable-static=no vista-2.2.0: ./configure --enable-shared=yes --enable-static=no ODIN can be compiled with following options: ./configure --enable-shared=yes --enable-static=no * MacOS X 10.4(Tiger), 10.5(Leopard) -Install the development tools from Apple, i.e. XCode 2.4 or later -Use fink 0.8.0 and set the following environment variables: export FINKDIR=/sw export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FINKDIR/lib export LIBRARY_PATH=$LIBRARY_PATH:$FINKDIR/lib export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$FINKDIR/include -Install qt-mac-opensource, 4.1.x or later, use the source code distribution, otherwise qwt cannot be compiled (with the qmake of the dmg binary distribution) For a minimal Qt sufficient for Odin, configure Qt with ./configure -prefix $QT_INSTALL_DIR -no-qt3support -release -no-xmlpatterns -no-phonon -no-svg -no-webkit -no-nis -no-cups -no-dbus -nomake "tools examples demos docs" Set the variable QTDIR to point to the source-code directory of Qt -Additionally, install the following libraries: -qwt5 (adapt qwtconfig.pri: INSTALLBASE and headers.path = $$INSTALLBASE/include/qwt, comment out QwtDesigner) -gsl (fink package) -blitz++ (current CVS checkout with CVSROOT=:pserver:anonymous@blitz.cvs.sourceforge.net:/cvsroot/blitz cvs co blitz), for configuration,use 'LIBTOOLIZE=glibtoolize autoreconf -fiv' (aborts with error, but creates configure which works fine) If necessary, create directory blitz/apple and therein link to blitz/gnu/bzconfig.h (also in the installed blitz headers) -Optionally, install the following libraries: -vista-2.2.0 (from ODIN download page) -dcmtk 3.5.4 (run make install-lib install-support, run ranlib manually, as requested) -Use the script ./install.macos to configure/compile/install ODIN Troubleshooting: ================ * During compilation I get a message '/usr/bin/moc: commamd not found' -> You must specify the directory where the Qt library is installed by setting the $QTDIR system variable, i.e. the headers should be found under $QTDIR/include, the libs under $QTDIR/lib and, most important for this problem the binaries (for example moc) under $QTDIR/bin. * During configuration I get a message 'configure: error: Can't find ....' or 'Please install ...' -> The configure script knows (mostly) what is needed, please install the missing packages. =============================================================================== And here are the generic installation instructions generated by the GNU autoconf package: Basic Installation ================== These are generic installation instructions. The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a `Makefile' in each directory of the package. It may also create one or more `.h' files containing system-dependent definitions. Finally, it creates a shell script `config.status' that you can run in the future to recreate the current configuration, a file `config.cache' that saves the results of its tests to speed up reconfiguring, and a file `config.log' containing compiler output (useful mainly for debugging `configure'). If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail diffs or instructions to the address given in the `README' so they can be considered for the next release. If at some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.in' is used to create `configure' by a program called `autoconf'. You only need `configure.in' if you want to change it or regenerate `configure' using a newer version of `autoconf'. The simplest way to compile this package is: 1. `cd' to the directory containing the package's source code and type `./configure' to configure the package for your system. If you're using `csh' on an old version of System V, you might need to type `sh ./configure' instead to prevent `csh' from trying to execute `configure' itself. Running `configure' takes a while. While running, it prints some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. Type `make install' to install the programs and any data files and documentation. 4. You can remove the program binaries and object files from the source code directory by typing `make clean'. Compilers and Options ===================== Some systems require unusual options for compilation or linking that the `configure' script does not know about. You can give `configure' initial values for variables by setting them in the environment. Using a Bourne-compatible shell, you can do that on the command line like this: CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure Or on systems that have the `env' program, you can do it like this: env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure Compiling For Multiple Architectures ==================================== You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their own directory. 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For packages that use the X Window System, `configure' can usually find the X include and library files automatically, but if it doesn't, you can use the `configure' options `--x-includes=DIR' and `--x-libraries=DIR' to specify their locations. Specifying the System Type ========================== There may be some features `configure' can not figure out automatically, but needs to determine by the type of host the package will run on. Usually `configure' can figure that out, but if it prints a message saying it can not guess the host type, give it the `--host=TYPE' option. TYPE can either be a short name for the system type, such as `sun4', or a canonical name with three fields: CPU-COMPANY-SYSTEM See the file `config.sub' for the possible values of each field. If `config.sub' isn't included in this package, then this package doesn't need to know the host type. If you are building compiler tools for cross-compiling, you can also use the `--target=TYPE' option to select the type of system they will produce code for and the `--build=TYPE' option to select the type of system on which you are compiling the package. Sharing Defaults ================ If you want to set default values for `configure' scripts to share, you can create a site shell script called `config.site' that gives default values for variables like `CC', `cache_file', and `prefix'. `configure' looks for `PREFIX/share/config.site' if it exists, then `PREFIX/etc/config.site' if it exists. Or, you can set the `CONFIG_SITE' environment variable to the location of the site script. A warning: not all `configure' scripts look for a site script. Operation Controls ================== `configure' recognizes the following options to control how it operates. `--cache-file=FILE' Use and save the results of the tests in FILE instead of `./config.cache'. Set FILE to `/dev/null' to disable caching, for debugging `configure'. `--help' Print a summary of the options to `configure', and exit. `--quiet' `--silent' `-q' Do not print messages saying which checks are being made. `--srcdir=DIR' Look for the package's source code in directory DIR. Usually `configure' can determine that directory automatically. `--version' Print the version of Autoconf used to generate the `configure' script, and exit. `configure' also accepts some other, not widely useful, options. odin-1.8.5/ChangeLog0000644000175000017500000010145111735132611011153 00000000000000ChangeLog for ODIN Version 1.8.5: -------------- New Features: - Writing of multiple VTK files for dynamic data sets - Storing protocol together with z-maps in miview fMRI - Added dialect 'tcourse' to ASCII fileio - SeqSimMonteCarlo now supports multi-threaded simulation - Added gamma variate fitting function - Added filter steps 'quantilmask' and 'resample' - Filter steps 'minip', 'maxip' and 'proj' now with direction argument - Added option 'weightmask' to micalc - Added reco step 'qcspike' to detect spikes in signal - Added reco steps 'driftcalc/driftcorr' for correction of field drift - Added GSL-based DownhillSimplex optimizer Internal Changes: - Added thread-local storage to ThreadedLoop - Removed usage of liboil - Removed FileIO of Lipsia/Vista - Rewrote filter_splice - Adapted to libpng 1.5.x - New implementation of unwrap_phase() function with variable startindex Version 1.8.4: -------------- New Features: - Calculating reductions (maximum, minimum and sum projection) by one filter step - Added write option 'fnamepar' to create file names of datasets based on arbitrary protocol parameters - Added parameter to weight phase by exponent of magnitude when combining multi-channel data - Added filter 'automask' to create mask using histogram-based threshold Internal Changes: - Fixes for DCMTK 3.6.0 - Combination of files with different bit representations in autoread - Using presence of DICOM trigger time to set PhysioTrigger - Accounting for different TRs in gated mode when combining data Version 1.8.3: -------------- New Features: - PhysioTrigger flag in GUI - Partial Fourier acquisition in readout direction - Reordering of phase lists API Changes: - Changed constructors of SeqAcqRead and SeqGradEcho to allow for partial Fourier acquisition in readout direction. Internal Changes: - Now using PREFIX/share/odin to install sequences, samples and coils - Constructors of SeqGradTrapez and SeqAcqRead now account for rastered duration of of constant part - Taking SeqVecIter objects into account when creating recoInfo Version 1.8.2: -------------- New Features: - Read-only display of parameter blocks by a table - Support for time varying samples to simulate fMRI, for instance - (Re-)added SeqMagnReset to reset magnetization in simulation - New FileIO plugin for ODIN measurement protocols API Changes: - Changed parameter order of Sample::resize() - Removed obsolete B1 map in Sample - Sample has extra time dimension (frames) Internal Changes: - Fixed noise generator of MRI simulator Version 1.8.1: -------------- New Features: - 3D phase encoded PROPELLER sequence - Support for diffusion tensor imaging - New parameters for odinreco to fine-tune odinreco of PROPELLER data - Added 3D mode to SeqGradEcho API Changes: - New operators /= for SeqGradChanParallel - Moved set_gradrotmatrixvector() from SeqParallel to SeqObjList Internal Changes: - Using userdef dimension for messer/gesse sequence - Separate functor for phase correction of blades Version 1.8.0: -------------- New Features: - odinprop now possible with ramp sampling - Dialect 'siemens' for DICOM read/write plugins Internal Changes: - Removed scanner-specific drivers from public distribution. Version 1.7.3: -------------- New Features: - Auto-detecting number of cores for odinreco. - Added functor 'fmri' to odinreco (fMRI localizer). - Optimized trapezoidal gradient pulses. - Added filter 'detrend' to remove slow drift over time. - Added filter 'merge' to merge datasets into one. - Added filter 'usemask' to generate 1D array using a mask. - Multi-threaded simulation of MR signal. API Changes: - SeqPulsar::set_rephased() now accepts an optional argument to set the rephaser strength. Internal Changes: - New template class ThreadedLoop for parallelized loops. Version 1.7.2: -------------- New Features: - New sequence 'odinprop' and appropriate reconstruction for PROPPELLER acquisition. Internal Changes: - Auto-generating manpages using 'help2man'. - Added --enable/disable- to configure for 3rd part libraries. Version 1.7.1: -------------- New Features: - Added residual-based robustness filter to GRAPPA reconstruction. - New filter 'align' to register the data of one dataset to the geometry of another. Internal Changes: - Added reverseSlice to Geometry to account for different handness of coordinate system. - Removed sonames of libraries. - Filters now operate on whole maps of protocol-data pairs. Version 1.7.0: -------------- New Features: - Full support for arbitrary oversampling on all platforms. - Added ScanDate and ScanTime members to Study. - New filters for intensity masks (genmask) and slice tiling (tile). - Added SeqHalt for physiological triggering. API Changes: - Parameter for oversampling factor can now be specified in SeqAcq* constructors. - Removed obsolete 'gradshift' from SeqAcqEPI constructor. Internal Changes: - Added configure option --enable-debug, release mode is now the default Version 1.6.9: -------------- New Features: - Added common method SeqFreqChanInterface::set_phasespoiling() for RF spoiling. - Added code for iterative GRAPPA interpolation in two phase encoding directions. - New file formats in FileIO: 3db (Iris3D binary data), png (PNG image), reg (Ansoft HFSS ASCII). API Changes: - Removed obsolete get/set_attenuation() of pulse classes. - Renamed SeqPulsNdim::get/set_wave() -> SeqPulsNdim::get/set_rfwave() and SeqPulsNdim::get/set_Gx/y/z() -> SeqPulsNdim::get/set_gradwave() - Merged enums read/phase/sliceChannel and read/phase/sliceDirection into read/phase/sliceDirection - New member 'methpars' in Protocol to accomodate custom sequence parameters. Internal Changes: - The protocol is now embedded in recoInfo instead of a separate file on disk. - Using Siemens Ice(Configurator) to store raw data on disk. Version 1.6.8: -------------- New Features: - Most of the tracing is now displayed directly in the messages window of Odin instead of the console. API Changes: - Replaced Debug module (in files tjutils/tjdebug*) by Log module (in files tjutils/tjlog*) Internal Changes: - Replaced most of uses of cout/cerr by using new Log module Version 1.6.7: -------------- New Features: - Ported to Siemens IDEA VB15 - odinreco can reconstruct Twix-exported raw data from some Siemens sequences (EPI, FLASH) Internal Changes: - New ostringstream-based debugging framework which now supports standard ostream output to be redirected to the debug object Version 1.6.6: -------------- New Features: - New class SeqGradPhaseEncFlowComp for 1st order flow-compensated phase encoding. - Implemented 3D mode for SeqFieldMap. - New framework for filter steps operating on datasets-protocols pairs in odindata/filter*. Internal Changes: - Added libodinreco in order to support external recos with a custom reader. - Common template base classes for filter and reco steps in odindata/step.*. Version 1.6.5: -------------- New Features: - Support for GNU-Zip compressed files in FileIO, e.g. files ending with nii.gz can be read directly. - Oscilloscope in sequence plotter. - New Mode 'B1' in odinquant and functor b1fit to produce B1 maps. - Added true half fourier reco to odinreco/homodyne.* - Ported to Siemens Numaris4 VB12 API Changes: - JDXyesno renamed to JDXbool. Internal Changes: - Uniform handling of arguments and options of reco steps (functors) via a single set of parameters per step. - Storing and using ReadoutShape instead of RegridMatrix for ramp-sampling correction. - Using MinGW patch so that ODIN can be used on Windows Vista. - Using name 'odindebug' as a uniform name for all local Debug objects. - Renamed SeqMethodInterface/SeqPlatformInterface to SeqMethodProxy/SeqPlatformProxy. - Extra configure option to include/exclude unit test. - New simple list-based memory manager for custom heap. Version 1.6.4: -------------- New Features: - Monte-Carlo simulator 'SeqSimMonteCarlo' to simulate diffusional averaging. Both simulators, 'SeqSimMagsi' and 'SeqSimMonteCarlo', are now accessible via a common interface 'SeqSimAbstract'. - New sequence 'odinswi' and reco functor 'swi' for susceptibilty weighted imaging. - New reco functor 'filter' and 'zerofill' for k-space filtering and zero filling. - Input/output plugin for the Matlab ASCII file format in FileIO module. - Improved Vista input/output plugin which is now compatible with Lipsia. - Improved NIFTI input/output which now supports different data representation types and correctly handles slice orientations. - New LAPACK-based linear algebra functions 'pseudo_inverse' and 'eigenvalues' in odindata/linalg.h. - More filter plugins for JDXfilter API Changes: - Renamed header seqmagn.h to seqsim.h and class 'SeqMagn' to 'SeqSimMagsi'. - Data::convert_to() has more convenient autoscaleOption instead of scale/offset. - New parameter RFSpoiling in commonPars Internal Changes: - Increased efficiency of the tokenizer and STL replacement. - Using liboil when available for array conversion. Version 1.6.3: -------------- New Features: - Direct FT with conjugate-phase reconstruction for spiral imaging. - Yet another optimized spiral trajectory (BoernertSpiral) as described in Boernert et al, MAGMA 9:29-41(1999). - Support for NIFTI file format. Internal Changes: - Collected common code of different spirals into base class ArchimedianSpiral. - Simplified interface to Paravision: A scan can now be started directly from the ODIN GUI. Communication between ODIN and Paravision is now bases solely on pvcmd. Version 1.6.2: -------------- New Features: - Experimental support for VB* on Siemens. - Slice ordering of Sinc and Gauss pulses is now interleaved by default. - Added slice-time correction functor to odinreco. API Changes: - Now, the class SeqAcqEPI has an extra parameter 'reduction' in the constructor to realize GRAPPA encoding directly in the the SeqAcqEPI class in order to combine segmentation and parallel imaging of EPI. Version 1.6.1: -------------- New Features: - Graphical installer to install ODIN on IDEA. - Implemented partial Fourier acquisition: New sequence parameter 'PartialFourier', added support for partial Fourier acquisition in SeqGradPhaseEnc/SeqGradEcho and homodyne reconstruction in odinreco. API Changes: - Overloading SeqMethod::method_reco() to perform method-specific reconstruction is no longer supported. Instead, each method can register a set of functors via RecoPars::set_Recipe() and RecoPars::set_PostProc3D(). Internal Changes: - No longer providing Debian packages because of a bug in Blitz++, see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=369753 for details. Version 1.6.0: -------------- New Features: - New multi-threaded pipeline-based reconstruction 'odinreco' which replaces good old 'autoreco' as the image reconstruction framework within ODIN. - Added components for multi-threading in tjutils/tjthread.h. - New class SeqVecIter to iterate manually through vectors (e.g. phaselists). API Changes: - Removed Nyquist correction for EPI in favour of simple 1D phase correction. Internal Changes: - Renamed library for data processing from 'odinreco' to 'odindata'. Version 1.5.1: -------------- New Features: - The FileIO module and the tools based on it (miconv,miview) now support datasets with differing protocols. These protocol-data pairs are now processed simultaneously. They are read from and written to a single file if the file format supports this option (e.g. Vista). - Spiral trajectories with a free parameter can be optimized for minimum readout length using downhill simplex optimization. - Various improvements to spiral reco: Faster k-space gridding, magnitude correction, optional reco by matrix inversion, ... API Changes: - Added ramp steepness as parameter to SeqGradTrapez and SeqAcqEPI. - Restructured FileIO functionality: Instea of separate 'read/write_*_file' functions for each file format, the class Data now has single functions 'autoread/autowrite' to import/export data from different file formats. - The FileIO module now handles lists of protocol-data pairs: Data with differing protocols can be read in and written out simultaneously. - New gridding and coodinate transform functors 'Gridding' and 'CoordTransformation' which are nitialized once and can be applied multiple times. Internal Changes: - Using fast(!) LAPACK routines for SVD instead of those of GSL if LAPACK is available. Version 1.5.0: -------------- New Features: - Added new sequence parameter GradientIntro which will automatically generate a 'tok tok tok' sound prior to the actual sequence if activated. - New encodind scheme 'maxDistEncoding' which creates max distance between consecutive elements of a vector, e.g. for multi-slice excitation with minimum overlap. - New class 'Study' and sub-object 'study' in class 'Protocol' to hold info about current study, i.e. patient info, study name, etc. - Fully standard-compliant DICOM export. - To allow off-center FOV in read direction, oversampling will now be used to create a shift in autoreco before the FOV-band filter is applied. Internal Changes: - Migrated to subversion source code control - Renamed internal interface classes of sequence objects from Abstract to Interface - All Seq*Interface now implement automatic marshalling of virtual functions if a marshall is specified with set_marshall(). - Restructured type interface for amd64 bit compatability: Possible integer types are now s8bit, u8bit, s16bit, u16bit, s32bit, u32bit and will be mapped to the appropriate C types during './configure'. Version 1.4.3: -------------- API Changes: - Argument for direction of ComplexData::fft(...) changed to bool value - The function do_autoreco() is obsolete, autoreco is always performed prior to calling sequence-specific method_reco(). New Features: - Added SeqPulsar::get_reph_gradintegral() to obtain rephasing integrals without creating a new gradient object. - Ported ODIN to Windows using MinGW. Internal Changes: - Using GSL FFT instead of FFTW -> No more FFTW dependency Version 1.4.2: -------------- API Changes: - Removed obsolete flag 'templateScan' from constructor of SeqAcqEPI New Features: - Added optimization code for RF pulses - New constructor flag 'rephase' for SeqAcqDeph to create post-acquisition rephasing gradients. Internal Changes: - Many bug fixes Version 1.4.1: -------------- API Changes: - Memory mapping of complex raw data has changed: The block can be reshaped at each load_block. New Features: - The EPI module now supports multiple echoes for each line in k-space. This is useful for field-map scans. - Added EPI-based module for field-map pre-scan to odinspir sequence. Internal Changes: - Better integration into the Paravision PVM framework. - Tagging of dimensions for reco is now performed mainly in autoreco for better performance. Version 1.4.0: -------------- New Features: - Added support for multi-shot (segmented) EPI. - Parallel imaging using GRAPPA. A new parameter 'ReductionFactor' can be used to specify an acceleration factor and the class 'SeqGradPhaseEnc' is able to create undersampled phase encoding with auto-calibration lines. - Embedded 1D plots (e.g. in Pulsar) can be detached by an entry in their context menu. API Changes: - The sub-elements of the Protocol class (system, geometry and seqpars) are no longer pointers, but actual objects. - All 'set_*_vector' member functions of SeqAcqAbstract derived classes are now replaced by a single function 'set_reco_vector' which takes the desired dimension as its first argument via a 'recoDim' parameter. - The simple macro ODINMETHOD_ENTRY_POINT is now used in every sequence file/module instead of the old ODINMAIN function code. - Changed constructor of SeqAcqEPI to support multi-shot (segmented) EPI - Changed constructor of 2D SeqGradEcho: More convenient constructor with matrix sizes and FOVs instead of gradient strengths. - Changed constructor of 'SeqGradPhaseEnc' to support parallel imaging. - Removed property digitizerMode from the API, i.e. from all constructors of SeqAcq* objects. Internal Changes: - Removed tjview - Using PVM instead of IMND interface on Paravision/Bruker. - Various changes to use optimum filter/digitizer settings on Paravision/Bruker. Version 1.3.2: -------------- New Features: - Added scale to all 2D plots Internal Changes: - Unit test of components is now handled by UnitTest and derived classes - Fixed broken Debian package. Version 1.3.1: -------------- API Changes: - Argument to get/set_spatial_offset of OdinPulse/SeqPulsarPinWheel is now channelNo enum instead of axis enum. - Moved image.h/image.cpp from odinreco to odinpara lib. - Renamed SeqRotMatrix to RotMatrix - The argument to set_gradrotmatrix() is now RotMatrix, instead of a 3x3 float array - Renamed set_mode/get_mode of JDX classes to set_compat_mode/get_compat_mode - The default compatability mode of parameters is now 'notBroken' instead of 'bruker' - The pre-defined frequency list 'pl90' is obsolete, use 'set_phase(90.0)' instead. New Features: - Multiple test cases are now supported for each sequence to cover more use cases during sequence test. - ODIN image file format now contains additional information about the slice geometry. - Added new program 'miview' which will eventually replace the good old, but messy 'tjview' - It is now possible to display images as color map in tjview/miview via the '-color' command-line option. - Any ImageSet (image.jdx) can be used as a background in geoedit Internal Changes: - Ported to Qt4 and Qwt5 - Ported to MacOS - The class name of a sequences/methods is now set by the define METHOD_CLASS in the method code to change the class name dynamically, which is required on MacOS. - Improved DICOM im/export - Navigator data set is now stored in ImageSet instead of obsolete PilotScan - The global parameter 'EchoTime' is now a vector of doubles internally to support multi-echo sequences. However, in the UI it still appears as a scalar parameter. - The sum immages of autoreco are now produced by averaging complex images instead of image magnitudes for better noise compensation. Version 1.3.0: -------------- API Changes: - Location and name of headers have changed: tjutils/tjdx*.h -> odinpara/jdx* tjutils/tjreco.h -> odinpara/reco.h odinseq/seqgeo.h -> odinpara/geometry.h odinseq/seqsys.h -> odinpara/system.h odinseq/seqpars.h -> odinpara/seqpars.h - Renamed classes: SeqGeo -> Geometry SeqSys -> System SeqReco -> RecoPars - Splitted SeqMagn into two separate classes Sample (in odinpara/sample.h) and SeqMagn (in odinseq/seqmagn.h) to separate the logic of sample properties and magnetization - Changed member functions of PilotScan: Now only one function with an enum 'sliceOrientation' as first argument instead of 3 functions - Constructor and redim functions of tjarray changed: Giving a dim parameter as first arg is no longer necessary, dim is determined from the number of args New Features: - A debugger can be attached to the running or newly started Odin process in order to debug sequences. It can be switched on/off under Preferences->Settings->AttachDebugger - DICOM support added via dcmtk: reading/writing of DICOM files is now possible within the Data class - new input/output functions autoread/autowrite in odinreco/fileio.h which detect the file format automatically according to the file extension - rawcalc/micalc now handles a variety of file formats - tjview is now capable of displaying DICOM files - Added new class Protocol which is used to hold the whole protocol of one experiment - Introduced new cmdline program 'miconv' which replaces the functionality of raw2vista, raw2vtk, vistasplit, etc. The file types are recognized according to file extension - Simulation of MR sequences can now be done via cmdline-action 'simulate' - Started work on drivers for GE (code generator for EPIC), drivers will be compiled in by default - Added write support for MetaImage (mhd) file format to FileIO::autowrite Internal Changes: - New library odinpara which holds JCAMP-DX implementation and parameter classes for the MR protocol (geometry, system, sequence parameters) - Added support for new version (3.x) of FFTW - Removed obsolete intermediate class SeqClassSys Misc: - Windows version of tjview no longer available - The parameters in ODIN user interface are now separated: commonPars and methodPars both have their own widget - The sequence-label prefix is removed from parameter names in commonPars when written to disk (e.g. odinepi_FlipAngle is now simply FlipAngle) - renamed command-line utilities: genphantom -> gensample rawcalc -> micalc Version 1.2.2: -------------- New Features: - rawcalc/micalc: It is now possible to use numbers instead of arrays to perform arithmetics with scalar numbers and arrays - Added RandomDist, a class to calculate random number distributions. - New header 'odinreco/linalg.h' and function 'solve_linear' to solve sets of linear equations using the singular value decomposition of GSL - New function polynomial_fit in header 'odinreco/fitting.h' to fit polynomes at each point of an array - New function transform in header 'odinreco/gridding.h' to perform coordinate transformation of Arrays (i.e. rotation, flipping, scaling, shifting) - Made sequence plotting more convenient: Empty channels are discarded and signal curves are displayed right after simulation - It is now possible to specify coil sensitivities for transmission and acquisition Internal Changes: - Now ComplexData::fft swaps quadrants before and after fftw (to obtain smooth phasemaps in the image) - Automated test of autoreco - Added unit tests for components in odinreco (gridding, fitting, statistics, fft) Version 1.2.1: -------------- New Features: - Improved simulation of intra-voxel dephasing by using intra-voxel magnetization gradients - Added vtk-support (writing 3D files) - New cmdline util raw2vtk to convert raw data to vtk files - Added TrueFISP sequence odinfisp - Improved plotting/printing of sequences: Thicker lines while printing, wheels for y-axes to select y-range - Added indication of x/y position when drawing profiles in tjview - The home page now contains a list of avaiable sequences together with their descritions. This list is automatically generated from the source code files in the sequences dir. Internal Changes: - Fixed resizing/margins of JDX widgets on newer Qt versions - Automated release and test procedure (make release / make test) Version 1.2.0: -------------- API Changes: - replaced value 'paravision1_1' of enum 'odinPlatform' by 'paravision' to indicate support of (hopefully) all Paravision versions. New Features: - Adapted ODIN to Paravision 3 - It is now possible to iterate through a list of flip angles via the set_flipangles() and get_flipangle_vector() functions of SeqPulsAbstract (and its derived classes) - Added horizontal/vertical-only zoom tool to sequence plot - Increased max number of pulses on Paravision from 16 to 32 - Printing of sequence plot is now black on white - Added Settings to sequence plot to select whether axes, grid, markers should be plotted Internal Changes: - Removed Qwt source code -> Qwt widget library has to be installed separately. - Debian Sarge is now the reference platform on Linux. Version 1.1.0: -------------- API Changes: - rewrote fitting framework in odinreco: Better usability with custom model functions via virtual functions instead of template classes New Features: - New class Image to handle image data. Data is stored on disk in compressed JCAMP-DX format. It is produced by 'autoreco' or by 'raw2image' and can be viewed with 'tjview'. - All parameters which are relevant for the measurement (systemInfo, geometryInfo, sequencePars) are now stored together with the raw data in a single file 'protocol'. The old files systemInfo, geometryInfo, and sequencePars are still available. - Added integration.* in odinreco for easy integration of functions using the GSL - New files utils.* in odinreco to hold spezialized utility functions for reconstruction Internal Changes: - Moved platform-specific processing of cmdline options to platform drivers - New class OdinProcess to encapsulate platform-specific process creation/execution - Singletons are now managed by SingletonHandler template class to solve problems with DLLs on windows - New class OdinConf to hold/manage platform-specific configuration options Version 1.0.0: -------------- - small bug fixes - Fixed geometry handling on IDEA - improved geoedit GUI - added Store/Load-Buttons to store ODIN protocols on Paravision - added -s to rels action on Paravision to set parameters via the command line Version 0.9.9: -------------- - cleaned up Paravision interface of ODIN - adaption of ODIN to NUMARIS VA25 - fixed calculation of composite pulses - added calculation of eddy currents to plotting module - added SeqSnapshot sequence object to dump magnetization at a specified point in time during simulation Version 0.9.8: -------------- - bug fixes - moved saturation pulse into separate files seqsat.* - new virtual samples for quality phantom - different modes for geometry: slicepack and 3Dvoxel - new Nyquist correction for EPI scans Version 0.9.7: -------------- - bug fixes Version 0.9.6: -------------- - Refectored magnetization class SeqSimMagn and its simulation. - Implemented new sequence plotting/simulation framework in the ODIN GUI. - Removed obsolete SeqDigitised class and audiofile generation which were formerly used to display sequences. Version 0.9.5: -------------- - Modified tjview so that it can be compiled for Windows - New plotting facility to visualize sequences using a new StandAlone platform and the QwtPlot class - Every platform has now its own systemInfo struct, but the interface does not change: systemInfo-> will be relayed to the particular systemInfo of the current platform. - Refactored reorder vector: SeqVector now contains a pointer to its reordering vector so that every vector class can now be reordered. Version 0.9.4: -------------- - Cleaned up stream replacement and debugging facility - Decreased memory usage of recoInfo structure - Support for multi-channel acquisition (phased-array coils) added - Cleaned up JCAMP-DX implementation - Replaced tjstring by STD_string, which is simply a macro for std::string on platforms with a working STL - Replaced tjcomplex by STD_complex, which is simply a macro for std::complex on platforms with a working STL Version 0.9.3: -------------- - Moved C-standard-header includes into a single new file tjcstd.h - Fixed performance problem when dealing with recoInfo of many-repetition scans Version 0.9.2: -------------- - Added recoInfo data structure to store reconstruction parameters - Added autoreco executable to perform an automatic reconstruction based on recoInfo - Improved STL-replacement: now true doubly linked list, list::sort() and list::unique() implemented - Fully implemented hardware drivers (SeqGradTrapez and SeqGradChanParallel) Version 0.9.1: -------------- - Implemented hardware drivers by pure virtual driver base classes and their derivations for each platform - Removed obsolete class SeqGradObjList and SeqGradObjLoop Version 0.9.0: -------------- - Added User Manual for ODIN user interface - Now using Qwt for plotting 1D-graphs - Improved handling of different nuclei, fixed decoupling class - Added interpolation function to Data class Version 0.8.4: -------------- - Improved ODIN user interface - Even more bug fixes Version 0.8.3: -------------- - Bug fixes! Version 0.8.2: -------------- - Improved release generation Version 0.8.1: -------------- - Bug fixes - Improved fMRI analysis in tjview Version 0.8.0: -------------- - Restructured source code tree - compilation for IDEA now uses autoconf/automake - new library odinreco instead of recopp_blitz Version 0.7.1: -------------- - improved ODIN GUI: k-space display, etc. - rewrote framework for JDXfunctions for minimal memory usage - accelerated performance in the Siemens enviroment - SeqRotMatrixVector now coupled to SeqParallel to be used with IDEA - Started spiral sequence Version 0.7.0: -------------- - ODIN now contains a nice GUI for interactive sequence design - complete rewrite of audio file generation Version 0.6.2: -------------- - Better integration of ODIN into Siemens GUI (TE/TR feedback) - Now using release compilation on Siemens host/mpcu to decrease library size - Added fMRI analysis to tjview Version 0.6.1: -------------- - Added custom memory manager for real time OS to avoid memory leaks - Finished implementation of rotation matrix vector - Reworked EPI implementation: different drivers for different platforms - EPI reco now in separate function Version 0.6.0: -------------- - Improved automatic reconstruction via ICE - Reworked implementation of reordering schemes for Bruker - Fixed serious bug in frequency list generation Version 0.5.3: -------------- - Reordering schemes introduced - Added code to ODIN that allows automatic reconstruction via the ICE framework - bug fixes Version 0.5.2: -------------- - Improved method interface - bug fixes Version 0.5.1: -------------- - New root classes SeqIdea and SeqParavision added that deal with the different scanner hardware - bug fixes - Partial fourier added to EPI module - Program 'genmakefile' added that creates Makefiles for the methods on different platforms - ICE program added that writes raw data to disk Version 0.5.0: -------------- - ODIN works together with IDEA! - bug fixes - global object 'commonPars' added that contains parameters found in nearly every sequence (TE,TR,..) Version 0.4.9: -------------- - ODIN now compiles with GCC3.2 - Various bug fixes Version 0.4.8: -------------- - Improved Pulsar Version 0.4.6: -------------- - Added ramp sampling for EPI Version 0.4.4: -------------- - Bug fixes for previous version Version 0.4.3: -------------- - Improved manual - Added more stuff for IDEA support Version 0.4.2: -------------- - subsystem for gradient channel handling replaced: gradient channel objects can now be played out asynchroniously - Improved EPI reco - Predefined fat saturation pulse added Version 0.4.1: -------------- - Support for import/export of Vista files added. - Frequency and delay lists for Bruker are now calculated by iterating through the sequence and retrieving their values. - Gradient waveforms and gradient vectors (phase encoding) are now copied to the PARX parameter space via a predefined list of float arrays to minimise IMND compilation. - Predefined sinc and Gauss pulse added. Version 0.4.0: -------------- - Support for IDEA added. ODIN now compiles with VC++ and the VxWorks cross-compiler. - Added a rough but working STL replacement for platforms where STL is broken (VxWorks). - ODIN Homepage improved: Download section now contains binaries for different platforms. - IDE for this release was KDevelop 2.1 Version 0.3.3: -------------- - Various bug fixes - Documentation updated - Composite pulses added to OdinPulse/Pulsar Version 0.3.2: -------------- - Simulation of sequences is now possible by using the 'simulate' option on the command line - Sequences can now be stored as 6 channel AIFF files by using the 'audio' command line switch - The command line switches 'events' and 'tree' for sequences print the events along the time axis or the hierachical sequence tree. - Added variable delay vector SeqDelayVector - renamed method tj_read_d to odingrech (basic gradient echo sequence) Version 0.3.1: -------------- - New debugging framework. Functions are debugged by generating a local Debug object. Additional messages can be emitted by a stream-like syntax. - The sequence library is distributed over a whole bunch of new files - The static members systemInfo and geometryInfo are now pointers due to problems in initialising the libraries when they are loaded - Added new program JdxEdit, an interactive editor for JCAMP-DX files Version 0.3.0: -------------- - Advanced pulses are now managed by a new class OdinPulse which allows adding new pulse shape, trajectory and filter functions via a plug-in style mechanism. - The Pulsar user interface has been completely rewritten to make use of the OdinPulse class and of new mechanism of automatically building a widget from a given JCAMP-DX parameter set. - Simulation of a sequence is now handled by two classes: SeqDigitised represents the digitised RF and gradient waveforms of the sequence and SeqSimMagn holds the magnetisation array. Both are then connected by a simulate function. - The simulation of relaxation effects (T1,T2) were added by Robert Trampel - The following methods are now part of ODIN: -odinmdeft : MDEFT sequence -odinonep : onepulse experiment - IDE for this release was KDevelop 2.1 odin-1.8.5/COPYING0000644000175000017500000004311011322062355010430 00000000000000 GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. 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These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. odin-1.8.5/odin.nsi0000644000175000017500000000713311322062355011046 00000000000000; Script to generate a distributable Odin package for Windows ; using the Nullsoft installer ; odin.nsi ;-------------------------------- ; The name of the installer Name "Odin" ; The file to write OutFile "odin-VERSION.exe" SetCompressor bzip2 ; The default installation directory ;InstallDir $PROGRAMFILES\Odin InstallDir C:\Odin DirText "IMPORTANT: Please uninstall any previous version of Odin and chose a directory path name WITHOUT space characters for installation!" ;-------------------------------- Function IsUserAdmin Push $R0 Push $R1 Push $R2 ClearErrors UserInfo::GetName IfErrors Win9x Pop $R1 UserInfo::GetAccountType Pop $R2 StrCmp $R2 "Admin" 0 Continue StrCpy $R0 "true" Goto Done Continue: StrCmp $R2 "" Win9x StrCpy $R0 "false" ;MessageBox MB_OK 'User "$R1" is in the "$R2" group' Goto Done Win9x: ;MessageBox MB_OK "Error! This DLL can't run under Windows 9x!" StrCpy $R0 "true" Done: ;MessageBox MB_OK 'User= "$R1" AccountType= "$R2" IsUserAdmin= "$R0"' Pop $R2 Pop $R1 Exch $R0 FunctionEnd ;-------------------------------- ; Registry key to check for directory (so if you install again, it will ; overwrite the old one automatically) InstallDirRegKey HKLM "Software\Odin" "Install_Dir" ;-------------------------------- ; Pages Page components Page directory Page instfiles UninstPage uninstConfirm UninstPage instfiles ;-------------------------------- Section "" Call IsUserAdmin Pop $R0 ; at this point $R0 is "true" or "false" StrCmp $R0 "false" 0 +3 MessageBox MB_OK|MB_ICONEXCLAMATION "Please install with Administrator rights." Quit SectionEnd ;-------------------------------- ; The stuff to install Section "Odin (required)" SectionIn RO ; Set output path to the installation directory. SetOutPath $INSTDIR ; Put file there File /r "bin" File /r "include" File /r "lib" File /r "share" File /r "src" File /r "mingw32" File /r "msys" ; Write the installation path into the registry WriteRegStr HKLM SOFTWARE\Odin "Install_Dir" "$INSTDIR" ; Write the uninstall keys for Windows WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Odin" "DisplayName" "NSIS Odin" WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Odin" "UninstallString" '"$INSTDIR\uninstall.exe"' WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Odin" "NoModify" 1 WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Odin" "NoRepair" 1 WriteUninstaller "uninstall.exe" SectionEnd ; Optional section (can be disabled by the user) Section "Start Menu Shortcuts" CreateDirectory "$SMPROGRAMS\Odin" CreateShortCut "$SMPROGRAMS\Odin\Uninstall.lnk" "$INSTDIR\uninstall.exe" CreateShortCut "$SMPROGRAMS\Odin\Odin.lnk" "$INSTDIR\bin\odin.exe" CreateShortCut "$SMPROGRAMS\Odin\Pulsar.lnk" "$INSTDIR\bin\pulsar.exe" ; CreateShortCut "$SMPROGRAMS\Odin\MiView.lnk" "$INSTDIR\bin\miview.exe" ; CreateShortCut "$SMPROGRAMS\Odin\GeoEdit.lnk" "$INSTDIR\bin\geoedit.exe" CreateShortCut "$SMPROGRAMS\Odin\Manual.lnk" "$INSTDIR\share\doc\odin\manual\html\index.html" CreateShortCut "$SMPROGRAMS\Odin\Shell.lnk" "$INSTDIR\bin\shell.bat" "$INSTDIR" SectionEnd ;-------------------------------- ; Uninstaller Section "Uninstall" ; Remove registry keys DeleteRegKey HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\Odin" DeleteRegKey HKLM SOFTWARE\Odin ; Remove files and uninstaller Delete "$INSTDIR\*.*" RMDir /r "$INSTDIR\*" ; Remove shortcuts, if any Delete "$SMPROGRAMS\Odin\*.*" ; Remove directories used RMDir "$SMPROGRAMS\Odin" RMDir "$INSTDIR" SectionEnd odin-1.8.5/odindata/0000755000175000017500000000000011735135551011250 500000000000000odin-1.8.5/odindata/filter_shift.h0000644000175000017500000000263011322062337014015 00000000000000/*************************************************************************** filter_shift.h - description ------------------- begin : Fri Nov 21 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_SHIFT_H #define FILTER_SHIFT_H #include class FilterShift : public FilterStep { JDXfloat shift[n_directions]; STD_string label() const {return "shift";} STD_string description() const {return "Shift data spatially";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterShift();} void init(); }; #endif odin-1.8.5/odindata/filter_reduction.cpp0000644000175000017500000000003611665172216015235 00000000000000#include "filter_reduction.h" odin-1.8.5/odindata/complexdata.h0000644000175000017500000002672111734622163013651 00000000000000/*************************************************************************** complexdata.h - description ------------------- begin : Fri Apr 6 2001 copyright : (C) 2001 by Thies Jochimsen & Michael von Mengershausen email : jochimse@cns.mpg.de mengers@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef COMPLEXDATA_H #define COMPLEXDATA_H #include #include /** * @addtogroup odindata * @{ */ /////////////////////////////////////////////////////// /** * This template class holds multidimensional complex data, most suitable for NMR signal. * In addition to functionality provided by the Data Array class, * it offers advanced numerical routines (FFT) and block-wise * processing of large data files. */ template class ComplexData : public Data { public: /** * Default constructor */ ComplexData() {} /** * Constructs a complex array with the given dimensionality */ ComplexData(const TinyVector& dimvec, const STD_complex& val=0) : Data(dimvec) {(*this)=val;} /** * Constructor with a variable list of arguments to specify the extend * in each dimension, the number of args must match N_rank */ // resolve ambiguities due to other constructors ComplexData(int extent1) : Data(extent1) {} ComplexData(int extent1, int extent2) : Data(extent1,extent2) {} ComplexData(int extent1, int extent2,int extent3) : Data(extent1,extent2,extent3) {} ComplexData(int extent1, int extent2,int extent3,int extent4) : Data(extent1,extent2,extent3,extent4) {} ComplexData(int extent1, int extent2,int extent3,int extent4,int extent5) : Data(extent1,extent2,extent3,extent4,extent5) {} ComplexData(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6) : Data(extent1,extent2,extent3,extent4,extent5,extent6) {} ComplexData(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7) : Data(extent1,extent2,extent3,extent4,extent5,extent6,extent7) {} ComplexData(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7,int extent8) : Data(extent1,extent2,extent3,extent4,extent5,extent6,extent7,extent8) {} ComplexData(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7,int extent8,int extent9) : Data(extent1,extent2,extent3,extent4,extent5,extent6,extent7,extent8,extent9) {} /** * Copy constructor */ ComplexData(const ComplexData& cd) : Data(cd) {} /** * Copy constructor from Data */ ComplexData(const Data& a) : Data(a) {} /** * Assignment operator */ ComplexData& operator = (const ComplexData& d) {Data::operator=(d); return *this;} /** * Assignment operator from Blitz::Array */ ComplexData& operator = (const Array& a) {Array::operator=(a); return *this;} /** * Fills all elements with 'val' */ ComplexData& operator = (const STD_complex& val) {Data::operator=(val); return *this;} /** * Assignment operator for expression templates */ template inline ComplexData& operator = (BZ_ETPARM(_bz_ArrayExpr) expr) { typedef _bz_typename T_expr::T_numtype T_numtype; evaluate(expr, _bz_update()); return *this; } /** * Element-wise + operator for 2 arrays */ Array operator + (const ComplexData& b) const { return Array(Array(*this)+Array(b)); } /** * Element-wise - operator for 2 arrays */ Array operator - (const ComplexData& b) const { return Array(Array(*this)-Array(b)); } /** * Element-wise * operator for 2 arrays */ Array operator * (const ComplexData& b) const { return Array(Array(*this)*Array(b)); } /** * Element-wise / operator for 2 arrays */ Array operator / (const ComplexData& b) const { return Array(Array(*this)/Array(b)); } /** * Performs an in-place FFT with the following properties: * - forward: Whether to do a forward (true) or backward (false) FFT * - cyclic_shift: Whether to shift data cyclically so that zero frequency * is in the middle of the array after FFT */ void fft(bool forward=true, bool cyclic_shift=true); /** * Performs an in-place FFT over a partial number of dimensions with the following properties: * - do_fft: A vector where the index should be set to 'true' if the FFT should be performed for the corresponding dimension * - forward: Whether to do a forward (true) or backward (false) FFT * - cyclic_shift: Whether to shift data cyclically so that zero frequency * is in the middle of the array after FFT */ void partial_fft(const TinyVector& do_fft, bool forward=true, bool cyclic_shift=true); /** * Modulate a phase gradient onto the array so that after FFT, the data will be shifted * in each dimension by 'rel_offset' which is given as a fraction relative to the full size, * i.e. a value of 0.5 shifts the array by half its size. * */ void modulate_offset(const TinyVector& rel_offset); /** * Shift the data by the number of pixels given in 'shiftvec' for each dimension using the FFT, * i.e. this is possible even with fractions. */ void shift_subpixel(const TinyVector& shiftvec); /** * Returns the phase of the complex array, whereby the phase is unwrapped in the last dimension */ Data phasemap() const; }; /** @} */ /////////////////////////////////////////////////////// template void ComplexData::fft(bool forward, bool cyclic_shift) { Log odinlog("ComplexData","fft"); TinyVector do_fft=true; ComplexData::partial_fft(do_fft, forward, cyclic_shift); } /////////////////////////////////////////////////////// // call FFT of GSL struct GslFftWorkSpace; // forward declaration class GslFft { public: GslFft(int length); ~GslFft(); void fft1d(double* complex_data, bool forward_fft); private: GslFftWorkSpace* ws; }; /////////////////////////////////////////////////////// template void ComplexData::partial_fft(const TinyVector& do_fft, bool forward, bool cyclic_shift) { Log odinlog("ComplexData","partial_fft"); TinyVector myshape(Array::shape()); TinyVector cyclshift=(ComplexData::shape())/2; // Shift (back) prior to FFT to get flat phasemap if(cyclic_shift) { for(int irank=0; irank::shift(irank,-cyclshift(irank)); } } TinyVector indexvec; for(int irank=0; irank ortho_shape(myshape); ortho_shape(irank)=1; int oneline_size=myshape(irank); double *complex_data= new double[2*oneline_size]; GslFft gslfft(oneline_size); // The total number of elements in the orthogonal subspace unsigned long n_ortho=product(ortho_shape); ODINLOG(odinlog,normalDebug) << "oneline_size/irank/n_ortho=" << oneline_size << "/" << irank << "/" << n_ortho << STD_endl; for(unsigned long iortho=0; iortho(ortho_shape,iortho); for(int j=0; j index; for(int i=0; i::numElements(); i++) { index=Data::create_index(i); (*this)(index)*=exp(float2imag(-2.0*PII*sum(rel_offset*index))); } } /////////////////////////////////////////////////////// template void ComplexData::shift_subpixel(const TinyVector& shiftvec) { fft(true); unsigned int totalsize=Array::numElements(); TinyVector index; for(unsigned int i=0; i::create_index(i); float im=0.0; for(int idim=0; idim::extent(idim)); } STD_complex phase(0,im); (*this)(index)*=exp(phase); } fft(false); } /////////////////////////////////////////////////////// template Data ComplexData::phasemap() const { Range all=Range::all(); const ComplexData& indata=*this; TinyVector myshape(indata.shape()); Data result(myshape); TinyVector ortho_shape(myshape); ortho_shape(N_rank-1)=1; int nlast=myshape(N_rank-1); Data phasevec(nlast); Data unwrapped(nlast); TinyVector indexvec; for(int iortho=0; iortho(ortho_shape,iortho); int ilast; for(ilast=0; ilast& data, Protocol& prot) const { data=where(Array(data)(data)); return true; } /////////////////////////////////////////////////// void FilterMax::init(){ thresh.set_description("Maximum value"); append_arg(thresh,"thresh"); } bool FilterMax::process(Data& data, Protocol& prot) const { data=where(Array(data)>thresh, float(thresh), Array(data)); return true; } /////////////////////////////////////////////////// void FilterType::init(){ type.set_description("Datatype"); append_arg(type,"type"); } float FilterType::getThresh(bool upper)const{ if( IS_TYPE( u8bit,type)) return upper ? std::numeric_limits::max(): std::numeric_limits::min(); else if(IS_TYPE( s8bit,type)) return upper ? std::numeric_limits::max(): std::numeric_limits::min(); else if(IS_TYPE(u16bit,type)) return upper ? std::numeric_limits::max():std::numeric_limits::min(); else if(IS_TYPE(s16bit,type)) return upper ? std::numeric_limits::max():std::numeric_limits::min(); else if(IS_TYPE(u32bit,type)) return upper ? std::numeric_limits::max():std::numeric_limits::min(); else if(IS_TYPE(s32bit,type)) return upper ? std::numeric_limits::max():std::numeric_limits::min(); else if(IS_TYPE(float,type)) return upper ? std::numeric_limits::max(): std::numeric_limits::min(); else if(IS_TYPE(double,type)) return upper ? std::numeric_limits::max():std::numeric_limits::min(); return 0.0; } bool FilterTypeMax::process(Data& data, Protocol& prot) const { float thresh=getThresh(true); data=where(Array(data)>thresh, thresh, Array(data)); return true; } bool FilterTypeMin::process(Data& data, Protocol& prot) const { float thresh=getThresh(false); data=where(Array(data)(data)); return true; } odin-1.8.5/odindata/fileio_raw.cpp0000644000175000017500000000624511322062337014014 00000000000000#include "fileio.h" #include "complexdata.h" ////////////////////////////////////////////////////////////// template struct RawFormat : public FileFormat { STD_string description() const { STD_string descr=TypeTraits::type2label((T)0); if(descr.find("bit")!=STD_string::npos) { descr=replaceStr(descr, "s", "signed "); descr=replaceStr(descr, "u", "unsigned "); descr=replaceStr(descr, "bit", " bit"); } descr+=" raw data"; return descr; } svector suffix() const { svector result; result.resize(1); result[0]=TypeTraits::type2label((T)0); return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("RawFormat","read"); TinyVector newshape; newshape=1; unsigned long typesize=sizeof(T); if( int(opts.cplx)>0 ) typesize*=2; int fsize=filesize(filename.c_str())-opts.skip; newshape(0)=prot.seqpars.get_NumOfRepetitions(); newshape(3)=prot.seqpars.get_MatrixSize(readDirection); newshape(2)=prot.seqpars.get_MatrixSize(phaseDirection); newshape(1)=(unsigned int)secureDivision(fsize,typesize*product(newshape)); ODINLOG(odinlog,normalDebug) << "fsize/typesize/newshape(1)=" << fsize << "/" << typesize << "/" << newshape(1) << STD_endl; if(!product(newshape)) { ODINLOG(odinlog,errorLog) << "wrong size: " << newshape << STD_endl; return -1; } data.resize(newshape); if(int(opts.cplx)>0 ) { ComplexData<4> data_cplx(newshape); if(data_cplx.Data::read(filename,opts.skip)<0) return -1; // extra scop for MinGW if(opts.cplx=="abs") data=cabs(data_cplx); if(opts.cplx=="pha") data=phase(data_cplx); if(opts.cplx=="real") data=creal(data_cplx); if(opts.cplx=="imag") data=cimag(data_cplx); } else { prot.system.set_data_type(TypeTraits::type2label((T)0)); if(data.Data::read(filename,opts.skip)<0) return -1; // extra scop for MinGW } return data.extent(0)*data.extent(1); } int write(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) { autoscaleOption scaleopt=autoscale; const STD_string type(prot.system.get_data_type()); if(type!="float" && type!="double")scaleopt=noupscale; if(opts.append) { Data data_copy; data.Data::convert_to(data_copy,scaleopt); return data_copy.write(filename,appendMode); } else return data.Data::write(filename,scaleopt); } }; ////////////////////////////////////////////////////////////// void register_raw_format() { static RawFormat s8f; static RawFormat u8f; static RawFormat s16f; static RawFormat u16f; static RawFormat s32f; static RawFormat u32f; static RawFormat floatf; static RawFormat doublef; s8f.register_format(); u8f.register_format(); s16f.register_format(); u16f.register_format(); s32f.register_format(); u32f.register_format(); floatf.register_format(); doublef.register_format(); } odin-1.8.5/odindata/step_code.h0000644000175000017500000001273611322062337013310 00000000000000#include template T* Step::clone() const { T* result=allocate(); result->init(); result->args.copy_ldr_vals(args); return result; } template void Step::set_args(const STD_string& argstr) { Log odinlog(c_label(),"set_args"); unsigned int nargs=args.numof_pars(); if(!nargs) return; // Just a flag svector toks(tokens(argstr,',','(',')')); for(unsigned int i=0; i STD_string Step::args_description() const { int nargs=args.numof_pars(); STD_string result; for(int i=0; i void Step::append_opts(JcampDxBlock& parblock) { parblock.merge(args); } template void Step::append_arg(JcampDxClass& arg, const STD_string& arglabel) { arg.set_label(label()+"_"+arglabel); args.append(arg); } /////////////////////////////////////////////////////////////////////////////////// template StepFactory::StepFactory(JcampDxBlock* parblock) { STD_list steplist; T::create_templates(steplist); for(typename STD_list::const_iterator it=steplist.begin(); it!=steplist.end(); ++it) { T* p=(*it); p->init(); if(parblock) p->append_opts(*parblock); templates[p->label()]=p; } } template StepFactory::~StepFactory() { for(typename StepMap::iterator it=templates.begin(); it!=templates.end(); ++it) delete it->second; for(typename STD_list::iterator it=garbage.begin(); it!=garbage.end(); ++it) delete (*it); } template T* StepFactory::create(const STD_string& label) const { Log odinlog("StepFactory","create"); T* result=0; typename StepMap::const_iterator it=templates.find(label); if(it!=templates.end()) { result=it->second->clone(); } else { ODINLOG(odinlog,errorLog) << "Step with label >" << label << "< not found" << STD_endl; return 0; } garbage.push_back(result); return result; } // Helper class for managing step entries in the manual struct StepDoc { STD_string label; STD_string description; STD_string in; STD_string out; STD_string options; }; template STD_string StepFactory::manual() const { STD_string result; STD_map > strmap; for(typename StepMap::const_iterator it=templates.begin(); it!=templates.end(); ++it) { const char* classtype=typeid(*(it->second)).name(); while( (*classtype) >='0' && (*classtype) <='9' ) classtype++; // strip off leading numbers (GCC) STD_string classname(classtype); classname=rmblock(classname,"IL",""); // strip off template parameters (GCC) StepDoc doc; doc.label=it->first; doc.description=it->second->description(); T::interface_description(it->second, doc.in, doc.out); JcampDxBlock parblock; it->second->append_opts(parblock); int nargs=parblock.numof_pars(); for(int i=0; i >::const_iterator it=strmap.begin(); it!=strmap.end(); ++it) { result+="/**\n"; result+=" * \\class "+it->first+"\n"; STD_string labels; STD_string descr; // assume the same for all for(STD_list::const_iterator docit=it->second.begin(); docit!=it->second.end(); ++docit) { if(labels!="") labels+=", "; labels+="\\b "+docit->label; descr=docit->description; } result+=" * \\brief "+labels+": "+descr+"\n\n"; for(STD_list::const_iterator docit=it->second.begin(); docit!=it->second.end(); ++docit) { result+=" * Functor label: \\b "+docit->label+"\n\n"; if(docit->in!="" || docit->out!="") { result+=" * Interface of \\b "+docit->label+":\n"; result+=" * - input: "+docit->in+"\n"; result+=" * - output: "+docit->out+"\n"; } result+=" *\n"; result+=" *\n"; if(docit->options!="") { result+=" * Options of \\b "+docit->label+":\n"; result+=" * \\verbatim \n"; result+=docit->options; result+=" \\endverbatim \n\n"; } } result+=" */\n\n"; } result+="/** @}\n"; result+=" */\n"; return result; } template STD_string StepFactory::get_cmdline_usage(const STD_string& lineprefix)const{ STD_string ret; for(typename StepMap::const_iterator it=templates.begin(); it!=templates.end(); ++it) { const T* st=it->second; ret += lineprefix+"-"+st->label(); STD_string argsdescr=st->args_description(); if(argsdescr!="") ret += " <"+argsdescr+">"; ret += " : "+st->description()+"\n"; } return ret; } odin-1.8.5/odindata/filter_merge.h0000644000175000017500000000264211322062337014002 00000000000000/*************************************************************************** filter_merge.h - description ------------------- begin : Mon May 25 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_MERGE_H #define FILTER_MERGE_H #include class FilterMerge: public FilterStep { STD_string label() const {return "merge";} STD_string description() const {return "Merge datasets into a single dataset by expanding the time dimension";} bool process(FileIO::ProtocolDataMap& pdmap) const; FilterStep* allocate() const {return new FilterMerge();} void init() {} }; #endif odin-1.8.5/odindata/data.cpp0000644000175000017500000003375211734622163012616 00000000000000#include "data.h" #include "fileio.h" #include "utils.h" #include ////////////////////////////////////////////////// int fileio_autowrite(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol* prot) { FileIO::ProtocolDataMap pdmap; if(prot) { pdmap[*prot].reference(data); } else { Protocol prot; // set extensions in the protocol prot.seqpars.set_NumOfRepetitions(data.extent(0)); prot.geometry.set_nSlices(data.extent(1)); prot.seqpars.set_MatrixSize(phaseDirection,data.extent(2)); prot.seqpars.set_MatrixSize(readDirection,data.extent(3)); pdmap[prot].reference(data); } return FileIO::autowrite(pdmap, filename, opts); } int fileio_autoread(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol* prot, ProgressMeter* progmeter) { Log odinlog("","fileio_autoread"); FileIO::ProtocolDataMap pdmap; ODINLOG(odinlog,normalDebug) << "data/filename/prot=" << data.shape() << "/" << filename << "/" << prot << STD_endl; Protocol protocol_template; // set defaults for reading raw data protocol_template.seqpars.set_MatrixSize(readDirection,1); protocol_template.seqpars.set_MatrixSize(phaseDirection,1); protocol_template.seqpars.set_MatrixSize(sliceDirection,1); if(prot) protocol_template=(*prot); int result=FileIO::autoread(pdmap, filename, opts, protocol_template, progmeter); if(result<0) return -1; FileIO::ProtocolDataMap::const_iterator it=pdmap.begin(); if(it!=pdmap.end()) { if(prot) (*prot)=it->first; data.reference(it->second); } else { ODINLOG(odinlog,errorLog) << "Empty protocol-data map" << STD_endl; return -1; } return result; } ////////////////////////////////////////////////// // Unit Test #ifndef NO_UNIT_TEST class DataTest : public UnitTest { public: DataTest() : UnitTest("Data") {} private: template bool conversion_test(const Data& testarray) const { Log odinlog(this,"conversion_test"); Data dst; testarray.convert_to(dst); STD_string prefix=STD_string("convert_to<")+TypeTraits::type2label((Type)0)+","+itos(Rank)+"> failed, "; TinyVector expected_shape; expected_shape=1; expected_shape(Rank-1)*=testarray.extent(1); expected_shape(STD_max(0,Rank-2))*=testarray.extent(0); if(expected_shape!=dst.shape()) { ODINLOG(odinlog,errorLog) << prefix << "wrong shape=" << dst.shape() << ", but expected " << expected_shape << STD_endl; return false; } if(std::numeric_limits::is_integer) { // just check whether numeric range is fully covered for full-scale mode float minnum=std::numeric_limits::min(); float maxnum=std::numeric_limits::max(); float deltanum=maxnum-minnum; float minval=min(dst); float maxval=max(dst); float relmaxdiff_plus=fabs(maxval-maxnum)/deltanum; float relmaxdiff_minus=fabs(minval-minnum)/deltanum; if(relmaxdiff_plus>.02 && relmaxdiff_minus>.02) { ODINLOG(odinlog,errorLog) << prefix << "auto-scale range relmaxdiff=" << relmaxdiff_minus << "/" << relmaxdiff_plus << STD_endl; ODINLOG(odinlog,errorLog) << "minval/maxval=" << minval << "/" << maxval << STD_endl; ODINLOG(odinlog,errorLog) << "minnum/maxnum=" << minnum << "/" << maxnum << STD_endl; return false; } // Convert back to float Data dstfloat; dst.convert_to(dstfloat); minval=min(dstfloat); maxval=max(dstfloat); relmaxdiff_plus=fabs(maxval-maxnum)/deltanum; relmaxdiff_minus=fabs(minval-minnum)/deltanum; if(relmaxdiff_plus>.02 && relmaxdiff_minus>.02) { ODINLOG(odinlog,errorLog) << prefix << "convert-back relmaxdiff=" << relmaxdiff_minus << "/" << relmaxdiff_plus << STD_endl; ODINLOG(odinlog,errorLog) << "minval/maxval=" << minval << "/" << maxval << STD_endl; ODINLOG(odinlog,errorLog) << "minnum/maxnum=" << minnum << "/" << maxnum << STD_endl; return false; } // Test down-scaling separately Data largevals(testarray.copy());largevals(3,3)=minnum-100.0;largevals(2,2)=maxnum+100.0; // Make sure data is out of range of Type largevals.convert_to(dst); minval=min(dst); maxval=max(dst); relmaxdiff_plus=fabs(maxval-maxnum)/deltanum; relmaxdiff_minus=fabs(minval-minnum)/deltanum; if(relmaxdiff_plus>.02 && relmaxdiff_minus>.02) { ODINLOG(odinlog,errorLog) << prefix << "down-scale range relmaxdiff=" << relmaxdiff_minus << "/" << relmaxdiff_plus << STD_endl; ODINLOG(odinlog,errorLog) << "minval/maxval=" << minval << "/" << maxval << STD_endl; ODINLOG(odinlog,errorLog) << "minnum/maxnum=" << minnum << "/" << maxnum << STD_endl; return false; } // Test up-scaling Data smallvals(testarray.copy()); smallvals*=0.001/STD_max(fabs(min(testarray)),fabs(max(testarray))); smallvals.convert_to(dst); minval=min(dst); maxval=max(dst); relmaxdiff_plus=fabs(maxval-maxnum)/deltanum; relmaxdiff_minus=fabs(minval-minnum)/deltanum; if(relmaxdiff_plus>.02 && deltanum>.02) { ODINLOG(odinlog,errorLog) << prefix << "up-scale range relmaxdiff=" << relmaxdiff_minus << "/" << relmaxdiff_plus << STD_endl; ODINLOG(odinlog,errorLog) << "smallvals=" << smallvals << STD_endl; ODINLOG(odinlog,errorLog) << "minval/maxval=" << minval << "/" << maxval << STD_endl; ODINLOG(odinlog,errorLog) << "minnum/maxnum=" << minnum << "/" << maxnum << STD_endl; return false; } // Test non-upscaled conversion of small numbers smallvals.convert_to(dst,noupscale); minval=min(dst); maxval=max(dst); if(minval || maxval) { // should be zero ODINLOG(odinlog,errorLog) << prefix << "noupscale failed" << STD_endl; ODINLOG(odinlog,errorLog) << "smallvals=" << smallvals << STD_endl; ODINLOG(odinlog,errorLog) << "minval/maxval=" << minval << "/" << maxval << STD_endl; ODINLOG(odinlog,errorLog) << "minnum/maxnum=" << minnum << "/" << maxnum << STD_endl; return false; } // do an additional test without auto-scaling if data is signed if(std::numeric_limits::is_signed) { testarray.convert_to(dst,noscale); float sumdiff=sum(dst)-sum(testarray); if(fabs(sumdiff)>0.1) { ODINLOG(odinlog,errorLog) << prefix << "no-scale sum sumdiff=" << sumdiff << STD_endl; ODINLOG(odinlog,errorLog) << "dst=" << dst << STD_endl; ODINLOG(odinlog,errorLog) << "testarray=" << testarray << STD_endl; return false; } } } else { for(int i=0; i testindex=testarray.create_index(i); TinyVector dstindex=dst.create_index(i); if(testarray(testindex)!=dst(dstindex)) { ODINLOG(odinlog,errorLog) << prefix << "value mismatch at index " << testindex << STD_endl; ODINLOG(odinlog,errorLog) << testarray(testindex) << " != " << dst(dstindex) << STD_endl; return false; } } } return true; } template bool readwrite_mmap_test(const Data& testarray) const { Log odinlog(this,"readwrite_mmap_test"); Data dst; testarray.convert_to(dst); STD_string prefix=STD_string("read/write/mmap<")+TypeTraits::type2label((Type)0)+"> failed, "; STD_string testfname(tempfile()); // Testing (f)write against filemap int testoffset=10000; // bytes Data(testfname, false, testoffset); // Create offset if(dst.write(testfname, appendMode)) { // append to offset ODINLOG(odinlog,errorLog) << prefix << "write(" << testfname <<")" << STD_endl; return false; } Data mmappedarray(testfname, true, testarray.shape(), testoffset); if(!mmappedarray.is_filemapped()) { ODINLOG(odinlog,errorLog) << prefix << "filemap of >" << testfname << "<" << STD_endl; return false; } if(mmappedarray.shape()!=dst.shape()) { ODINLOG(odinlog,errorLog) << prefix << "wrong shape=" << mmappedarray.shape() << ", but expected " << dst.shape() << STD_endl; return false; } for(int i=0; i index=dst.create_index(i); if(mmappedarray(index)!=dst(index)) { ODINLOG(odinlog,errorLog) << prefix << "mmap value mismatch at index " << index << STD_endl; ODINLOG(odinlog,errorLog) << mmappedarray(index) << " != " << dst(index) << STD_endl; return false; } } // Cross-wise testing of template vs. format read/write if(testarray.write(TypeTraits::type2label((Type)0),testfname,autoscale)) { // implicit conversion, use full range of integer ODINLOG(odinlog,errorLog) << prefix << "write(" << TypeTraits::type2label((Type)0) << "," << testfname <<")" << STD_endl; return false; } #if __GNUC__ > 3 // The following gives parse error on earlier GCC versions Data testread(testarray.shape()); testread=0.0; if(testread.read(testfname)) { ODINLOG(odinlog,errorLog) << "read<" << TypeTraits::type2label((Type)0) << ">(" << testfname <<")" << STD_endl; return false; } if(std::numeric_limits::is_integer) { // Check wheter full range was used float minnum=std::numeric_limits::min(); float maxnum=std::numeric_limits::max(); float deltanum=maxnum-minnum; float minval=min(testread); float maxval=max(testread); float relmaxdiff_plus=fabs(maxval-maxnum)/deltanum; float relmaxdiff_minus=fabs(minval-minnum)/deltanum; if(relmaxdiff_plus>.02 && relmaxdiff_minus>.02) { ODINLOG(odinlog,errorLog) << prefix << "read relmaxdiff=" << relmaxdiff_minus << "/" << relmaxdiff_plus << STD_endl; ODINLOG(odinlog,errorLog) << "minval/maxval=" << minval << "/" << maxval << STD_endl; ODINLOG(odinlog,errorLog) << "minnum/maxnum=" << minnum << "/" << maxnum << STD_endl; return false; } } else { if(testarray.shape()!=testread.shape()) { ODINLOG(odinlog,errorLog) << prefix << "shape mismatch: " << testarray.shape() << " != " << testread.shape() << STD_endl; return false; } for(int i=0; i index=testarray.create_index(i); if(testarray(index)!=testread(index)) { ODINLOG(odinlog,errorLog) << prefix << "read/write value mismatch at index " << index << STD_endl; ODINLOG(odinlog,errorLog) << testarray(index) << " != " << testread(index) << STD_endl; return false; } } } #endif return true; } bool check() const { Log odinlog(this,"check"); int testsize=10; Data testarray(testsize,testsize); // checking create_index against create_linear_index, thereby filling testarray TinyVector indexvec; for(int i=0; i testarray_copy(testarray); testarray_copy.makeUnique(); // test cyclical identitiy shift testarray.shift(1,3); float diff=sum(abs(testarray-testarray_copy)); if(!diff) { ODINLOG(odinlog,errorLog) << "shift ineffective, zero diff" << STD_endl; return false; } testarray.shift(1,4); testarray.shift(1,3); diff=sum(abs(testarray-testarray_copy)); if(diff) { ODINLOG(odinlog,errorLog) << "cyclical shift failed, diff=" << diff << STD_endl; return false; } if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; if(!conversion_test(testarray)) return false; // Testing complex conversion and convert_from_ptr() simultaneously Data cmplxarr; testarray.convert_to(cmplxarr); Data testarray2; convert_from_ptr(testarray2, cmplxarr.c_array(), testarray.shape()); diff=sum(testarray-testarray2); if(diff) { ODINLOG(odinlog,errorLog) << "convert_to/from_ptr failed, diff=" << diff << STD_endl; ODINLOG(odinlog,errorLog) << "testarray=" << testarray << STD_endl; ODINLOG(odinlog,errorLog) << "cmplxarr="; for(int i=0; i3) result.z=0.5*sqrt(double(n-3))*log(argument); // http://www.fmrib.ox.ac.uk/~stuart/thesis/chapter_6/section6_4.html } return result; } ///////////////////////////////////////////////////////////////////////// /** * Kendall's rank-correlation between vectors 'x' and 'y' re-implemented from NRC, section 14.6 * */ template correlationResult kendall(const Array& x, const Array& y) { Log odinlog("","kendall"); correlationResult result; if(x.shape()!=y.shape()) { ODINLOG(odinlog,errorLog) << "Shape mismatch" << STD_endl; return result; } int n=x.size(); int nx=0; int ny=0; int diff=0; for(int j=0; j ii=index2extent(x.shape(),i); TinyVector jj=index2extent(x.shape(),j); float dx=x(jj)-x(ii); float dy=y(jj)-y(ii); if(dx) nx++; if(dy) ny++; float dd=dx*dy; if(dd>0.0) diff++; if(dd<0.0) diff--; } } double tau=secureDivision(diff,sqrt(double(nx))*sqrt(double(ny))); result.r=tau; result.z=3.0*tau*sqrt( secureDivision(n*(n-1),2*(2*n+5) ) ); // Eq. 30.4 in Handbook of Parametric and Nonparametric Statistical Procedures return result; } ///////////////////////////////////////////////////////////////////////// /** * Results of an fMRI analysis * */ struct fmriResult { fmriResult() : Sbaseline(0.0), Srest(0.0), Sstim(0.0), rel_diff(0.0), rel_err(0.0) {} /** * Signal during baseline (leading timesteps with zeroes in design file) */ float Sbaseline; /** * Signal during rest */ float Srest; /** * Signal during stimulation */ float Sstim; /** * Relative signal change */ float rel_diff; /** * Error of relative signal change */ float rel_err; }; ///////////////////////////////////////////////////////////////////////// /** * Returns an fMRI analysis of 'timecourse' using 'designvec' * */ fmriResult fmri_eval(const Data& timecourse, const Data& designvec); /** @} */ #endif odin-1.8.5/odindata/filter_nan.cpp0000644000175000017500000000113511322062337014006 00000000000000// // C++ Implementation: filter_nan // // Description: // // // Author: , (C) 2007 // // Copyright: See COPYING file that comes with this distribution // // #include "filter_nan.h" void FilterNaN::init(){ replace=0; replace.set_description("Replacement value"); append_arg(replace,"replace"); } bool FilterNaN::process(Data& data, Protocol& prot)const{ //replace all elements by replace where element does NOT equal itself (which is only true for NaN) data=where(Array(data) == Array(data), Array(data), (float)replace ); return true; } odin-1.8.5/odindata/complexdata.cpp0000644000175000017500000001107011670202076014167 00000000000000#include "complexdata.h" #include #ifdef HAVE_LIBGSL #include struct GslFftWorkSpace { int length_cache; gsl_fft_complex_wavetable* wavetable; gsl_fft_complex_workspace* workspace; }; GslFft::GslFft(int length) : ws(new GslFftWorkSpace) { ws->length_cache=length; ws->wavetable=gsl_fft_complex_wavetable_alloc(length); ws->workspace=gsl_fft_complex_workspace_alloc(length); } GslFft::~GslFft() { gsl_fft_complex_wavetable_free(ws->wavetable); gsl_fft_complex_workspace_free(ws->workspace); delete ws; } void GslFft::fft1d(double* complex_data, bool forward_fft) { if(forward_fft) gsl_fft_complex_forward (complex_data, 1, ws->length_cache, ws->wavetable, ws->workspace); else gsl_fft_complex_backward(complex_data, 1, ws->length_cache, ws->wavetable, ws->workspace); } #else #error "GNU Scientific library is missing!" #endif ////////////////////////////////////////////////// // Unit Test #ifndef NO_UNIT_TEST class ComplexDataTest : public UnitTest { public: ComplexDataTest() : UnitTest("ComplexData") {} private: bool check() const { Log odinlog(this,"check"); int testsize=11; // Use odd number for more thourough testing ComplexData<2> testarray(testsize,testsize); TinyVector index; for(int i=0; i original(testarray); original.makeUnique(); // test FFT by back and forth transform testarray.fft(true); testarray.fft(false); float diff=sum(cabs(testarray-original)); if(diff>1e-4) { // Data(cabs(testarray)).autowrite("testarray.jdx"); // Data(cabs(original)).autowrite("original.jdx"); ODINLOG(odinlog,errorLog) << "FFT test failed, diff=" << diff << STD_endl; return false; } // Test Data::shift against ComplexData::modulate_offset ComplexData<2> shifttest1(original.shape()); shifttest1=original; ComplexData<2> shifttest2(original.shape()); shifttest2=original; int shiftpix=3; shifttest1.shift(0, shiftpix); shifttest2.fft(true); float relshift=float(shiftpix)/float(testsize); shifttest2.modulate_offset(TinyVector(relshift, 0.0)); shifttest2.fft(false); diff=sum(cabs(shifttest1)-cabs(shifttest2)); // take magnitude difference as modulate_offset adds extra phase if(diff>0) { // Data(cabs(shifttest1)).autowrite("shifttest1.jdx"); // Data(cabs(shifttest2)).autowrite("shifttest2.jdx"); ODINLOG(odinlog,errorLog) << "modulate_offset failed, diff=" << diff << STD_endl; return false; } // Test Data::convert_to complex->complex ComplexData<3> data3d; original.convert_to(data3d); ComplexData<2> convtest; data3d.convert_to(convtest); diff=sum(cabs(original-convtest)); if(diff>0.0) { ODINLOG(odinlog,errorLog) << "convert_to(complex->complex) failed, diff=" << diff << STD_endl; ODINLOG(odinlog,errorLog) << "original " << original << STD_endl; ODINLOG(odinlog,errorLog) << "convtest " << convtest << STD_endl; return false; } // Testing convert_to with byte->complex->float int nbytes=4; Data bytedata(nbytes); for(int i=0; i cplxdst; bytedata.convert_to(cplxdst); Data floatdst; cplxdst.convert_to(floatdst); for(int i=0; i& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterResize();} void init(); }; ///////////////////////////////////////////////////////////////////////// class FilterResample : public FilterStep { JDXint newsize; STD_string label() const {return "resample";} STD_string description() const {return "Temporal resize of image data";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterResample();} void init(); }; ///////////////////////////////////////////////////////////////////////// class FilterIsotrop : public FilterStep { JDXfloat size; STD_string label() const {return "isotrop";} STD_string description() const {return "make image voxels isotrop through interpolation (image geometry will not change)";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterIsotrop();} void init(); }; #endif odin-1.8.5/odindata/filter_scale.cpp0000644000175000017500000000051111322062337014316 00000000000000#include "filter_scale.h" void FilterScale::init(){ slope=1.0; slope.set_description("Slope"); append_arg(slope,"slope"); offset=0.0; offset.set_description("Offset"); append_arg(offset,"offset"); } bool FilterScale::process(Data& data, Protocol& prot) const { data=slope*data+offset; return true; } odin-1.8.5/odindata/fileio_hfss.cpp0000644000175000017500000000624711322062337014170 00000000000000#include "fileio.h" #ifndef STREAM_REPLACEMENT struct HFSSFormat : public FileFormat { STD_string description() const {return "Ansoft HFSS ASCII";} svector suffix() const { svector result; result.resize(1); result[0]="reg"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("HFSSFormat","read"); STD_ifstream ifs(filename.c_str()); if(ifs.bad()) { ODINLOG(odinlog,errorLog) << "Cannot open file " << filename << STD_endl; return -1; } // Read header STD_string firstline,secondline; if(!(getline(ifs,firstline) && getline(ifs,secondline)) ) { ODINLOG(odinlog,errorLog) << "Cannot read header" << STD_endl; return -1; } ODINLOG(odinlog,normalDebug) << "firstline=" << firstline << STD_endl; ODINLOG(odinlog,normalDebug) << "secondline=" << secondline << STD_endl; svector dimstrings=tokens(firstline,':'); if(dimstrings.size()!=4) { ODINLOG(odinlog,errorLog) << "Format error in 1st line" << STD_endl; return -1; } svector minstring =tokens(extract(dimstrings[1],"[","]")); svector maxstring =tokens(extract(dimstrings[2],"[","]")); svector gridstring=tokens(extract(dimstrings[3],"[","]")); TinyVector hfss_minpos, hfss_maxpos, hfss_res, hfss_FOV; TinyVector hfss_size; float scale_factor=1000.0; // convert m to mm for(int i=0; i<3; i++) { hfss_res[2-i]=scale_factor*atof(gridstring[i].c_str()); hfss_minpos[2-i]=scale_factor*atof(minstring[i].c_str())-0.5*hfss_res[2-i]; hfss_maxpos[2-i]=scale_factor*atof(maxstring[i].c_str())+0.5*hfss_res[2-i]; hfss_FOV[2-i]=fabs(hfss_maxpos[2-i]-hfss_minpos[2-i]); hfss_size(2-i)=int( hfss_FOV[2-i]/hfss_res[2-i]+0.5); } ODINLOG(odinlog,normalDebug) << "hfss_minpos=" << hfss_minpos << STD_endl; ODINLOG(odinlog,normalDebug) << "hfss_maxpos=" << hfss_maxpos << STD_endl; ODINLOG(odinlog,normalDebug) << "hfss_res=" << hfss_res << STD_endl; ODINLOG(odinlog,normalDebug) << "hfss_FOV=" << hfss_FOV << STD_endl; ODINLOG(odinlog,normalDebug) << "hfss_size=" << hfss_size << STD_endl; // Fill Grid data.resize(1,hfss_size(0),hfss_size(1),hfss_size(2)); data=0.0; TinyVector index; index(0)=0; TinyVector pos; float val; while(ifs >> pos[2] >> pos[1] >> pos[0] >> val) { for(int i=0; i<3; i++) index(1+i)=int((scale_factor*pos[i]-hfss_minpos[i])/hfss_res[i]); data(index)=val; } // Adjust protocol prot.geometry.set_Mode(voxel_3d) .set_FOV(sliceDirection, hfss_FOV[0]) .set_FOV(phaseDirection, hfss_FOV[1]) .set_FOV(readDirection, hfss_FOV[2]) .set_offset(sliceDirection, 0.5*(hfss_minpos[0]+hfss_maxpos[0])) .set_offset(phaseDirection, 0.5*(hfss_minpos[1]+hfss_maxpos[1])) .set_offset(readDirection, 0.5*(hfss_minpos[2]+hfss_maxpos[2])); return hfss_size(0); } }; #endif ////////////////////////////////////////////////////////////// void register_hfss_format() { #ifndef STREAM_REPLACEMENT static HFSSFormat hf; hf.register_format(); #endif } odin-1.8.5/odindata/filter_reslice.cpp0000644000175000017500000001150111322062337014656 00000000000000#include "filter_reslice.h" bool swapdim(Data& data, Geometry& geo,const direction newread,const direction newphase,const direction newslice,const int newread_mult,const int newphase_mult,const int newslice_mult) { Log odinlog("","swapdim"); ODINLOG(odinlog,normalDebug) << "newread/newphase/newslice=" << newread << "/" << newphase << "/" << newslice << STD_endl; // Checking input if(newread==newphase || newread==newslice || newphase==newslice) { ODINLOG(odinlog,errorLog) << "Direction used more than once: newread/newphase/newslice=" << newread << "/" << newphase << "/" << newslice << STD_endl; return false; } const dvector vects[n_directions]={geo.get_readVector(),geo.get_phaseVector(),geo.get_sliceVector()}; double fov[n_directions]; //store i,j and k of the image coordinate system in scanner coordinate system ODINLOG(odinlog,normalDebug) << "get_readVector:" << vects[readDirection] << " => " << (vects[newread]*newread_mult).printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "get_phaseVector:" << vects[phaseDirection] << " => " << (vects[newphase]*newphase_mult).printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "get_sliceVector:" << vects[sliceDirection] << " => " << (vects[newslice]*newslice_mult).printbody() << STD_endl; //switch to 3d mode (we cannot deal with slice gaps) geo.set_Mode(voxel_3d); //get the size of the image for(direction i=readDirection;i& data, Protocol& prot)const{ direction read,phase,slice; int swap[3]; if(! (selChannel( newslice,slice,swap[0]) && selChannel( newphase,phase,swap[1]) && selChannel(newread,read,swap[2])) ) return false; return swapdim(data,prot.geometry,read,phase,slice,swap[2],swap[1],swap[0]); } bool FilterSwapdim::selChannel(STD_string name, direction &dir, int& sign){ Log odinlog("FilterSwapdim","selChannel"); sign=1; dir=readDirection; bool result=true; if(name.length()>0) { size_t minus=name.find('-'),plus=name.find('+'); if(plus!=STD_string::npos)name.erase(plus,1); else if(minus!=STD_string::npos){ name.erase(minus,1); sign=-1; } if(name[0]=='r')dir=readDirection; else if(name[0] == 'p')dir=phaseDirection; else if(name[0] == 's')dir=sliceDirection; else result=false; } else { result=false; } if(!result) ODINLOG(odinlog,errorLog) << "Error parsing direction string >" << name << "<" << STD_endl; return result; } ///////////////////////////////////////////////////////////////////////////// void FilterReSlice::init(){ orient.add_item("axial",axial); orient.add_item("sagittal",sagittal); orient.add_item("coronal",coronal); orient.set_description("requested orientation"); append_arg(orient,"orientation"); } bool FilterReSlice::process(Data& data, Protocol& prot)const{ sliceOrientation sorient=prot.geometry.get_orientation(); if(sorient==int(orient)) return true; Geometry &geo=prot.geometry; switch(int(orient)) { case axial: if(sorient == sagittal) return swapdim(data,geo,sliceDirection,readDirection,phaseDirection,1,1,1); else if(sorient == coronal) return swapdim(data,geo,readDirection,sliceDirection,phaseDirection,1,1,-1); break; case sagittal: if(sorient==axial) return swapdim(data,geo,phaseDirection,sliceDirection,readDirection,-1,-1,1); else if(sorient==coronal) return swapdim(data,geo,sliceDirection,phaseDirection,readDirection,-1,1,1); break; case coronal: if(sorient==axial) return swapdim(data,geo,readDirection,sliceDirection,phaseDirection,1,-1,1); else if(sorient==sagittal) return swapdim(data,geo,sliceDirection,phaseDirection,readDirection,-1,1,1); break; } return true; } odin-1.8.5/odindata/fileio_dicom.cpp0000644000175000017500000013030311712547771014324 00000000000000#include "fileio.h" #include "utils.h" #include #ifdef DICOMSUPPORT /////////////////////////////////////////////////////////////////////////// // Because we have 2 config.h files, one from ODIN and one from DCMTK, // Undefine doubly defined before include of DCMTK headers #undef PACKAGE_BUGREPORT #undef PACKAGE_NAME #undef PACKAGE_STRING #undef PACKAGE_TARNAME #undef PACKAGE_VERSION //#include #include #include #include #include #include #include #include #include #include #include // fix for use of possesive 's' across different versions of dcmtk #ifdef DCM_PatientsName #define DCM_PAT_NAME DCM_PatientsName #else #define DCM_PAT_NAME DCM_PatientName #endif #ifdef DCM_PatientsBirthDate #define DCM_PAT_BIRTHDATE DCM_PatientsBirthDate #else #define DCM_PAT_BIRTHDATE DCM_PatientBirthDate #endif #ifdef DCM_PatientsSex #define DCM_PAT_SEX DCM_PatientsSex #else #define DCM_PAT_SEX DCM_PatientSex #endif #ifdef DCM_PatientsWeight #define DCM_PAT_WEIGHT DCM_PatientsWeight #else #define DCM_PAT_WEIGHT DCM_PatientWeight #endif #ifdef DCM_PerformingPhysiciansName #define DCM_PERF_PHYS DCM_PerformingPhysiciansName #else #define DCM_PERF_PHYS DCM_PerformingPhysicianName #endif #ifdef DCM_ReferringPhysiciansName #define DCM_REF_PHYS DCM_ReferringPhysiciansName #else #define DCM_REF_PHYS DCM_ReferringPhysicianName #endif /////////////////////////////////////// enum dicom_field_importance{optional=0,warning,error}; bool check_status(const char* func, const char* call, const OFCondition& status, const dicom_field_importance severity=error) { Log odinlog("DicomFormat","check_status"); if(status.bad()) { logPriority loglevel=noLog; switch(severity){ case optional: loglevel=normalDebug;break; case warning: loglevel=warningLog;break; case error: loglevel=errorLog;break; } ODINLOG(odinlog,loglevel) << func << "(" << call << ")" << ": " << status.text() << STD_endl; return true; } return false; } /////////////////////////////////////// bool check_dict(const char* func) { Log odinlog("DicomFormat",func); if (!dcmDataDict.isDictionaryLoaded()) { ODINLOG(odinlog,errorLog) << "No data dictionary loaded, check environment variable " << DCM_DICT_ENVIRONMENT_VARIABLE << STD_endl; return true; } return false; } /////////////////////////////////////// bool insert_uint16_hack(DcmDataset *dataset, const DcmTagKey &key, u16bit value) { // Hack to insert uint16 numbers on pre-3.5.4 dcmtk versions, code taken from dcmtk forum // the preprocessor directive of the following line does not work with DCMTK 3.6.0 where OFFIS_DCMTK_VERSION_NUMBER is a string //#if OFFIS_DCMTK_VERSION_NUMBER > 353 dataset->putAndInsertUint16(key,value); //#else // DcmElement *us = new DcmUnsignedShort(DcmTag(key, EVR_US)); // if (us != NULL) { // if(check_status("insert_uint16_hack","putUint16",us->putUint16(value))) {return false;} // if(check_status("insert_uint16_hack","insert",dataset->insert(us, OFTrue /*replaceOld*/))) {return false;} // } else return false; //#endif return true; } template void copy(const DiPixel *pix, Data &dst,const TinyVector &shape,int mosaic_mult){ Log odinlog("DicomFormat","copy"); T* src=(T*)pix->getData(); const Range all=Range::all(); if(shape(1)>1) { // Sort Siemens Mosaic data dst.resize(shape); Data indata; TinyVector inshape(mosaic_mult,shape(2),mosaic_mult,shape(3)); convert_from_ptr(indata,src,inshape); for(int n=0; n DST endian(const BASE *b){ DST ret=0; #if __BYTE_ORDER == __LITTLE_ENDIAN for(short i=0;i<(short)sizeof(DST);i++) #elif __BYTE_ORDER == __BIG_ENDIAN for(short i=(short)sizeof(DST)-1;i>=0;i--) #else #error "Sorry your endianess is not supported. What the heck are you comiling on ??" #endif ret+=b[i]< odinlog("DicomFormat","fetch_from_MR_CSA_Header"); svector ret; Uint8 *array; csaHeader->getUint8Array(array); for(STD_string::size_type pos=0;pos<=csaHeader->getLength();){ STD_string dummy((char*)array+pos); STD_string::size_type found=dummy.find(label); if(found==STD_string::npos) { pos+=dummy.length()+1; } else { pos+=found+0x40; //len of the name is 0x20 plus 0x20 "I dont know what the hell this is supposed to be" /*Sint32 &vm=*((Sint32*)array+pos);*/pos+=sizeof(Sint32); /*char *vr=(char*)array+pos;*/pos+=0x4; /*Sint32 syngodt=endian(array+pos);*/pos+=sizeof(Sint32); Sint32 nitems=endian(array+pos);pos+=sizeof(Sint32); if(nitems) { pos+=sizeof(Sint32); //77 Sint32 len=0; for(unsigned short n=0;n(array+pos);pos+=sizeof(Sint32);//the length of this element pos+=3*sizeof(Sint32); //whatever if(!len)continue; const unsigned s=ret.size();ret.resize(s+1); ret[s]=STD_string((char*)array+pos);//store the text if the is some pos+=((len+sizeof(Sint32)-1)/sizeof(Sint32))*sizeof(Sint32);//increment pos by len aligned to sizeof(Sint32) } ODINLOG(odinlog,normalDebug) << "Found \""+label+"\" in CSA header: \"" << ret.printbody() << "\"" << STD_endl; } else { ODINLOG(odinlog,normalDebug) << "Found empty \""+label+"\" in CSA header" << STD_endl; } return ret; } } ODINLOG(odinlog,normalDebug) << "Could not find\""+label+"\" in CSA header: " << STD_endl; return ret; } ////////////////////////////////////////////////////////////// struct DicomFormat : public FileFormat { STD_string description() const {return "DICOM";} svector suffix() const { svector result; result.resize(4); result[0]="dcm"; result[1]="mag"; result[2]="ph"; result[3]="ima"; return result; } svector dialects() const { svector result; result.resize(1); result[0]="siemens"; return result; } int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("DicomFormat","read"); ODINLOG(odinlog,normalDebug) << "filename=" << filename << STD_endl; Range all=Range::all(); const char* func="DicomFormat::read"; if(check_dict(func)) return -1; if(JDXfileName(filename).get_basename()=="DICOMDIR") return 0; // ignore DICOMDIR #ifdef OFLOG_H OFLog::configure(OFLogger::WARN_LOG_LEVEL); // reset logging (in dcmtk 3.6.0 info logging is somehow enabled sometimes) #endif DcmFileFormat fileformat; DcmDataset* dset=0; if(check_status(func,"loadFile",fileformat.loadFile(filename.c_str()))) { ODINLOG(odinlog,errorLog) << "Unable to get dataset" << STD_endl; return -1; } dset=fileformat.getDataset(); if(!dset) { ODINLOG(odinlog,errorLog) << "fileformat.getDataset() failed" << STD_endl; return -1; } DcmElement* csaHeader=0; if(dset->findAndGetElement(DcmTagKey(0x0029,0x1010),csaHeader).good()) { ODINLOG(odinlog,normalDebug) << "found Siemens-specific CSA Header" << STD_endl; /* Uint8* array=0; csaHeader->getUint8Array(array); if(array) { DcmElement* csaData=0; if(dset->findAndGetElement(DcmTagKey(0x7fe1,0x1010),csaData).good()) { ODINLOG(odinlog,infoLog) << "csaData->getLength()=" << csaData->getLength() << STD_endl; STD_string csaHeaderStr((const char*)array, csaHeader->getLength()); STD_cout << csaHeaderStr << STD_endl; } } */ } DicomImage img(dset, EXS_Unknown, CIF_IgnoreModalityTransformation); // apply modality transform manually to get higher floating point accuracy EI_Status status=img.getStatus(); if(status!=EIS_Normal) { const char* errmsg="Unknown Error"; if(status==EIS_NoDataDictionary) errmsg="NoDataDictionary"; if(status==EIS_InvalidDocument) errmsg="InvalidDocument"; if(status==EIS_MissingAttribute) errmsg="MissingAttribute"; if(status==EIS_InvalidValue) errmsg="InvalidValue"; if(status==EIS_NotSupportedValue) errmsg="NotSupportedValue"; if(status==EIS_MemoryFailure) errmsg="MemoryFailure"; if(status==EIS_InvalidImage) errmsg="InvalidImage"; if(status==EIS_OtherError) errmsg="OtherError"; ODINLOG(odinlog,errorLog) << "Unable to load DICOM image " << filename << " - " << errmsg << STD_endl; return -1; } TinyVector shape; shape=1; // default shape(2)=img.getHeight(); shape(3)=img.getWidth(); ODINLOG(odinlog,normalDebug) << "shape=" << shape << STD_endl; OFString valstr; STD_string image_type; if(!check_status(func,"ImageType",dset->findAndGetOFStringArray(DCM_ImageType, valstr),warning)) image_type=valstr.c_str(); ODINLOG(odinlog,normalDebug) << "image_type=" << image_type << STD_endl; // Hack for Siemens Mosaic int mosaic_mult=1; Sint16 mosaic_slices=1; //try to find 0x0019,100a (images per mosaic) if(image_type.find("MOSAIC")!=STD_string::npos) { if(dset->findAndGetSint16(DcmTagKey(0x0019,0x100a),mosaic_slices).good()){ ODINLOG(odinlog,normalDebug) << "Found \"NumberOfImagesInMosaic\" in 0x0019,0x100a: " << mosaic_slices << STD_endl; } else { if(csaHeader) { //othwise find NumberOfImagesInMosaic in Siemens shadow Header 0x0029,0x1010 svector csa_mosaic=fetch_from_MR_CSA_Header(csaHeader,"NumberOfImagesInMosaic"); if(csa_mosaic.size()) { mosaic_slices=atoi(csa_mosaic[0].c_str()); ODINLOG(odinlog,normalDebug) << "Found \"NumberOfImagesInMosaic\" in CSADataInfo: " << mosaic_slices << STD_endl; } } } if(mosaic_slices>1) { mosaic_mult=(int)ceil(sqrt((double)mosaic_slices)); ODINLOG(odinlog,normalDebug) << "mosaic_mult=" << mosaic_mult << STD_endl; ODINLOG(odinlog,normalDebug) << "mosaic_slices=" << mosaic_slices << STD_endl; shape(3)/=mosaic_mult; shape(2)/=mosaic_mult; shape(1)=mosaic_slices; } else { ODINLOG(odinlog,warningLog) << "\"NumberOfImagesInMosaic\" not available. Mosaic won't be split up" << STD_endl; shape(1)=1; } } //Get Diffusion Data Float64 Bvalue; OFCondition foundB=dset->findAndGetFloat64(DCM_DiffusionBValue,Bvalue); //in case someone actually used the right Tag if(foundB.bad() && opts.dialect=="siemens"){//fallback for siemens OFString buff; foundB=dset->findAndGetOFString(DcmTagKey(0x0019,0x100c), buff); Bvalue=atof(buff.c_str()); } //@todo fallback for GE/Philips if(foundB.good()){//we got the b_value JDXtriple bvector(0,0,0,"Diffusion_bVector"); if(Bvalue){ const Float64 *dir;unsigned long count; OFCondition foundD=dset->findAndGetFloat64Array(DCM_DiffusionGradientOrientation,dir,&count); //in case someone actually used the right Tag if(foundD.bad() && opts.dialect=="siemens") foundD=dset->findAndGetFloat64Array( DcmTagKey(0x0019,0x100e),dir,&count);//siemens fallback if(foundD.good()) { for(unsigned long i=0;i" << filename << "<"<< STD_endl; } else ODINLOG(odinlog,warningLog) << "no diffusion direction found in >" << filename << "<"<< STD_endl; } prot.methpars.append_copy(bvector); } //detect pixel datatype and copy pixel data //@todo: Transpose data and geometry in plane according to DCM_InPlanePhaseEncodingDirection if(!img.isMonochrome()){ ODINLOG(odinlog,errorLog) << "only gray value images are supportet"<< STD_endl; return -1; } const DiPixel *pix=img.getInterData(); switch(pix->getRepresentation()){ case EPR_Uint8: copy (pix,data,shape,mosaic_mult); prot.system.set_data_type(TypeTraits::type2label((u8bit)0)); break; case EPR_Uint16: copy (pix,data,shape,mosaic_mult); prot.system.set_data_type(TypeTraits::type2label((u16bit)0)); break; case EPR_Uint32: copy (pix,data,shape,mosaic_mult); prot.system.set_data_type(TypeTraits::type2label((u32bit)0)); break; case EPR_Sint8: copy (pix,data,shape,mosaic_mult); prot.system.set_data_type(TypeTraits::type2label((s8bit)0)); break; case EPR_Sint16: copy (pix,data,shape,mosaic_mult); prot.system.set_data_type(TypeTraits::type2label((s16bit)0)); break; case EPR_Sint32: copy (pix,data,shape,mosaic_mult); prot.system.set_data_type(TypeTraits::type2label((s32bit)0)); break; default: ODINLOG(odinlog,errorLog) << "pixel representation not supportet"<< STD_endl; } #ifdef ODIN_DEBUG double min,max; img.getMinMaxValues(min,max); ODINLOG(odinlog,normalDebug) << "image range is " << min << " - " << max << STD_endl; ODINLOG(odinlog,normalDebug) << "datatype set to " << prot.system.get_data_type() << STD_endl; #endif //ODIN_DEBUG // rescale data, if necessary float intercept=0; float slope=1.0; if(!check_status(func,"RescaleIntercept",dset->findAndGetOFString(DCM_RescaleIntercept, valstr),optional)) { intercept=atof(valstr.c_str()); } if(!check_status(func,"RescaleSlope",dset->findAndGetOFString(DCM_RescaleSlope, valstr),optional)) { slope=atof(valstr.c_str()); } if(intercept!=0.0 || slope!=1.0) { ODINLOG(odinlog,normalDebug) << "rescaling data with intercept/slope=" << intercept << "/" << slope << STD_endl; data=data*slope+intercept; } STD_string unknown="Unknown"; // Date/time stuff STD_string scandate; STD_string scantime; if(!check_status(func,"SeriesDate",dset->findAndGetOFString(DCM_SeriesDate, valstr),warning)) { scandate=valstr.c_str(); } if(!check_status(func,"SeriesTime",dset->findAndGetOFString(DCM_SeriesTime, valstr),warning)) { svector toks=tokens(valstr.c_str(), '.'); if(toks.size()) scantime=toks[0]; } prot.study.set_DateTime(scandate,scantime); // Get patient stuff STD_string pname(unknown); if(!check_status(func,"PatientsName",dset->findAndGetOFString(DCM_PAT_NAME, valstr),warning)) { pname=valstr.c_str(); pname=replaceStr(pname,"^"," "); pname=valstr.c_str(); } STD_string pid(unknown); if(!check_status(func,"PatientID",dset->findAndGetOFString(DCM_PatientID, valstr),warning)) { pid=valstr.c_str(); } STD_string pdbirth(ODIN_DATE_LENGTH,'0'); if(!check_status(func,"PatientsBirthDate",dset->findAndGetOFString(DCM_PAT_BIRTHDATE, valstr),warning)) { pdbirth=valstr.c_str(); } char psex='M'; if(!check_status(func,"PatientsSex",dset->findAndGetOFString(DCM_PAT_SEX, valstr),warning)) { if(valstr.length()) psex=valstr[0]; } float pweight=50.0; if(!check_status(func,"PatientsWeight",dset->findAndGetOFString(DCM_PAT_WEIGHT, valstr),warning)) { if(valstr.length()) pweight=atof(valstr.c_str()); } prot.study.set_Patient(pid, pname, pdbirth, psex, pweight); // Get study stuff STD_string studydescr(unknown); if(!check_status(func,"StudyDescription",dset->findAndGetOFString(DCM_StudyDescription, valstr),warning)) { studydescr=valstr.c_str(); } STD_string physician(unknown); if(!check_status(func,"PerformingPhysiciansName",dset->findAndGetOFString(DCM_PERF_PHYS, valstr),optional)) { physician=valstr.c_str(); } prot.study.set_Context(studydescr,physician); // Get series stuff STD_string seriesdescr(unknown); if(!check_status(func,"SeriesDescription",dset->findAndGetOFString(DCM_SeriesDescription, valstr),warning)) { seriesdescr=valstr.c_str(); } int seriesno=1; if(!check_status(func,"SeriesNumber",dset->findAndGetOFString(DCM_SeriesNumber, valstr),warning)) { seriesno=atoi(valstr.c_str()); } if(opts.dialect=="siemens") { // Quick hack to produce different datasets for different channels on Siemens if(dset->findAndGetOFString(DcmTagKey (0x0051, 0x100f), valstr).good()) { seriesdescr+="_"+STD_string(valstr.c_str()); } } prot.study.set_Series(seriesdescr,seriesno); // get Pixel Spacing and FOV float FOVread=200.0,psize_read; if(!check_status(func,"PixelSpacing(read)",dset->findAndGetOFString(DCM_PixelSpacing, valstr, 0), warning)) { psize_read=atof(valstr.c_str()); FOVread=psize_read*shape(3); prot.geometry.set_FOV(readDirection, FOVread); }else psize_read=FOVread/shape(3); float FOVphase=200.0,psize_phase; if(!check_status(func,"PixelSpacing(phase)",dset->findAndGetOFString(DCM_PixelSpacing, valstr, 1), warning)) { psize_phase=atof(valstr.c_str()); FOVphase=psize_phase*shape(2); prot.geometry.set_FOV(phaseDirection, FOVphase); }else psize_phase=FOVphase/shape(2); // Get the slice orientation, i.e. the vectors of read and phase direction dvector readvec(3); readvec[0]=1.0; dvector phasevec(3); phasevec[1]=1.0; dvector slicevec(3); slicevec[2]=1.0; // The following does not work with dcmtk since we can only access the first 3 elements of ImageOrientationPatient dvector offset(3); offset = -0.5*(FOVread-psize_read)*readvec - 0.5*(FOVphase-psize_phase)*phasevec; for(int i=0; i<3; i++) { if(!check_status(func,("ImageOrientationPatient("+itos(i)+")").c_str(),dset->findAndGetOFString(DCM_ImageOrientationPatient, valstr,i))) { readvec[i]=atof(valstr.c_str()); } // Does not work in dcmtk if(!check_status(func,("ImageOrientationPatient("+itos(3+i)+")").c_str(),dset->findAndGetOFString(DCM_ImageOrientationPatient, valstr,3+i))) { phasevec[i]=atof(valstr.c_str()); } if(!check_status(func,("ImagePositionPatient("+itos(i)+")").c_str(),dset->findAndGetOFString(DCM_ImagePositionPatient, valstr,i))) { offset[i]=atof(valstr.c_str()); } } //remove the additional mosaic offset //eg. if there is a 10x10 Mosaic, substract the half size of 9 Images from the offset for(int i=0;i<3;i++) { offset[i]+=(mosaic_mult-1)*FOVread*.5*readvec[i] + (mosaic_mult-1)*FOVphase*.5*phasevec[i]; } //Following DICOM standard ImagePositionPatient is the _middle_ of the first vector so we would //use (FOV-voxelsize)/2 to get the center. dvector center_offset= offset + 0.5*(FOVread-psize_read)*readvec + 0.5*(FOVphase-psize_phase)*phasevec; //But siemens seems to store the outer edge of the first voxel. So... if(opts.dialect=="siemens") center_offset= offset + 0.5*FOVread*readvec + 0.5*FOVphase*phasevec; dvector transform(3); transform[0]=-1.0; transform[1]=-1.0; transform[2]=1.0; // default: x- and y-axis are inverted when converting from DICOM coord system to ODIN coord system (as defined in geometry.h) if(!check_status(func,"PatientPosition",dset->findAndGetOFString(DCM_PatientPosition, valstr),optional)) { bool known_position=false; if(valstr=="HFP") { transform[0]=-transform[0]; transform[1]=-transform[1]; known_position=true; } if(valstr=="HFS") { // use default known_position=true; } if(!known_position) { ODINLOG(odinlog,normalDebug) << "Unknown PatientPosition=" << valstr << STD_endl; } } readvec*=transform; phasevec*=transform; center_offset*=transform; slicevec=Data(vector_product(Data(readvec), Data(phasevec))); // has correct handness for ODIN ODINLOG(odinlog,normalDebug) << "psize_read/phase=" << psize_read << "/" << psize_phase << STD_endl; ODINLOG(odinlog,normalDebug) << "offset=" << offset.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "center_offset=" << center_offset.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "readvec=" << readvec.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "phasevec=" << phasevec.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "slicevec=" << slicevec.printbody() << STD_endl; prot.geometry.set_orientation_and_offset(readvec, phasevec, slicevec, center_offset); if(!check_status(func,"SliceThickness",dset->findAndGetOFString(DCM_SliceThickness, valstr),warning)) { prot.geometry.set_sliceThickness(atof(valstr.c_str())); } float space=0; if(!check_status(func,"SpacingBetweenSlices",dset->findAndGetOFString(DCM_SpacingBetweenSlices, valstr),optional)) { space+=atof(valstr.c_str()); prot.geometry.set_sliceDistance(space); } // Calculate slice offset, do not use DCM_SliceLocation since it is based on variable handness // also take in account, that for mosaic the slice position is given for the first image of the mosaic float sliceproj=(slicevec*center_offset).sum(); prot.geometry.set_offset(sliceDirection,sliceproj+(mosaic_slices-1)*space/2); STD_string modality("MR"); if(!check_status(func,"Modality",dset->findAndGetOFString(DCM_Modality, valstr),warning)) { modality=valstr.c_str(); } if(modality=="MR") { // avoid useles error messages with non-MR modalities // Get system stuff if(!check_status(func,"ImagingFrequency",dset->findAndGetOFString(DCM_ImagingFrequency, valstr),warning)) { prot.system.set_B0_from_freq(1000.0*atof(valstr.c_str())); } if(!check_status(func,"TransmitCoilName",dset->findAndGetOFString(DCM_TransmitCoilName, valstr),warning)) { prot.system.set_transmit_coil_name(valstr.c_str()); } // Sequence stuff if(!check_status(func,"PixelBandwidth",dset->findAndGetOFString(DCM_PixelBandwidth, valstr),warning)) { prot.seqpars.set_AcqSweepWidth(0.001*atof(valstr.c_str())*shape(3)); } if(!check_status(func,"RepetitionTime",dset->findAndGetOFString(DCM_RepetitionTime, valstr),warning)) { prot.seqpars.set_RepetitionTime(atof(valstr.c_str())); } if(!check_status(func,"EchoTime",dset->findAndGetOFString(DCM_EchoTime, valstr),warning)) { prot.seqpars.set_EchoTime(atof(valstr.c_str())); } if(!check_status(func,"FlipAngle",dset->findAndGetOFString(DCM_FlipAngle, valstr),warning)) { prot.seqpars.set_FlipAngle(atof(valstr.c_str())); } prot.seqpars.set_PhysioTrigger(dset->findAndGetOFString(DCM_TriggerTime, valstr).good()); // presence of TriggerTime indicates gating, at least on Siemens if(!check_status(func,"SequenceName",dset->findAndGetOFString(DCM_SequenceName, valstr),warning)) { STD_string seqname(valstr.c_str()); // Add sequence variant/options STD_string seqopts; if(!check_status(func,"ScanningSequence",dset->findAndGetOFString(DCM_ScanningSequence, valstr),warning)) { seqopts+=valstr.c_str(); } if(!check_status(func,"SequenceVariant",dset->findAndGetOFStringArray(DCM_SequenceVariant, valstr),warning)) { if(seqopts!="" && valstr!="") seqopts+="_"; seqopts+=replaceStr(valstr.c_str(),"\\","_"); } if(!check_status(func,"ScanOptions",dset->findAndGetOFStringArray(DCM_ScanOptions, valstr),warning)) { if(seqopts!="" && valstr!="") seqopts+="_"; seqopts+=replaceStr(valstr.c_str(),"\\","_"); } if(seqopts!="") seqname+="_"+seqopts; prot.seqpars.set_Sequence(seqname); } } // Timestamp temporal sorting of multi-file DICOMs prot.seqpars.set_AcquisitionStart(-1.0); // inidicates no useful value if(dset->findAndGetOFString(DCM_FrameReferenceTime, valstr).good()){ // for dynamic PET data prot.seqpars.set_AcquisitionStart(atof(valstr.c_str())); } else { if(dset->findAndGetOFString(DCM_InstanceNumber, valstr).good()) { prot.seqpars.set_AcquisitionStart(atof(valstr.c_str())); } else { if(dset->findAndGetOFString(DCM_AcquisitionTime, valstr).good()){// Try timestamp field first //@todo backward compatibility missing (http://idlastro.gsfc.nasa.gov/idl_html_help/Value_Representations.html#TM) int hh=atoi(valstr.substr(0,2).c_str()); int mm=atoi(valstr.substr(2,2).c_str()); double ss=atof(valstr.substr(4,7).c_str()); ODINLOG(odinlog,normalDebug) << "hh/mm/ss=" << hh << "/" << mm << "/" << ss << STD_endl; prot.seqpars.set_AcquisitionStart( 1000.0*(ss + 60*mm + 3600*hh) ); } } } return shape(0)*shape(1); } /////////////////////////////////////////////////////// int write(const FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts) { Log odinlog("DicomFormat","write"); Range all=Range::all(); STD_string delimiter("\\"); const char* func="DicomFormat::write"; if(check_dict(func)) return -1; JDXfileName fname(filename); #ifdef OFLOG_H OFLog::configure(OFLogger::WARN_LOG_LEVEL); // reset logging (in dcmtk 3.6.0 info logging is somehow enabled sometimes) #endif // Create directory to store DICOMS DicomDirInterface dicomdir; JDXfileName dstdir; dstdir.set_dir(true); dstdir=fname.get_dirname()+SEPARATOR_STR+fname.get_basename_nosuffix()+STD_string("_dcm"); if( createdir(dstdir.c_str()) && (!checkdir(dstdir.c_str())) ) { ODINLOG(odinlog,errorLog) << "Cannot create directoy " << dstdir << STD_endl; return -1; } STD_string dcmdirfname=dstdir+SEPARATOR_STR+"DICOMDIR"; if(check_status(func,"createNewDicomDir",dicomdir.createNewDicomDir(DicomDirInterface::AP_GeneralPurpose,dcmdirfname.c_str()))) return -1; // Iterate over protocol-data pairs unsigned int index=0; for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) { Protocol prot(pdit->first); // writable copy to adjust FOV const Data& data=pdit->second; DcmFileFormat fileformat; // The meta-info stuff not provided by dcmtk DcmMetaInfo* metainfo=fileformat.getMetaInfo(); if(check_status(func,"MediaStorageSOPClassUID", metainfo->putAndInsertString(DCM_MediaStorageSOPClassUID,UID_MRImageStorage))) return -1; // The dataset stuff DcmDataset *dataset=fileformat.getDataset(); // The static UIDs char uid[100]; if(check_status(func,"SOPClassUID", dataset->putAndInsertString(DCM_SOPClassUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT)))) return -1; if(check_status(func,"FrameOfReferenceUID", dataset->putAndInsertString(DCM_FrameOfReferenceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT)))) return -1; if(check_status(func,"SeriesInstanceUID", dataset->putAndInsertString(DCM_SeriesInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT)))) return -1; // Common stuff if(check_status(func,"ImageType", dataset->putAndInsertString(DCM_ImageType,("ORIGINAL"+delimiter+"PRIMARY"+delimiter+"OTHER").c_str()))) return -1; if(check_status(func,"SpecificCharacterSet", dataset->putAndInsertString(DCM_SpecificCharacterSet,"ISO_IR 100"))) return -1; if(check_status(func,"SOPClassUID", dataset->putAndInsertString(DCM_SOPClassUID,UID_MRImageStorage))) return -1; // Pixel data stuff if(check_status(func,"SamplesPerPixel", dataset->putAndInsertUint16(DCM_SamplesPerPixel, 1))) return -1; if(check_status(func,"PhotometricInterpretation",dataset->putAndInsertString(DCM_PhotometricInterpretation, "MONOCHROME2"))) return -1; if(check_status(func,"BitsAllocated", dataset->putAndInsertString(DCM_BitsAllocated, "16"))) return -1; if(check_status(func,"BitsStored", dataset->putAndInsertString(DCM_BitsStored, "16"))) return -1; if(check_status(func,"HighBit", dataset->putAndInsertString(DCM_HighBit, "15"))) return -1; if(check_status(func,"PixelRepresentation", dataset->putAndInsertString(DCM_PixelRepresentation, "0"))) return -1; // Sequence type stuff if(check_status(func,"ScanningSequence", dataset->putAndInsertString(DCM_ScanningSequence, "RM"))) return -1; // research mode if(check_status(func,"SequenceVariant", dataset->putAndInsertString(DCM_SequenceVariant, "NONE"))) return -1; if(check_status(func,"ScanOptions", dataset->putAndInsertString(DCM_ScanOptions, ""))) return -1; // bogus value if(check_status(func,"MRAcquisitionType", dataset->putAndInsertString(DCM_MRAcquisitionType, "2D"))) return -1; if(check_status(func,"EchoTrainLength", dataset->putAndInsertString(DCM_EchoTrainLength, "1"))) return -1; // bogus value // date/time of scan, will be used for all DICOM timestamps STD_string scandate; STD_string scantime; prot.study.get_DateTime(scandate,scantime); // Patient stuff STD_string pname; STD_string pid; STD_string pdbirth; char psex; float pweight; prot.study.get_Patient(pid, pname, pdbirth, psex, pweight); pdbirth[ODIN_DATE_LENGTH]='\0'; pname=replaceStr(pname," ","^"); if(pid=="") pid="Zero"; // dicomdir.addDicomFile does not like zero-size string if(check_status(func,"PatientsName", dataset->putAndInsertString(DCM_PAT_NAME, pname.c_str()))) return -1; if(check_status(func,"PatientID", dataset->putAndInsertString(DCM_PatientID, pid.c_str()))) return -1; if(check_status(func,"PatientsBirthDate", dataset->putAndInsertString(DCM_PAT_BIRTHDATE, pdbirth.c_str()))) return -1; if(check_status(func,"PatientsSex", dataset->putAndInsertString(DCM_PAT_SEX, STD_string(1,psex).c_str()))) return -1; if(check_status(func,"PatientsWeight", dataset->putAndInsertString(DCM_PAT_WEIGHT, ftos(pweight).c_str()))) return -1; // Study stuff STD_string studydescr; STD_string physician; prot.study.get_Context(studydescr, physician); studydescr=replaceStr(studydescr," ","^"); physician=replaceStr(physician," ","^"); STD_string studyid(studydescr); if(studyid=="") studyid="0"; // Mangle date, PatientID and study description into unique Study UID STD_string studyinstanceuid; studyinstanceuid+=scandate; for(unsigned int i=0; i64) studyinstanceuid=studyinstanceuid.substr(0,64); if(check_status(func,"StudyInstanceUID", dataset->putAndInsertString(DCM_StudyInstanceUID, studyinstanceuid.c_str()))) return -1; if(check_status(func,"StudyDate", dataset->putAndInsertString(DCM_StudyDate, scandate.c_str()))) return -1; if(check_status(func,"StudyTime", dataset->putAndInsertString(DCM_StudyTime, scantime.c_str()))) return -1; if(check_status(func,"PerformingPhysiciansName", dataset->putAndInsertString(DCM_PERF_PHYS, physician.c_str()))) return -1; if(check_status(func,"ReferringPhysiciansName", dataset->putAndInsertString(DCM_REF_PHYS, physician.c_str()))) return -1; if(check_status(func,"StudyID", dataset->putAndInsertString(DCM_StudyID, studyid.c_str()))) return -1; if(check_status(func,"StudyDescription", dataset->putAndInsertString(DCM_StudyDescription, studydescr.c_str()))) return -1; if(check_status(func,"AccessionNumber", dataset->putAndInsertString(DCM_AccessionNumber, ""))) return -1; // Series stuff STD_string seriesdescr; int seriesno; prot.study.get_Series(seriesdescr, seriesno); seriesdescr=replaceStr(seriesdescr," ","^"); if(seriesno<=0) seriesno=1; if(check_status(func,"Modality", dataset->putAndInsertString(DCM_Modality, "MR"))) return -1; if(check_status(func,"SeriesDescription",dataset->putAndInsertString(DCM_SeriesDescription, seriesdescr.c_str()))) return -1; // must have value for DICOMDIR if(check_status(func,"ProtocolName",dataset->putAndInsertString(DCM_ProtocolName, seriesdescr.c_str()))) return -1; if(check_status(func,"SeriesNumber",dataset->putAndInsertString(DCM_SeriesNumber, itos(seriesno).c_str()))) return -1; // must have value for DICOMDIR if(check_status(func,"SeriesDate", dataset->putAndInsertString(DCM_SeriesDate, scandate.c_str()))) return -1; if(check_status(func,"SeriesTime", dataset->putAndInsertString(DCM_SeriesTime, scantime.c_str()))) return -1; // Other date/time stuff if(check_status(func,"AcquisitionDate", dataset->putAndInsertString(DCM_AcquisitionDate, scandate.c_str()))) return -1; if(check_status(func,"ContentDate", dataset->putAndInsertString(DCM_ContentDate, scandate.c_str()))) return -1; if(check_status(func,"ContentTime", dataset->putAndInsertString(DCM_ContentTime, scantime.c_str()))) return -1; // Frame of Reference stuff if(check_status(func,"PositionReferenceIndicator",dataset->putAndInsertString(DCM_PositionReferenceIndicator, ""))) return -1; int xsize=data.extent(3); int ysize=data.extent(2); if(opts.dialect=="siemens") { // Siemens screws up with some non-quadratic image sizes, so we will use next-power-of-2-sized quadratic images int quadsize = 1 << (int)(ceil( log(double(STD_max(data.extent(2),data.extent(3))))/ log(2.0))); ODINLOG(odinlog,normalDebug) << "Fixing matrix size for siemens: " << xsize << "x" << ysize << " -> " << quadsize << "x" << quadsize << STD_endl; xsize=ysize=quadsize; } int xoffset=(xsize-data.extent(3))/2; int yoffset=(ysize-data.extent(2))/2; ODINLOG(odinlog,normalDebug) << "xsize/ysize/xoffset/yoffset=" << xsize << "/" << ysize << "/" << xoffset << "/" << yoffset << STD_endl; // adjust FOV in protocol to new matrix size float FOVread= secureDivision(xsize,data.extent(3))*prot.geometry.get_FOV(readDirection); float FOVphase=secureDivision(ysize,data.extent(2))*prot.geometry.get_FOV(phaseDirection); prot.geometry.set_FOV(readDirection, FOVread); prot.geometry.set_FOV(phaseDirection, FOVphase); // Matrix size if(check_status(func,"Rows", dataset->putAndInsertUint16(DCM_Rows, ysize))) return -1; if(check_status(func,"Columns",dataset->putAndInsertUint16(DCM_Columns, xsize))) return -1; // seqpars stuff if(check_status(func,"RepetitionTime", dataset->putAndInsertString(DCM_RepetitionTime, ftos(prot.seqpars.get_RepetitionTime()).c_str()))) return -1; if(check_status(func,"TemporalResolution",dataset->putAndInsertString(DCM_TemporalResolution, ftos(prot.seqpars.get_RepetitionTime()).c_str()))) return -1; if(check_status(func,"EchoTime", dataset->putAndInsertString(DCM_EchoTime, ftos(prot.seqpars.get_EchoTime()).c_str()))) return -1; // if(check_status(func,"NumberOfAverages",dataset->putAndInsertString(DCM_NumberOfAverages, itos(prot.seqpars.get_NumOfRepetitions()).c_str()))) return -1; float pixelbw=secureDivision(1000.0*prot.seqpars.get_AcqSweepWidth(),prot.seqpars.get_MatrixSize(readDirection)); if(check_status(func,"PixelBandwidth", dataset->putAndInsertString(DCM_PixelBandwidth, ftos(pixelbw).c_str()))) return -1; if(check_status(func,"FlipAngle", dataset->putAndInsertString(DCM_FlipAngle, ftos(prot.seqpars.get_FlipAngle()).c_str()))) return -1; if(check_status(func,"SequenceName", dataset->putAndInsertString(DCM_SequenceName, prot.seqpars.get_Sequence().c_str()))) return -1; // system stuff if(check_status(func,"TransmitCoilName", dataset->putAndInsertString(DCM_TransmitCoilName, prot.system.get_transmit_coil_name().c_str()))) return -1; if(check_status(func,"ImagedNucleus", dataset->putAndInsertString(DCM_ImagedNucleus, prot.system.get_main_nucleus().c_str()))) return -1; if(check_status(func,"MagneticFieldStrength",dataset->putAndInsertString(DCM_MagneticFieldStrength, ftos(0.001*prot.system.get_B0()).c_str()))) return -1; if(check_status(func,"ImagingFrequency", dataset->putAndInsertString(DCM_ImagingFrequency, ftos(0.001*prot.system.get_nuc_freq()).c_str()))) return -1; STD_string swstring=STD_string(PACKAGE)+"-"+VERSION; if(check_status(func,"SoftwareVersions", dataset->putAndInsertString(DCM_SoftwareVersions, swstring.c_str()))) return -1; // Manufacturer stuff if(check_status(func,"Manufacturer",dataset->putAndInsertString(DCM_Manufacturer, prot.system.get_platform_str().c_str()))) return -1; STD_string fieldstr=ftos(0.001*prot.system.get_B0(),1)+" Tesla"; // Use field strength to label station if(check_status(func,"StationName",dataset->putAndInsertString(DCM_StationName, fieldstr.c_str()))) return -1; // geometry stuff float xspacing=secureDivision(FOVread, xsize); float yspacing=secureDivision(FOVphase, ysize); STD_string pixstr=ftos(xspacing)+delimiter+ftos(yspacing); if(check_status(func,"PixelSpacing",dataset->putAndInsertString(DCM_PixelSpacing, pixstr.c_str()))) return -1; if(check_status(func,"NumberOfSlices",dataset->putAndInsertString(DCM_NumberOfSlices, itos(prot.geometry.get_nSlices()).c_str()))) return -1; if(check_status(func,"SliceThickness",dataset->putAndInsertString(DCM_SliceThickness, ftos(prot.geometry.get_sliceThickness()).c_str()))) return -1; if(check_status(func,"SpacingBetweenSlices",dataset->putAndInsertString(DCM_SpacingBetweenSlices, ftos(prot.geometry.get_sliceDistance()).c_str()))) return -1; // DTI JcampDxClass* bptr=prot.get_parameter("Diffusion_bVector"); if(bptr) { JDXtriple* bvec=0; bvec=bptr->cast(bvec); if(bvec) { fvector fbvec(*bvec); float bval=norm3(fbvec[0],fbvec[1],fbvec[2]); ODINLOG(odinlog,normalDebug) << "bval=" << bval << STD_endl; if(check_status(func,"DiffusionBValue",dataset->putAndInsertString(DCM_DiffusionBValue, ftos(bval).c_str()))) return -1; if(bval) fbvec/=bval; STD_string borient=ftos(fbvec[0])+delimiter+ftos(fbvec[1])+delimiter+ftos(fbvec[2]); if(check_status(func,"DiffusionGradientOrientation", dataset->putAndInsertString(DCM_DiffusionGradientOrientation, borient.c_str()))) return -1; } } // for SliceLocation dvector slice_offset=prot.geometry.get_sliceOffsetVector(); // Image orientation // Note: x- and y-axis are inverted when converting from ODIN coord system (as defined in geometry.h) to DICOM coord system int digits=12; // Need high accuracy, otherwise DICOMs won't import on Siemens... dvector linvec=prot.geometry.get_readVector(); dvector colvec=prot.geometry.get_phaseVector(); STD_string patort=ftos(-linvec[0],digits)+delimiter+ ftos(-linvec[1],digits)+delimiter+ ftos( linvec[2],digits)+delimiter+ ftos(-colvec[0],digits)+delimiter+ ftos(-colvec[1],digits)+delimiter+ ftos( colvec[2],digits); if(check_status(func,"ImageOrientationPatient", dataset->putAndInsertString(DCM_ImageOrientationPatient, patort.c_str()))) return -1; // fixed position in odin: head first supine if(check_status(func,"PatientPosition", dataset->putAndInsertString(DCM_PatientPosition, "HFS"))) return -1; // use get_cornerPoints() for ImagePositionPatient // account for DICOM's convention that the position is center of the 1st voxel: prot.geometry.set_FOV(readDirection, FOVread - xspacing); prot.geometry.set_FOV(phaseDirection, FOVphase - yspacing); darray cornerpoints=prot.geometry.get_cornerPoints(Geometry(),0); ODINLOG(odinlog,normalDebug) << "cornerpoints" << STD_string(cornerpoints.get_extent()) << "=" << cornerpoints.printbody() << STD_endl; Data u16bitdata; const STD_string type(prot.system.get_data_type()); if(type!="float" && type!="double")data.convert_to(u16bitdata,noupscale); else data.convert_to(u16bitdata); if(opts.dialect=="siemens") { // clip data for viewer on host u16bit thresh=std::numeric_limits::max()-10; Array u16bitdata_copy(u16bitdata); u16bitdata_copy=where(u16bitdata_copy>thresh, thresh, u16bitdata_copy); u16bitdata=u16bitdata_copy; } u16bit minval=min(u16bitdata); u16bit maxval=max(u16bitdata); Data oneslice_padded(ysize,xsize); for(int iframe=0; iframeputAndInsertString(DCM_SOPInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT)))) return -1; if(check_status(func,"InstanceNumber",dataset->putAndInsertString(DCM_InstanceNumber, itos(index+1).c_str()))) return -1; // timestamp double timestamp_s=double(iframe)*0.001*prot.seqpars.get_RepetitionTime(); int hours=int(timestamp_s)/3600; timestamp_s-=hours*3600; int minutes=int(timestamp_s)/60; timestamp_s-=minutes*60; int seconds=int(timestamp_s); timestamp_s-=seconds; int fract=int(timestamp_s*1.0e6); char timestr[100]; snprintf(timestr, 100, "%02i%02i%02i.%06i", hours, minutes, seconds, fract); if(check_status(func,"AcquisitionTime",dataset->putAndInsertString(DCM_AcquisitionTime, timestr))) return -1; // Set slice location of this image // Note: x- and y-axis are inverted when converting from ODIN coord system (as defined in geometry.h) to DICOM coord system STD_string patpos=ftos(-cornerpoints(iplane,0,0,0,0))+delimiter+ftos(-cornerpoints(iplane,0,0,0,1))+delimiter+ftos(cornerpoints(iplane,0,0,0,2)); ODINLOG(odinlog,normalDebug) << "patpos(" << iframe << "," << iplane << ")=" << patpos << STD_endl; if(check_status(func,"ImagePositionPatient", dataset->putAndInsertString(DCM_ImagePositionPatient, patpos.c_str()))) return -1; if(check_status(func,"SliceLocation",dataset->putAndInsertString(DCM_SliceLocation, ftos(slice_offset[iplane]).c_str()))) return -1; oneslice_padded=0; oneslice_padded(Range(yoffset,yoffset+data.extent(2)-1), Range(xoffset,xoffset+data.extent(3)-1))=u16bitdata(iframe,iplane,all,all); if(!insert_uint16_hack(dataset, DCM_SmallestImagePixelValue, minval)) return -1; if(!insert_uint16_hack(dataset, DCM_LargestImagePixelValue, maxval)) return -1; if(check_status(func,"PixelData",dataset->putAndInsertUint16Array(DCM_PixelData, oneslice_padded.c_array(), oneslice_padded.numElements()))) return -1; STD_string basename(itos(index,10000000)); // Filenames with eight digits STD_string singlefname=dstdir+SEPARATOR_STR+basename; // only upper-case letters, no dot, max 8 chars allowed here if(check_status(func,"saveFile",fileformat.saveFile(singlefname.c_str(), EXS_LittleEndianExplicit))) return -1; // file must be stored before adding to DCOMDIR if(check_status( func, (STD_string("addDicomFile \"")+dstdir+"/"+basename+"\"").c_str(), dicomdir.addDicomFile(basename.c_str(),dstdir.c_str()) )) return -1; index++; } } } // End iterating over protocol-data pairs if(check_status(func,"writeDicomDir",dicomdir.writeDicomDir())) return -1; return index; } }; #endif void register_dicom_format() { #ifdef DICOMSUPPORT static DicomFormat df; df.register_format(); #endif } odin-1.8.5/odindata/filter_range.cpp0000644000175000017500000000207111713467630014337 00000000000000#include "filter_range.h" bool str2range(const STD_string& str, Range& range, int srcsize) { Log odinlog("","str2range"); if(str=="") return false; int increment=1; svector tokscol=tokens(str,':'); int colsize=tokscol.size(); if(colsize<1 || colsize>2) return false; if(colsize==2) increment=atoi(tokscol[1].c_str()); svector toks=tokens(tokscol[0],'-'); bool result=false; if(toks.size()==2) {range=Range(atoi(toks[0].c_str()),atoi(toks[1].c_str()),increment); result=true;} if(toks.size()==1) {range=Range(atoi(toks[0].c_str()),atoi(toks[0].c_str()),increment); result=true;} if(!result) { ODINLOG(odinlog,errorLog) << "Error parsing range string >" << str << "<" << STD_endl; } if(result) { if(range.first()>range.last()) result=false; if(range.first()<0 || range.first()>=srcsize) result=false; if(range.last()<0 || range.last()>=srcsize) result=false; if(!result) { ODINLOG(odinlog,errorLog) << "selected " << range << " out of valid range (0," << (srcsize-1) << ")" << STD_endl; } } return result; } odin-1.8.5/odindata/fileio_mat.cpp0000644000175000017500000002404011322062337013775 00000000000000#include "fileio.h" #ifdef MATLABSUPPORT #include #include #include #include #include #include "complexdata.h" ////////////////////////////////////////////////////////////// typedef std::pair > PDpair; class LibMatSingleton{ public: bool initialized; LibMatSingleton(){ Log odinlog("LibMatSingleton","LibMatSingleton"); /* Initialize Matlab */ const char *oplist[]={"-nojvm"}; if (!mclInitializeApplication((const char **)oplist,1)){ ODINLOG(odinlog,errorLog) << "Could not initialize MATLAB interface" << STD_endl; initialized=false; } else { ODINLOG(odinlog,infoLog) << "MATLAB interface initialized " << STD_endl; initialized=true; } } ~LibMatSingleton(){ Log odinlog("LibMatSingleton","~LibMatSingleton"); ODINLOG(odinlog,infoLog) << "Shuting down MATLAB interface" << STD_endl; mclTerminateApplication(); } }; struct MatlabBinFormat : public FileFormat { MATFile *fp; mxArray *root; FileWriteOpts w_opts; static bool initialized; MatlabBinFormat():fp(0){} STD_string description() const {return "binary data for Matlab";} svector suffix() const { svector result; result.resize(1); result[0]="mat"; return result; } svector dialects() const {return svector();} bool init() { static LibMatSingleton single; return single.initialized; } template mxArray *dat2array(Data dat,mxClassID classID) { Log odinlog("MatlabBinFormat","dat2array"); mxArray *ret; const TinyVector shape(dat.shape()); unsigned short dims; if(shape(0)>1) dims=4; else if(shape(1)>1) dims=3; else if(shape(2)>1) dims=2; else dims=1; mwSize size[dims]; for(int i=0;i odinlog("MatlabBinFormat","createMetaDataArray"); mxArray *ret; const mwSize dims[]={ydim,xdim}; if(!(ret=mxCreateNumericArray(2,dims,mxDOUBLE_CLASS,mxREAL))) { ODINLOG(odinlog,errorLog) << "could not create " << xdim << "x" << ydim << " array for Metadata" << STD_endl; return NULL; } else return ret; } bool saveVar(const mxArray *arr,STD_string name){ Log odinlog("MatlabBinFormat","saveVar"); if(matPutVariable(fp,name.c_str(),arr)!=0){ ODINLOG(odinlog,errorLog) << "could not add " << name << STD_endl; return false; } return true; } mxArray* vector2Array(const dvector vect){ const mwSize dim=vect.size(); mxArray *arr=createMetaDataArray(dim); if(!arr)return NULL; double* ptr=(double*)mxGetData(arr); for(unsigned short i=0;i odinlog("MatlabBinFormat","triple2Array"); mxArray *arr=createMetaDataArray(3); if(!arr){ ODINLOG(odinlog,errorLog) << "array creation failed" << STD_endl; return NULL; } double* ptr=(double*)mxGetData(arr); for(unsigned short i=0;i<3;i++) ptr[i]=triple[i]; return arr; } mxArray* rotMatrix2Array(const RotMatrix rot){ Log odinlog("MatlabBinFormat","rotMatrix2Array"); mxArray *arr=createMetaDataArray(3,3); if(!arr){ ODINLOG(odinlog,errorLog) << "array creation failed" << STD_endl; return NULL; } double* ptr=(double*)mxGetData(arr); for(unsigned short i=0;i<3*3;i++) ptr[i]=rot[i%3][i/3]; return arr; } mxArray *dat2mat(const PDpair &pdpair, const FileWriteOpts& opts){ Log odinlog("MatlabBinFormat","dat2mat"); const Protocol &prot=pdpair.first; const Data &dat=pdpair.second; mxArray *matArray=NULL; STD_string type=selectDataType(prot,opts); if(type=="s8bit") matArray=dat2array (dat,mxINT8_CLASS); else if(type=="u8bit") matArray=dat2array (dat,mxUINT8_CLASS); else if(type=="s16bit") matArray=dat2array(dat,mxINT16_CLASS); else if(type=="u16bit") matArray=dat2array(dat,mxUINT16_CLASS); else if(type=="s32bit") matArray=dat2array(dat,mxINT32_CLASS); else if(type=="u32bit") matArray=dat2array(dat,mxUINT32_CLASS); else if(type=="float") matArray=dat2array (dat,mxSINGLE_CLASS); else if(type=="double") matArray=dat2array(dat,mxDOUBLE_CLASS); else ODINLOG(odinlog,errorLog) << "datatype >" << type << "< unknown/unhandled" << STD_endl; return matArray; } template void array2dat(mxArray *matArray,Protocol &prot,Data &dat) { prot.system.set_data_type(TypeTraits::type2label(T())); //copy/convert data, scale only down and only when converted to integers convert_from_ptr(dat,(T*)mxGetData(matArray),dat.shape()); } const unsigned int mat2dat(Protocol &prot,Data &dat){ Log odinlog("MatlabBinFormat","mat2dat"); const char *name; mxArray *matArray= matGetNextVariable(fp, &name); if(!matArray)return 0; prot.seqpars.set_description(name); size_t dims=mxGetNumberOfDimensions(matArray); const mwSize *dim=mxGetDimensions(matArray); if(dims>2) { prot.seqpars.set_NumOfRepetitions(dim[2]); prot.geometry.set_nSlices(dim[2]); } if(dims>1) prot.seqpars.set_MatrixSize(phaseDirection,dim[1]); if(dims >0) prot.seqpars.set_MatrixSize(readDirection,dim[0]); switch(dims) { case 4:dat.resize(dim[3], dim[2], dim[1], dim[0]);break; case 3:dat.resize(dim[2], dim[1], dim[0], 1);break; case 2:dat.resize(dim[1], dim[0], 1, 1);break; case 1:dat.resize(dim[0], 1, 1, 1);break; default:ODINLOG(odinlog,errorLog) << dims << " Dimensions not (yet) supportted" << STD_endl; } switch(mxGetClassID(matArray)) { case mxINT8_CLASS: array2dat (matArray, prot, dat);break; case mxUINT8_CLASS: array2dat (matArray, prot, dat);break; case mxINT16_CLASS: array2dat (matArray, prot, dat);break; case mxUINT16_CLASS:array2dat (matArray, prot, dat);break; case mxINT32_CLASS: array2dat (matArray, prot, dat);break; case mxUINT32_CLASS:array2dat (matArray, prot, dat);break; /* case mxINT64_CLASS: array2dat (matArray, prot, dat);break; case mxUINT64_CLASS:array2dat (matArray, prot, dat);break;*/ case mxSINGLE_CLASS:array2dat (matArray, prot, dat);break; case mxDOUBLE_CLASS:array2dat (matArray, prot, dat);break; default: ODINLOG(odinlog,errorLog) << "Datatype \""<< mxGetClassName(matArray) << "\" not (yet) supportted" << STD_endl; dat.resize(0,0,0,0); break; } // matlab uses column-major ordering dat.transposeSelf(fourthDim,thirdDim,secondDim,firstDim); prot.geometry.set_Mode(voxel_3d); prot.geometry.set_FOV(readDirection,dat.shape()(3)); prot.geometry.set_FOV(phaseDirection,dat.shape()(2)); prot.geometry.set_FOV(sliceDirection,dat.shape()(1)); mxDestroyArray(matArray); return 1; } bool open(STD_string name,const char mode[]){ if(init() && (fp=matOpen(name.c_str(),mode)))return true; else return false; } void close(){ matClose(fp); } int read(FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template) { Log odinlog("MatlabBinFormat","read"); if(!open(filename,"r")){ ODINLOG(odinlog,errorLog) << "could not open " << filename << " for reading: " << strerror(errno) << STD_endl; return -1; } Data dat; Protocol prot(protocol_template); while(mat2dat(prot,dat)) { FileIO::ProtocolDataMap::const_iterator found=pdmap.find(prot); if(found!=pdmap.end()) ODINLOG(odinlog,warningLog) << "equal Protocols found, skipping" << STD_endl; else pdmap[prot].reference(dat); } close(); return 1; } void write(const PDpair &pair,unsigned short index, const FileWriteOpts& opts){ Log odinlog("MatlabBinFormat","write"); STD_string seqDesc; int seqNum; pair.first.study.get_Series(seqDesc,seqNum); mxSetField(root, index, "seqDesc", mxCreateString(seqDesc.c_str())); mxSetField(root, index, "seqNum", mxCreateDoubleScalar(seqNum)); mxSetField(root, index, "voxel", dat2mat(pair,opts)); mxSetField(root, index, "center",vector2Array(pair.first.geometry.get_center())); mxSetField(root, index, "rotation",rotMatrix2Array(pair.first.geometry.get_gradrotmatrix())); JDXtriple *diff=dynamic_cast(const_cast(pair.first).methpars.get_parameter("Diffusion_bVector")); if(diff)mxSetField(root, index, "bVector",triple2Array(*diff)); } int write(const FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts) { Log odinlog("MatlabBinFormat","write"); const char *field_names[] = {"bVector","voxel", "center","rotation","seqDesc","seqNum"}; if(!open(filename,"w")){ ODINLOG(odinlog,errorLog) << "could not open " << filename << " for writing: " << strerror(errno) << STD_endl; return -1; } unsigned short cnt=0; const mwSize dim = pdmap.size(); root=mxCreateStructArray(1, &dim, sizeof(field_names)/sizeof(char*), field_names); w_opts=opts; for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit,cnt++) write(*pdit,cnt,opts); saveVar(root,"root"); close(); return pdmap.size(); } }; bool MatlabBinFormat::initialized=0; #endif //MATLABSUPPORT ////////////////////////////////////////////////////////////// void register_mat_format() { #ifdef MATLABSUPPORT static MatlabBinFormat mat; mat.register_format(); #endif //MATLABSUPPORT } odin-1.8.5/odindata/filter_lowpass.cpp0000644000175000017500000000313011725203122014713 00000000000000#include "filter_lowpass.h" #include "complexdata.h" #include void FilterLowPass::init(){ freq=0.0; freq.set_unit("Hz").set_description("Cut-off frequency"); append_arg(freq,"freq"); } bool FilterLowPass::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); Range all=Range::all(); TinyVector shape=data.shape(); int nrep=shape(timeDim); ComplexData<4> cdata(float2real(data)); cdata.partial_fft( TinyVector(true,false,false,false), true); int centindex=nrep/2; float maxfreq_Hz=1000.0*secureDivision(1.0, prot.seqpars.get_RepetitionTime()); int cutoffindex=int(secureDivision(freq, maxfreq_Hz)*centindex+0.5); int plateauindex=int(0.8*cutoffindex+0.5); ODINLOG(odinlog,normalDebug) << "plateauindex/cutoffindex=" << plateauindex << "/" << cutoffindex << STD_endl; JDXfilter transition; transition.set_function("Gauss"); for(int i=0; i<(centindex+1); i++) { if(i>=plateauindex && i<=cutoffindex) { float relpos=secureDivision(i-plateauindex, cutoffindex-plateauindex); STD_complex factor(transition.calculate(relpos)); if((centindex-i)>=0) cdata(centindex-i, all, all, all)*=factor; if((centindex+i)cutoffindex) { if((centindex-i)>=0) cdata(centindex-i, all, all, all)=STD_complex(0.0); if((centindex+i)(true,false,false,false), false); data=creal(cdata); return true; } odin-1.8.5/odindata/filter_splice.h0000644000175000017500000000262711725203122014161 00000000000000/*************************************************************************** filter_reduction.h - description ------------------- begin : Fri Feb 17 2012 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_SPLICE_H #define FILTER_SPLICE_H #include "filter_step.h" class FilterSplice: public FilterStep { JDXenum dir; STD_string label() const {return "splice";} STD_string description() const {return "splices the image in the given direction";} bool process(FileIO::ProtocolDataMap& pdmap)const; FilterStep* allocate() const {return new FilterSplice();} void init(); }; #endif odin-1.8.5/odindata/filter_shift.cpp0000644000175000017500000000121211322062337014343 00000000000000#include "filter_shift.h" void FilterShift::init(){ for(int idir=0; idir& data, Protocol& prot) const { TinyVector subpixel_shift(0.0,shift[sliceDirection],shift[phaseDirection],shift[readDirection]); data.congrid(data.shape(), &subpixel_shift); for(int idir=0; idir #include #include /** * @addtogroup odindata * @{ */ /** * Options for autoread */ struct FileReadOpts : JcampDxBlock { FileReadOpts(); JDXenum format; JDXstring jdx; JDXenum cplx; JDXint skip; JDXstring dset; JDXstring filter; JDXstring dialect; JDXbool fmap; }; ////////////////////////////////////////////////////////////////////////// /** * Options for autowrite */ struct FileWriteOpts : JcampDxBlock { FileWriteOpts(); JDXenum format; JDXbool append; JDXstring wprot; JDXbool split; JDXstring dialect; JDXenum datatype; JDXstring fnamepar; }; /** @} */ #endif odin-1.8.5/odindata/filter_merge.cpp0000644000175000017500000000316611322062337014337 00000000000000#include "filter_merge.h" bool FilterMerge::process(FileIO::ProtocolDataMap& pdmap) const { Log odinlog(c_label(),"process"); Range all=Range::all(); STD_map acqstartmap; // Create a temporary protocol-data pair for each AcquisitionStart TinyVector shape=0; for(FileIO::ProtocolDataMap::const_iterator it=pdmap.begin();it!=pdmap.end();it++) { const Protocol& prot=it->first; const Data& data=it->second; shape(timeDim)+=data.extent(timeDim); for(int idim=sliceDim; idim result(shape); int repoffset=0; Protocol prot; bool prot_set=false; for(STD_map::const_iterator acqit=acqstartmap.begin();acqit!=acqstartmap.end();acqit++) { const FileIO::ProtocolDataMap& acqpdmap=acqit->second; for(FileIO::ProtocolDataMap::const_iterator it=acqpdmap.begin();it!=acqpdmap.end();it++) { if(!prot_set) {prot=it->first; prot_set=true;} // Use first protocol for dataset Data oneset(it->second); TinyVector newshape(shape); int nrep=oneset.extent(timeDim); newshape(timeDim)=nrep; oneset.congrid(newshape); ODINLOG(odinlog,normalDebug) << "newshape" << newshape << STD_endl; result(Range(repoffset,repoffset+nrep-1),all,all,all)=oneset; repoffset+=nrep; } } pdmap[prot].reference(result); return true; } odin-1.8.5/odindata/fileio.h0000644000175000017500000001362211734622163012613 00000000000000/*************************************************************************** fileio.h - description ------------------- begin : Fri Apr 6 2001 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILEIO_H #define FILEIO_H //shortcut to check for type from string (templated function doesn work well with mingw - so we use macro) #define IS_TYPE(type, name) (name==TypeTraits::type2label((type)0)) #include #include #define AUTODETECTSTR "autodetect" #define AUTOTDATAYPESTR "automatic" /** * @addtogroup odindata * @{ */ /** * The 4 dimensions of data arrays used in FileIO and Filter components, these dimensions are * - timeDim: Time direction * - sliceDim: Slice direction * - phaseDim: Phase direction * - readDim: Read direction */ enum dataDim { timeDim=0, sliceDim, phaseDim, readDim, n_dataDim }; static const char* dataDimLabel[]={"time", "slice", "phase", "read"}; /** * Structure to accomodate autoread/autwrite functionality. Please refer to (\ref fileio_doc ) for a detailed description of this module. */ class FileIO { public: /** * Type to associate protocols with tempo-spatial raw data via std::map */ typedef STD_map > ProtocolDataMap; /** * Reads in file 'filename' and appends all data sets found to protocol-data map 'pdmap', autodetects file format according to file extension. * Read options are given by 'opts' and 'protocol_template' contains defaults used by the decoder/encoder of the particular file format. * The progress meter 'progmeter' can be optionally specified to monitor the progress of the operation. * Returns number of slices, or -1 if it fails. */ static int autoread(ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template,ProgressMeter* progmeter=0); /** * Writes out protocol-data map 'pdmap' to file(s) filename, autodetects file format according to file extension. * Write options are given by 'opts'. * Returns number of slices sucessfully written, or -1 if it fails. */ static int autowrite(const ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts); /** * Returns possible file formats/extensions to autoread autowrite */ static svector autoformats(); /** * Returns possible file formats as string with comment */ static STD_string autoformats_str(const STD_string& indent=""); /** * Returns whether tracing via stdout is enabled/disabled */ static bool get_trace_status() {return do_trace;} /** * Enables/disables tracing via stdout */ static void set_trace_status(bool stat) {do_trace=stat;} static const char* get_compName(); // For debugging FilieIO component private: static logPriority loglevel() {if(do_trace) return infoLog; else return normalDebug;} static bool do_trace; static int read_dir(ProtocolDataMap& pdmap, const STD_string& dirname, const FileReadOpts& opts, const Protocol& protocol_template,ProgressMeter* progmeter=0); }; ////////////////////////////////////////////////////////////////////////// /** * Base class for file formats */ class FileFormat { public: /** * Use this function on a static instance to register the corresponding file format */ void register_format(); /** * creates unique filenames based on 'filename' for the protocol-data pairs in 'pdmap' using comma-separated list of additional parameters in 'par' */ static svector create_unique_filenames(const STD_string& filename, const FileIO::ProtocolDataMap& pdmap, const STD_string& par); /** * returns the voxel extent of the 'geometry' in the given 'direction' using a matrix size 'size'. */ static float voxel_extent(const Geometry& geometry, direction direction, int size); protected: virtual ~FileFormat() {} // avoid compiler warnings /** * Returns the spatial voxel extent in the given direction assuming the given size */ static STD_string selectDataType(const Protocol &prot,const FileWriteOpts& opts); private: // limit access friend class FileIO; virtual STD_string description() const = 0; virtual svector suffix() const = 0; virtual svector dialects() const = 0; virtual int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot); virtual int read(FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template); virtual int write(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot); virtual int write(const FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts); static STD_map formats; static STD_string analyze_suffix(const STD_string& filename); static FileFormat* get_format(const STD_string& filename, const STD_string& override_suffix); static svector possible_formats(); static STD_string formats_str(const STD_string& indent); static void format_error(const STD_string& filename); }; /** @} */ #endif odin-1.8.5/odindata/filter.h0000644000175000017500000000245011322062337012620 00000000000000// // C++ Interface: filter // // Description: // // // Author: , (C) 2008 // // Copyright: See COPYING file that comes with this distribution // // #ifndef FILTER_H #define FILTER_H #include /** * @addtogroup odindata * @{ */ // helper class for debugging the filter component struct Filter { static const char* get_compName(); }; ///////////////////////////////////////////////////////////////////////////// /** * A chain of filter functors. */ class FilterChain { public: /** * Create empty filter chain */ FilterChain() {} /** * Create filter chain from command line string. */ FilterChain(const STD_string& argstr) {init(argstr);} /** * Create filter chain from command line. */ FilterChain(int argc,char *argv[]); /** * Initialize filter chain using given command-line string. */ bool init(const STD_string& argstr) {return create(tokens(argstr,' ','\"','\"'));} /** * Apply filter chain to all elements in 'pdmap'. */ bool apply(FileIO::ProtocolDataMap& pdmap) const; /** * Apply filter chain to protocol-data pair. */ bool apply(Protocol& prot, Data& data) const; private: FilterFactory factory; STD_list filters; bool create(const svector& args); }; /** @} */ #endif odin-1.8.5/odindata/fileio_mhd.cpp0000644000175000017500000001102511322062337013763 00000000000000#include "fileio.h" ///////////////////////////////////////////////////////////// struct MhdFormat : public FileFormat { STD_string description() const {return "MetaImage";} svector suffix() const { svector result; result.resize(1); result[0]="mhd"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("MhdFormat","read"); STD_string mhdfile; ::load(mhdfile,filename); mhdfile=replaceStr(mhdfile,"=", " = "); // make sure key, value and '=' are separated by whitespaces svector toks=tokens(mhdfile); int ndims=-1; int i; int ntoks=toks.size(); for(i=0; i shape=data.shape(); farray fa(data); ndim nn=fa.get_extent(); nn.autosize(); // get rid of 1-size dims fvector res(nn.dim()); res=1.0; ODINLOG(odinlog,normalDebug) << "fa.dim()=" << fa.dim() << STD_endl; if(fa.dim()>2) { dvector soffset=prot.geometry.get_sliceOffsetVector(); ODINLOG(odinlog,normalDebug) << "soffset=" << soffset.printbody() << STD_endl; if(soffset.size()>1) res[nn.dim()-3]=fabs(soffset[1]-soffset[0]); else res[nn.dim()-3]=prot.geometry.get_sliceThickness(); } if(nn.dim()>1) res[nn.dim()-2]=secureDivision(prot.geometry.get_FOV(phaseDirection),prot.seqpars.get_MatrixSize(phaseDirection)); if(nn.dim()>0) res[nn.dim()-1]=secureDivision(prot.geometry.get_FOV(readDirection), prot.seqpars.get_MatrixSize(readDirection)); JDXfileName fname(filename); STD_string rawfname=fname.get_basename_nosuffix()+".raw"; STD_string header; header+="NDims = "+itos(nn.dim())+"\n"; header+="DimSize ="; for(unsigned int idim=0; idim(fname.get_dirname()+rawfname); } }; ////////////////////////////////////////////////////////////// void register_mhd_format() { static MhdFormat mf; mf.register_format(); } odin-1.8.5/odindata/fitting.h0000644000175000017500000004306111735132611013003 00000000000000/*************************************************************************** fitting.h - description ------------------- begin : Fri Apr 6 2001 copyright : (C) 2001 by Thies Jochimsen & Michael von Mengershausen email : jochimse@cns.mpg.de mengers@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FITTING_H #define FITTING_H #include // for MinimizationFunction #include #include #include /** * @addtogroup odindata * @{ */ /** * Structure representing a fitting paramater. */ struct fitpar { fitpar() : val(0.0), err(0.0) {} /** * Value of the fitting parameter which is varied during the fit. */ float val; /** * The error interval of the final result. */ float err; }; //////////////////////////////////////////////////////////////////////// /** * Base class of all multi-dimensional function classes which * are used for fitting. * The function has an independent variable 'x' (the argument to evaluate_f), * a dependent variable 'y' (the result of evaluate_f) and a number of * function parameters. * To use this class, derive from it and overload the virtual * functions 'evaluate_f' (function value), 'evaluate_df' (first derivative), * 'numof_fitpars', and 'get_fitpar'. * Parameters which are modified during the fit should be * members of type fitpar. */ class ModelFunction { public: /** * Returns the function value at position 'x'. */ virtual float evaluate_f(float x) const = 0; /** * Returns the first derivatives at position 'x'. */ virtual fvector evaluate_df(float x) const = 0; /** * Returns the number of independent fitting parameters. */ virtual unsigned int numof_fitpars() const = 0; /** * Returns reference to the i'th fitting parameter. */ virtual fitpar& get_fitpar(unsigned int i) = 0; /** * Fit the function to the given dataset. * The current parameters are taken as starting values. * Fits the function to the y-values 'yvals', and optionally * to the corresponding y-error bars 'ysigma' and x-vals 'xvals'. * If no error-bars are given, they are all set to 0.1 and if no * x-vals are given equidistant points with an increment of one are chosen, * i.e. xvals(i)=i; * A maximum of 'max_iterations' iterations and the given 'tolerance' * is used for the fit. * Returns true on success. */ bool fit(const Array& yvals, const Array& ysigma=defaultArray, const Array& xvals=defaultArray, unsigned int max_iterations=500, double tolerance=1.0e-4); /** * Returns the function values for x-values 'xvals'. */ Array get_function(const Array& xvals) const; // dummy array used for default arguments static const Array defaultArray; protected: ModelFunction() {} virtual ~ModelFunction() {} fitpar dummy_fitpar; }; //////////////////////////////////////////////////////////////////////// class ModelData; // forward declaration class GslData4Fit; // forward declaration /** * Class which is used for fitting of functions. */ class FunctionFit { public: /** * Prepare a non-linear least-square fit of function 'model_func' for 'nvals' values with a * maximum of 'max_iterations' iterations and the given 'tolerance'. */ FunctionFit(ModelFunction& model_func, unsigned int nvals, unsigned int max_iterations=500, double tolerance=1.0e-4); /** * Destructor */ ~FunctionFit(); /** * The fitting routine that takes the starting values from the model function, * y-values 'yvals', and optionally the corresponding y-error bars 'ysigma' * and x-vals 'xvals'. If no error-bars are given, they are all set to 0.1 and if no * x-vals are given equidistant points with an increment of one are chosen, * i.e. xvals(i)=i; * Returns true on success. */ bool fit(const Array& yvals, const Array& ysigma=defaultArray, const Array& xvals=defaultArray); // dummy array used for default arguments static const Array defaultArray; private: void print_state (size_t iter); ModelFunction& func; unsigned int max_it; double tol; GslData4Fit* gsldata; ModelData* data4fit; }; /////////////////////////////////////////////////////////////////////// /** * A function to fit an exponential curve to an 1D data set. * It uses the function * * A * exp(lambda * x) */ struct ExponentialFunction : public ModelFunction { fitpar A; fitpar lambda; // implementing virtual functions of ModelFunction float evaluate_f(float x) const; fvector evaluate_df(float x) const; unsigned int numof_fitpars() const; fitpar& get_fitpar(unsigned int i); }; /////////////////////////////////////////////////////////////////////// /** * A function to fit an exponential curve to an 1D data set. * It uses the function * * A * exp(lambda * x) + C */ struct ExponentialFunctionWithOffset : public ModelFunction { fitpar A; fitpar lambda; fitpar C; // implementing virtual functions of ModelFunction float evaluate_f(float x) const; fvector evaluate_df(float x) const; unsigned int numof_fitpars() const; fitpar& get_fitpar(unsigned int i); }; /////////////////////////////////////////////////////////////////////// /** * A function to fit an Gaussian curve to an 1D data set. * It uses the function * * A * exp( - 2 * ( (x-x0) / fwhm )^2 ) */ struct GaussianFunction : public ModelFunction { fitpar A; fitpar x0; fitpar fwhm; // implementing virtual functions of ModelFunction float evaluate_f(float x) const; fvector evaluate_df(float x) const; unsigned int numof_fitpars() const; fitpar& get_fitpar(unsigned int i); }; /////////////////////////////////////////////////////////////////////// /** * * Class for fitting sinus function to a 1D curve * * y= A*sin(m*x + c) */ struct SinusFunction : public ModelFunction { fitpar A; fitpar m; fitpar c; // implementing virtual functions of ModelFunction float evaluate_f(float x) const; fvector evaluate_df(float x) const; unsigned int numof_fitpars() const; fitpar& get_fitpar(unsigned int i); }; /////////////////////////////////////////////////////////////////////// /** * * Class for fitting gamma variate function to a 1D curve * * y= A*x^alpha*exp(-x/beta) */ struct GammaVariateFunction : public ModelFunction { /** * * Set parameters from a simplified set of parameters: xmax and ymax are the x- and y-values of the maximum (see Madsen, Phys. Med. Biol. 37, 1992) */ void set_pars(float alphaval, float xmax, float ymax); fitpar A; fitpar alpha; fitpar beta; // implementing virtual functions of ModelFunction float evaluate_f(float x) const; fvector evaluate_df(float x) const; unsigned int numof_fitpars() const; fitpar& get_fitpar(unsigned int i); }; /////////////////////////////////////////////////////////////////////// /** * * Class for polynomial fitting of function * * y= Sum_i a[i] x^i, with i in [0,N_rank] * * N_rank is the degree of the polynome to be fitted */ template struct PolynomialFunction { fitpar a[N_rank+1]; /** * * polynomial fitting routine. * Fits the function to the y-values 'yvals', and optionally * the corresponding error bars 'ysigma' and x-values 'xvals'. * If no error-bars are given they are all set to 1.0 and if no * x-vals are given equidistant points with an increment of one * are chosen, i.e. xvals(i)=i; * Returns true on success. */ bool fit(const Array& yvals, const Array& ysigma, const Array& xvals); bool fit(const Array& yvals, const Array& ysigma){ firstIndex fi; Array xvals(yvals.size()); xvals=fi; return fit(yvals,ysigma,xvals); }; bool fit(const Array& yvals){ Array ysigma(yvals.size()); ysigma=1.; return fit(yvals,ysigma); }; /** * Returns the polynomial function values for x-values 'xvals' * using the current polynomial coefficients. */ Array get_function(const Array& xvals) const; }; template bool PolynomialFunction::fit(const Array& yvals, const Array& ysigma, const Array& xvals) { int npol=N_rank+1; for(int i=0; i sigma(npts); if(ysigma.size()==npts) sigma=ysigma; else sigma=1.0; Array x(npts); if(xvals.size()==npts) x=xvals; else for(int ipt=0; ipt A(npts,npol); Array b(npts); for(int ipt=0; ipt coeff(solve_linear(A,b)); for(int ipol=0; ipol Array PolynomialFunction::get_function(const Array& xvals) const { int npts=xvals.size(); Array result(npts); result=0.0; for(int ipt=0; ipt& yvals, const Array& ysigma=defaultArray, const Array& xvals=defaultArray); /** * Returns the linear function values for x-values 'xvals' * using the current fit parameters. */ Array get_function(const Array& xvals) const; // dummy array used for default arguments static const Array defaultArray; }; /////////////////////////////////////////////////////////////////////// class GslData4DownhillSimplex; // forward declaration /** * downhill simplex optimizer */ class DownhillSimplex { public: /** * Construct downhill simplex optimizer * - function: Function to evaluate/minimize */ DownhillSimplex(MinimizationFunction& function); /** * Destructor */ ~DownhillSimplex(); /** * Returns parameter values which minimize function * - starting_points: Starting from this initial point * - step_size: The size of the initial trial steps * - ftol: Tolerannce * - nmax: Max number of iterations */ fvector get_minimum_parameters(const fvector& starting_points, const fvector& step_size, float ftol=1e-3, unsigned int nmax=1000); private: unsigned int ndim; GslData4DownhillSimplex* gsldata; }; /////////////////////////////////////////////////////////////////////// /** * Fits an N_rank-dimensional polynomial of order 'polynom_order' to each point of the * array using the values of its neighbours regarding their reliability * (i.e. their relative weight for the fit). Parameters are: * - value_map: The array to be fitted * - reliability_map: The reliability of each point * - polynom_order: Order of the polynom * - kernel_size: Size of the neighbourhood of the pixel which is * considered for the fit (using a Gaussian kernel with this FWHM) * - only_zero_reliability: Fit only pixel with zero reliabiliy * * This function returns the fitted array */ template Array polyniomial_fit(const Array& value_map, const Array& reliability_map, unsigned int polynom_order, float kernel_size, bool only_zero_reliability=false) { Log odinlog("","polyniomial_fit"); Data result(value_map.shape()); result=0.0; if(!same_shape(value_map,reliability_map)) { ODINLOG(odinlog,errorLog) << "size mismatch (value_map.shape()=" << value_map.shape() << ") != (reliability_map.shape()=" << reliability_map.shape() << ")" << STD_endl; return result; } if(min(reliability_map)<0.0) { ODINLOG(odinlog,errorLog) << "reliability_map must be non-negative" << STD_endl; return result; } int minsize=max(value_map.shape()); for(int idim=0; idim1) && (dimsize valshape(value_map.shape()); int nvals=value_map.numElements(); TinyVector polsize; polsize=polynom_order+1; Data polarr(polsize); int npol=polarr.numElements(); if(pow(kernel_size,float(N_rank)) neighbsize; neighbsize=2*neighb_pixel+1; TinyVector neighboffset; neighboffset=-neighb_pixel; Data neighbarr(neighbsize); // neighbour grid around root pixel int nneighb=neighbarr.numElements(); ODINLOG(odinlog,normalDebug) << "nvals/npol/nneighb=" << nvals << "/" << npol << "/" << nneighb << STD_endl; if(npol>nneighb) { ODINLOG(odinlog,warningLog) << "polynome order (" << npol << ") larger than number of neighbours (" << nneighb << ")" << STD_endl; } Array A(npol,npol); Array c(npol); Array b(npol); TinyVector valindex; TinyVector neighbindex; TinyVector currindex; TinyVector diffindex; TinyVector polindex; TinyVector polindex_sum; float epsilon=0.01; float relevant_radius=0.5*kernel_size*sqrt(double(N_rank))+epsilon; // iterate through pixels of value_map for(int ival=0; ival=valshape(irank)) valid_pixel=false; } // does the pixel have non-vanishing reliability float reliability=0.0; if(valid_pixel) reliability=reliability_map(currindex); if(reliability<=0.0) valid_pixel=false; if(valid_pixel) { diffindex=currindex-valindex; // (xk-x0,yk-y0,...) float radiussqr=sum(diffindex*diffindex); float weight=reliability*exp(-2.0*radiussqr/(kernel_size*kernel_size)); if(weight>0.0) { if(sqrt(radiussqr)<=relevant_radius) n_relevant_neighb_pixel++; // create b_i,j for(int ipol=0; ipol=npol) { // do we have enough pixel for the fit ? c=solve_linear(A,b); result(valindex)=c(0); } } else result(valindex)=value_map(valindex); } return result; } /** @} */ #endif odin-1.8.5/odindata/filter_align.cpp0000644000175000017500000000646511322062337014337 00000000000000#include "filter_align.h" #include "gridding.h" void FilterAlign::init(){ fname.set_description("filename"); append_arg(fname,"fname"); blowup.set_description("In-plane blowup factor"); append_arg(blowup,"blowup"); } bool FilterAlign::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); Range all=Range::all(); TinyVector inshape3d(data.extent(sliceDim),data.extent(phaseDim),data.extent(readDim)); int blowup_factor=STD_max(1,int(blowup)); // Load external file Data extdata; Protocol alignprot; if(extdata.autoread(fname, FileReadOpts(), &alignprot)<0) return false; TinyVector dst_shape(extdata.shape()(sliceDim),blowup_factor*extdata.shape()(phaseDim),blowup_factor*extdata.shape()(readDim)); ODINLOG(odinlog,normalDebug) << "dst_shape=" << dst_shape << STD_endl; extdata.free(); TinyVector dst_extent; for(int i=0; i<3; i++) dst_extent(2-i)=alignprot.geometry.get_FOV(direction(i)); ODINLOG(odinlog,normalDebug) << "dst_extent=" << dst_extent << STD_endl; int npts3d=product(inshape3d); ODINLOG(odinlog,normalDebug) << "npts3d=" << npts3d << STD_endl; STD_vector > src_coords(npts3d); dvector srcfov(3); dvector dstfov(3); dvector srcsize(3); dvector dstsize(3); for(int i=0; i index=index2extent(inshape3d, ipt); for(int i=0; i<3; i++) relpos[2-i]=secureDivision(0.5+index(i), inshape3d(i)); srcpos=srcfov*(relpos-0.5); dstpos=alignprot.geometry.transform( prot.geometry.transform(srcpos,false), true); src_coords[ipt].coord=TinyVector(dstpos[2],dstpos[1],dstpos[0]); ODINLOG(odinlog,normalDebug) << "src_coords(" << ipt << ")=" << src_coords[ipt].coord << STD_endl; } JDXfilter gridkernel; gridkernel.set_function("Gauss"); // Calculate kernel which covers both grids for(int i=0; i #ifdef HAVE_LIBGSL #include #include #include // data struct to be passed through GSL functions struct ModelData { ModelData(unsigned int size) {n=size; y=new float[size]; sigma=new float[size]; x=new float[size];} ~ModelData() {delete[] y; delete[] sigma; delete[] x;} ModelFunction* modelfunc; // model function unsigned int n; // number of points float* y; // function values float* sigma; // uncertainty of function values float* x; // arguments of function }; struct GslData4Fit { gsl_multifit_fdfsolver *solver; gsl_matrix *covar; }; //////////////////////////////////////////////////////////////// bool ModelFunction::fit(const Array& yvals, const Array& ysigma, const Array& xvals, unsigned int max_iterations, double tolerance) { FunctionFit ff(*this,yvals.extent(firstDim),max_iterations,tolerance); return ff.fit(yvals,ysigma,xvals); } Array ModelFunction::get_function(const Array& xvals) const { int n=xvals.extent(firstDim); Array result(n); for(int i=0; i ModelFunction::defaultArray; //////////////////////////////////////////////////////////////// // functions to be used by GSL solver int FunctionFit_func_f (const gsl_vector * gv, void *params, gsl_vector * f) { // get current model function ModelData* data=(ModelData*)params; ModelFunction* modelfunc=data->modelfunc; unsigned int n_fitpars=modelfunc->numof_fitpars(); // set the fitting parameters in the model function for(unsigned int i=0; iget_fitpar(i).val=gsl_vector_get(gv, i); } // calculate vector of values for this set of parameters for (unsigned int i = 0; i < data->n; i++) { float Yi = modelfunc->evaluate_f(data->x[i]); gsl_vector_set (f, i, (data->y[i] - Yi)/data->sigma[i]); } return GSL_SUCCESS; } int FunctionFit_func_df (const gsl_vector * gv, void *params, gsl_matrix * df) { // get current model function ModelData* data=(ModelData*)params; ModelFunction* modelfunc=data->modelfunc; unsigned int n_fitpars=modelfunc->numof_fitpars(); // set the fitting parameters in the model function for(unsigned int i=0; iget_fitpar(i).val=gsl_vector_get(gv, i); } // calculate vector of derivative values for this set of parameters fvector dYi(n_fitpars); for (unsigned int i = 0; i < data->n; i++) { dYi = modelfunc->evaluate_df(data->x[i]); float s = data->sigma[i]; for(unsigned int j=0; jmodelfunc=&model_func; gsldata=new GslData4Fit; // allocate and initialize GSL stuff gsldata->covar = gsl_matrix_alloc (func.numof_fitpars(), func.numof_fitpars()); gsldata->solver = gsl_multifit_fdfsolver_alloc (gsl_multifit_fdfsolver_lmsder, data4fit->n, func.numof_fitpars()); } FunctionFit::~FunctionFit() { // free GSL stuff gsl_multifit_fdfsolver_free(gsldata->solver); gsl_matrix_free(gsldata->covar); delete data4fit; delete gsldata; } bool FunctionFit::fit(const Array& yvals, const Array& ysigma, const Array& xvals) { Log odinlog("FunctionFit","fit"); bool haveSigma; bool haveXvals; // check input if(data4fit->n!=(unsigned)yvals.size() || data4fit->n<=0) { ODINLOG(odinlog,errorLog) << "size mismatch in yvals" << STD_endl; return false; } if((unsigned)ysigma.size()==data4fit->n) haveSigma=true; else { haveSigma=false; ODINLOG(odinlog,normalDebug) << "no error bars provided, taking uniform interval for all x" << STD_endl; } if((unsigned)xvals.size()==data4fit->n) haveXvals=true; else { haveXvals=false; ODINLOG(odinlog,normalDebug) << "no x values provided, taking index as x value" << STD_endl; } ODINLOG(odinlog,normalDebug) << "n/numof_fitpars=" << data4fit->n << "/" << func.numof_fitpars() << STD_endl; // copy Blitz arrays to data4fit for (unsigned long i=0;in;i++) { data4fit->y[i]=yvals(i); if(haveSigma) data4fit->sigma[i]=ysigma(i); else data4fit->sigma[i]=0.1; if(haveXvals) data4fit->x[i]=xvals(i); else data4fit->x[i]=(float)i; } ODINLOG(odinlog,normalDebug) << "copy arrays done" << STD_endl; // initialize GSL fitting function gsl_multifit_function_fdf gsl_func; gsl_func.f=&FunctionFit_func_f; gsl_func.df=&FunctionFit_func_df; gsl_func.fdf=&FunctionFit_func_fdf; gsl_func.n=data4fit->n; gsl_func.p=func.numof_fitpars(); gsl_func.params=(void *)data4fit; ODINLOG(odinlog,normalDebug) << "gsl_func done" << STD_endl; // starting values double x_init[func.numof_fitpars()]; for(unsigned int i=0; isolver, &gsl_func, &initial_guess.vector); ODINLOG(odinlog,normalDebug) << "initialize solver done" << STD_endl; unsigned int iter = 0; int status; do { // main loop ODINLOG(odinlog,normalDebug) << "iter= " << iter << STD_endl; iter++; status = gsl_multifit_fdfsolver_iterate (gsldata->solver); ODINLOG(odinlog,normalDebug) << "status(fit)= " << gsl_strerror (status) << STD_endl; print_state (iter); if (status!=GSL_SUCCESS) break; status = gsl_multifit_test_delta (gsldata->solver->dx, gsldata->solver->x, tol, tol); ODINLOG(odinlog,normalDebug) << "status(test)= " << gsl_strerror (status) << STD_endl; ODINLOG(odinlog,normalDebug) << "iter/max_it= " << iter << "/" << max_it << STD_endl; } while (status == GSL_CONTINUE && iter < max_it); if(status!=GSL_SUCCESS && status!=GSL_ENOPROG) { // ignoring error 'iteration is not making progress towards solution' and taking intermediate result as best fit ODINLOG(odinlog,errorLog) << gsl_strerror(status) << STD_endl; return false; } gsl_multifit_covar (gsldata->solver->J, 0.0, gsldata->covar); // copy results for(unsigned int i=0;isolver->x, i); func.get_fitpar(i).err=sqrt(gsl_matrix_get(gsldata->covar,i,i)); } return true; } void FunctionFit::print_state (size_t iter) { #ifdef ODIN_DEBUG Log odinlog("FunctionFit","fit"); ODINLOG(odinlog,normalDebug) << "iter=" << iter << STD_endl; for(unsigned int i=0;i s(n); Array x(n); if(haveSigma) s=ysigma; else s=1.0; if(haveXvals) x=xvals; else for(int i=0; i s2(n); s2=s*s; float S= sum(1.0/(s2)); float Sx= sum(x /(s2)); float Sxx=sum(x*x/(s2)); ODINLOG(odinlog,normalDebug) << "S/Sx/Sxx=" << S << "/" << Sx << "/" << Sxx << STD_endl; float Sy= sum(yvals/(s2)); float Sxy=sum(x*yvals/(s2)); ODINLOG(odinlog,normalDebug) << "Sy/Sxy=" << Sy << "/" << Sxy << STD_endl; float Delta=S*Sxx - Sx*Sx; ODINLOG(odinlog,normalDebug) << "Delta=" << Delta << STD_endl; float beta=secureDivision(S*Sxy-Sx*Sy, Delta); float alpha=secureDivision(Sxx*Sy-Sx*Sxy, Delta); ODINLOG(odinlog,normalDebug) << "alpha/beta=" << beta << "/" << beta << STD_endl; Array summand(n); summand=(yvals-beta*x-alpha); summand*=summand; float ystdev=sqrt(secureInv(double(n)-2.0)*sum( summand )); ODINLOG(odinlog,normalDebug) << "ystdev=" << ystdev << STD_endl; float betastdev=ystdev*sqrt(1.0/( sum(x*x) - secureInv(n)*sum(x)*sum(x) )); ODINLOG(odinlog,normalDebug) << "betastdev=" << betastdev << STD_endl; float alphastdev=betastdev*sqrt( secureInv(n)*sum(x*x) ); ODINLOG(odinlog,normalDebug) << "alphastdev=" << alphastdev << STD_endl; m.val=beta; m.err=betastdev; c.val=alpha; c.err=alphastdev; return true; } Array LinearFunction::get_function(const Array& xvals) const { return Array(m.val * xvals + c.val); } const Array LinearFunction::defaultArray; ////////////////////////////////////////////////////////////// struct GslData4DownhillSimplex { gsl_vector* x; gsl_vector* ss; gsl_multimin_function minex_func; gsl_multimin_fminimizer* s; }; double DownhillSimplex_func_f(const gsl_vector * gv, void *params) { // get current model function const MinimizationFunction* minfunc=(const MinimizationFunction*)params; unsigned int n_fitpars=minfunc->numof_fitpars(); fvector x(n_fitpars); for(unsigned int i=0; ievaluate(x); } DownhillSimplex::DownhillSimplex(MinimizationFunction& function) { ndim=function.numof_fitpars(); gsldata=new GslData4DownhillSimplex; gsldata->x = gsl_vector_alloc(ndim); gsldata->ss = gsl_vector_alloc(ndim); gsldata->minex_func.n = ndim; gsldata->minex_func.f = &DownhillSimplex_func_f; gsldata->minex_func.params = &function; gsldata->s = gsl_multimin_fminimizer_alloc(gsl_multimin_fminimizer_nmsimplex2, ndim); // newer algorithm, only available in recent GSL // gsldata->s = gsl_multimin_fminimizer_alloc(gsl_multimin_fminimizer_nmsimplex, ndim); } DownhillSimplex::~DownhillSimplex() { // free GSL stuff gsl_vector_free(gsldata->x); gsl_vector_free(gsldata->ss); gsl_multimin_fminimizer_free(gsldata->s); delete gsldata; } fvector DownhillSimplex::get_minimum_parameters(const fvector& starting_points, const fvector& step_size, float ftol, unsigned int nmax) { Log odinlog("DownhillSimplex","get_minimum_parameters"); fvector result(ndim); if(starting_points.size()!=ndim) { ODINLOG(odinlog,errorLog) << "size mismatch: starting_points.size()=" << starting_points.size() << ", ndim=" << ndim << STD_endl; return result; } if(step_size.size()!=ndim) { ODINLOG(odinlog,errorLog) << "size mismatch: starting_points.size()=" << starting_points.size() << ", ndim=" << ndim << STD_endl; return result; } for(unsigned int idim=0; idimx, idim, starting_points[idim]); gsl_vector_set (gsldata->ss, idim, step_size[idim]); } gsl_multimin_fminimizer_set (gsldata->s, &(gsldata->minex_func), gsldata->x, gsldata->ss); unsigned int niterations=0; int status; double size; do { niterations++; status = gsl_multimin_fminimizer_iterate(gsldata->s); if (status) break; size = gsl_multimin_fminimizer_size(gsldata->s); status = gsl_multimin_test_size(size, ftol); /* if (status == GSL_SUCCESS) { printf ("converged to minimum at\n"); } printf ("%5d %10.3e %10.3e f() = %7.3f size = %.3f\n", iter, gsl_vector_get (s->x, 0), gsl_vector_get (s->x, 1), s->fval, size); */ } while (status == GSL_CONTINUE && niterations < nmax); for(unsigned int idim=0; idims->x, idim); ODINLOG(odinlog,normalDebug) << "result" << result << STD_endl; ODINLOG(odinlog,normalDebug) << "min value=" << gsldata->s->fval << STD_endl; return result; } ////////////////////////////////////////////////////////////// // Unit test #ifndef NO_UNIT_TEST class DownhillSimplexTestFunction : public MinimizationFunction { unsigned int numof_fitpars() const {return 2;} float evaluate(const fvector& xvec) const {return pow(xvec[0]-2.0,2)+pow(xvec[1]-3.0,2);} }; class FunctionFitTest : public UnitTest { public: FunctionFitTest() : UnitTest("FunctionFit") {} private: bool check() const { Log odinlog(this,"check"); int numoftestvals=5; ExponentialFunctionWithOffset expf_offset; FunctionFit expfit_offset(expf_offset,numoftestvals); Array yvals(numoftestvals); Array ysigma(numoftestvals); Array xvals(numoftestvals); // some arbitrary values for testing xvals(0)=0.1; yvals(0)=12.4; ysigma(0)=0.7; xvals(1)=1.2; yvals(1)=8.4; ysigma(1)=1.2; xvals(2)=1.9; yvals(2)=6.1; ysigma(2)=0.9; xvals(3)=3.0; yvals(3)=5.0; ysigma(3)=0.8; xvals(4)=4.1; yvals(4)=5.0; ysigma(4)=1.0; expf_offset.A.val=1.0; // starting value expf_offset.lambda.val=-1.0; // starting value expf_offset.C.val=1.0; // starting value if(!expfit_offset.fit(yvals,ysigma,xvals)) { ODINLOG(odinlog,errorLog) << "ExponentialFunctionWithOffset fit failed" << STD_endl; return false; } float A_expected=8.74419; float A_err_expected=1.32811; float lambda_expected=-0.76985; float lambda_err_expected=0.37922; float C_expected=4.33682; float C_err_expected=1.31881; STD_string A_str =ftos(expf_offset.A.val) +"+-"+ftos(expf_offset.A.err); STD_string A_expected_str =ftos(A_expected ) +"+-"+ftos(A_err_expected); STD_string lambda_str =ftos(expf_offset.lambda.val) +"+-"+ftos(expf_offset.lambda.err); STD_string lambda_expected_str=ftos(lambda_expected)+"+-"+ftos(lambda_err_expected); STD_string C_str =ftos(expf_offset.C.val) +"+-"+ftos(expf_offset.C.err); STD_string C_expected_str =ftos(C_expected) +"+-"+ftos(C_err_expected); /* // gives different results depending on the GSL version if(A_str !=A_expected_str) {ODINLOG(odinlog,errorLog) << "FunctionFit_check: ExponentialFunctionWithOffset failed: A=" << A_str << ", but expected A=" << A_expected_str << STD_endl; return false;} if(lambda_str!=lambda_expected_str) {ODINLOG(odinlog,errorLog) << "FunctionFit_check: ExponentialFunctionWithOffset failed: lambda=" << lambda_str << ", but expected lambda=" << lambda_expected_str << STD_endl; return false;} if(C_str !=C_expected_str) {ODINLOG(odinlog,errorLog) << "FunctionFit_check: ExponentialFunctionWithOffset failed: C=" << C_str << ", but expected C=" << C_expected_str << STD_endl; return false;} */ ///////////////////////////////////////////////////// int numoftestvals2=100; ExponentialFunction expf; FunctionFit expfit(expf,numoftestvals2); // arbitrary values for testing A_expected=44.5; lambda_expected=0.78; expf.A.val=A_expected; expf.lambda.val=lambda_expected; yvals.resize(numoftestvals2); ysigma.resize(numoftestvals2); xvals.resize(numoftestvals2); for(int i=0; i(ysigma3).autowrite("ysigma3.asc"); if(!polyf.fit(yvals3,ysigma3,xvals3)) { ODINLOG(odinlog,errorLog) << "PolynomialFunction fit failed" << STD_endl; return false; } for(int i=0; i1.0e-3) { ODINLOG(odinlog,errorLog) << "PolynomialFunction failed: a[" << i << "]=" << fitval << ", but expected " << expval << STD_endl; return false; } } ///////////////////////////////////////////////////// Array values(3,3); values=10.0; values(1,1)=0.0; Array reliability(3,3); reliability=1.0; reliability(1,1)=0.0; Data pfresult(3,3); pfresult=polyniomial_fit(values,reliability,1,2.0); if(fabs(pfresult(1,1)-10.0)>1.0e-3) { ODINLOG(odinlog,errorLog) << "values=" << values << STD_endl; ODINLOG(odinlog,errorLog) << "reliability=" << reliability << STD_endl; ODINLOG(odinlog,errorLog) << "pfresult=" << pfresult << STD_endl; ODINLOG(odinlog,errorLog) << "polyniomial_fit failed" << STD_endl; return false; } int testsize=20; Data testarray(testsize,testsize); Data testrelia(testsize,testsize); TinyVector index; for(int i=0; i1.0e-3) { ODINLOG(odinlog,errorLog) << "polyniomial_fit failed, diff=" << diff << STD_endl; return false; } ///////////////////////////////////////////////////// DownhillSimplexTestFunction dstf; DownhillSimplex ds(dstf); fvector starting_points(2); starting_points=0.0; fvector step_size(2); step_size=1.0; fvector dsresult=ds.get_minimum_parameters(starting_points, step_size); fvector dsexpected(2); dsexpected[0]=2.0; dsexpected[1]=3.0; float maxdiff=(dsresult-dsexpected).maxabs(); ODINLOG(odinlog,normalDebug) << "maxdiff=" << maxdiff << STD_endl; if((dsresult-dsexpected).maxabs()>1.0e-3) { ODINLOG(odinlog,errorLog) << "DownhillSimplex failed, result" << dsresult << ", but expected" << dsexpected << STD_endl; return false; } return true; } }; void alloc_FunctionFitTest() {new FunctionFitTest();} // create test instance #endif ////////////////////////////////////////////////////////////// #else #error "GNU Scientific library is missing!" #endif odin-1.8.5/odindata/fileio.cpp0000644000175000017500000010175211734622162013147 00000000000000#include "fileio.h" #include "utils.h" #include "complexdata.h" // for unit test #include #include #include #include const char* FileIO::get_compName() {return "FileIO";} LOGGROUNDWORK(FileIO) /////////////////////////////////////////////////////////////////////////////// void FileFormat::register_format() { svector suffs=suffix(); for(unsigned int i=0; i& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("FileFormat","read"); ODINLOG(odinlog,errorLog) << this->description() << "::read not implemented" << STD_endl; return -1; } int FileFormat::read(FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template) { Data data; Protocol prot(protocol_template); int result=this->read(data, filename, opts, prot); if(result<0) return -1; if(result>0) pdmap[prot].reference(data); // Ignore zero-size data, e.g. DICOMDIR return result; } int FileFormat::write(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) { Log odinlog("FileFormat","write"); ODINLOG(odinlog,errorLog) << this->description() << "::write not implemented" << STD_endl; return -1; } int FileFormat::write(const FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts) { int result=0; svector fnames=create_unique_filenames(filename, pdmap, opts.fnamepar); int ifile=0; for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) { int writeresult=this->write(pdit->second, fnames[ifile], opts, pdit->first); if(writeresult<0) return writeresult; result+=writeresult; ifile++; } return result; } STD_string FileFormat::analyze_suffix(const STD_string& filename) { JDXfileName fname(filename); return fname.get_suffix(); } FileFormat* FileFormat::get_format(const STD_string& filename, const STD_string& override_suffix) { STD_string suffix; if(override_suffix==AUTODETECTSTR) { suffix=analyze_suffix(filename); } else { suffix=override_suffix; } if(formats.find(suffix)!=formats.end()) return formats[suffix]; return 0; } svector FileFormat::possible_formats() { svector result; result.resize(formats.size()); int index=0; for(STD_map::const_iterator it=formats.begin(); it!=formats.end(); ++it) { result[index]=it->first; index++; } return result; } STD_string FileFormat::formats_str(const STD_string& indent) { STD_string result; for(STD_map::const_iterator it=formats.begin(); it!=formats.end(); ++it) { result+=indent+(it->first)+" \t ("+it->second->description(); svector dialects=it->second->dialects(); if(dialects.size()) result+=", dialects: "+dialects.printbody(); result+=")\n"; } return result; } void FileFormat::format_error(const STD_string& filename) { Log odinlog("FileFormat","format_error"); ODINLOG(odinlog,errorLog) << "File extension >" << analyze_suffix(filename) << "< of file >" << filename << "< not recognized" << STD_endl; ODINLOG(odinlog,errorLog) << "Recognized file extensions (and formats) are" << STD_endl << formats_str("") << STD_endl; } svector FileFormat::create_unique_filenames(const STD_string& filename, const FileIO::ProtocolDataMap& pdmap, const STD_string& par) { Log odinlog("FileFormat","create_unique_filenames"); unsigned int nnames=pdmap.size(); svector result; result.resize(nnames); if(nnames==1) { result[0]=filename; return result; } STD_string serDesc; int serNum; // Get max series number int maxseries=0; for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) { pdit->first.study.get_Series(serDesc,serNum); maxseries=STD_max(maxseries,serNum); } svector pars; pars=tokens(par); int npars=pars.size(); // Create vector of strings "S[_]" STD_map namescount; svector unique_names; unique_names.resize(nnames); unsigned int iname=0; for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) { pdit->first.study.get_Series(serDesc,serNum); for(unsigned int i=0;ifirst.printval(pars[ipar]), "\n", ""); // truncate after first newline } } if(namescount.find(str)==namescount.end()) namescount[str]=0; else namescount[str]++; unique_names[iname]=str; iname++; } // Make sure filenames are unique by appending enumeration, if neccessary STD_map uniqueindex; // separate count for each non-unique filename for(unsigned int i=0; i0) { if(uniqueindex.find(str)==uniqueindex.end()) uniqueindex[str]=0; else uniqueindex[str]++; unique_names[i]+="_"+itos(uniqueindex[str],ncount); } } // Decompose file name to insert unique name before first known prefix JDXfileName fname(filename); svector fmts=FileIO::autoformats(); JDXfileName bname=fname.get_basename_nosuffix(); STD_string fnamesuff(fname.get_suffix()); STD_string suffixstr; if(fnamesuff!="") suffixstr="."+fname.get_suffix(); ODINLOG(odinlog,normalDebug) << "suffixstr=" << suffixstr << STD_endl; bool known_fmt=true; while(known_fmt) { // split filename from right to left as long as known file extensions are detected STD_string suff=bname.get_suffix(); known_fmt=false; for(unsigned int i=0; i odinlog("FileFormat","voxel_extent"); float result; if(direction==sliceDirection) { if(geometry.get_Mode()==voxel_3d) { result=secureDivision(geometry.get_FOV(direction), size); } else { if(geometry.get_nSlices()>1) result=geometry.get_sliceDistance(); else result=geometry.get_sliceThickness(); } } else { result=secureDivision(geometry.get_FOV(direction), size); } ODINLOG(odinlog,normalDebug) << "result(" << directionLabel[direction] << ")=" << result << STD_endl; return result; } STD_map FileFormat::formats; ////////////////////////////////////////////////////////////////////////// void register_asc_format(); void register_dicom_format(); void register_gzip_format(); void register_hfss_format(); void register_jdx_format(); void register_mhd_format(); void register_mat_format(); void register_nifti_format(); void register_png_format(); void register_raw_format(); void register_Iris3D_format(); void register_vtk_format(); ////////////////////////////////////////////////////////////// struct FileFormatCreator : public StaticHandler { // functions to initialize/delete static members by the StaticHandler template class static void init_static() { register_asc_format(); register_dicom_format(); register_gzip_format(); register_jdx_format(); register_mhd_format(); register_mat_format(); register_nifti_format(); register_png_format(); register_Iris3D_format(); register_raw_format(); register_hfss_format(); register_vtk_format(); } static void destroy_static() {} }; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; ////////////////////////////////////////////////////////////////////////// int FileIO::autoread(ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template,ProgressMeter* progmeter) { Log odinlog("FileIO","autoread"); if(!checkdir(filename.c_str()) && filesize(filename.c_str())<=0) { ODINLOG(odinlog,errorLog) << "File " << filename << " not found or is empty" << STD_endl; return -1; } FileFormatCreator ffc; // for some reason, we needed a named object here instead of a plain constructor // override file suffix if jdx option is given STD_string suffix=opts.format; if(opts.jdx!="") suffix="smp"; int result=-1; if(checkdir(filename.c_str())) { result=read_dir(pdmap, filename, opts, protocol_template,progmeter); if(result<0) return -1; } else { FileFormat* ff=FileFormat::get_format(filename,suffix); if(!ff) { FileFormat::format_error(filename); return -1; } ODINLOG(odinlog,loglevel()) << "Reading format " << ff->description() << STD_endl; result=ff->read(pdmap, filename, opts, protocol_template); if(result<0) { ODINLOG(odinlog,errorLog) << "Cannot read file " << filename << STD_endl; return -1; } } ODINLOG(odinlog,normalDebug) << "slicedist=" << pdmap.begin()->first.geometry.get_sliceDistance() << STD_endl; ProtocolDataMap pdmapin(pdmap); pdmap.clear();unsigned short cnt=0; for(ProtocolDataMap::const_iterator pdit=pdmapin.begin(); pdit!=pdmapin.end(); ++pdit) { if(!pdit->second.size()) { ODINLOG(odinlog,errorLog) << "Zero-size data while reading " << filename << STD_endl; return -1; } TinyVector shape=pdit->second.shape(); Protocol prot(pdit->first); // overwrite extent in protocol prot.seqpars.set_NumOfRepetitions(shape(timeDim)); if(prot.geometry.get_Mode()==slicepack) prot.geometry.set_nSlices(shape(sliceDim)); else prot.seqpars.set_MatrixSize(sliceDirection,shape(sliceDim)); prot.seqpars.set_MatrixSize(phaseDirection,shape(phaseDim)); prot.seqpars.set_MatrixSize(readDirection,shape(readDim)); // Adjust total duration of sequence, only if uninitialized ODINLOG(odinlog,normalDebug) << "ExpDuration=" << prot.seqpars.get_ExpDuration() << STD_endl; prot.seqpars.set_ExpDuration(STD_max(prot.seqpars.get_ExpDuration(), shape(0)*prot.seqpars.get_RepetitionTime()/(60.0*1000.0))); // Set label of protocol to filename STD_string postfix; if(pdmapin.size()>1) postfix=":"+itos(cnt,pdmapin.size()-1); prot.set_label("Protocol of "+filename+postfix); const Data& data=pdit->second; if(!opts.fmap && data.is_filemapped()) { ODINLOG(odinlog,normalDebug) << "filemapped" << STD_endl; pdmap[prot].reference(data.copy()); } else { pdmap[prot].reference(data); } STD_string cntstr; if(pdmapin.size()>1) cntstr="#"+itos(cnt)+" "; ODINLOG(odinlog,loglevel()) << "Read dataset " << cntstr << "from file " << filename << " with dimensions " << shape << STD_endl; cnt++; } ODINLOG(odinlog,normalDebug) << "mem(read): " << Profiler::get_memory_usage() << STD_endl; // Extract only a certain dataset if requested int dset2extract=-1; if(opts.dset!="") { dset2extract=atoi(opts.dset.c_str()); if(dset2extract>=int(pdmap.size()) || dset2extract<0) { ODINLOG(odinlog,errorLog) << "Dataset to extract (" << dset2extract << ") out of range (" << pdmap.size() << ")" << STD_endl; return -1; } } if(dset2extract>=0) { ODINLOG(odinlog,loglevel()) << "Extracting dataset with index " << dset2extract << STD_endl; ProtocolDataMap pdmap_copy(pdmap); pdmap.clear(); int iset=0; for(ProtocolDataMap::const_iterator pdit=pdmap_copy.begin(); pdit!=pdmap_copy.end(); ++pdit) { if(dset2extract==iset) pdmap[pdit->first].reference(pdit->second); iset++; } } // filter on certain parameters in protocol if(opts.filter!="") { svector toks=tokens(opts.filter,'='); if(toks.size()==2) { ODINLOG(odinlog,loglevel()) << "Filtering data where parameter " << toks[0] << " contains " << toks[1] << STD_endl; ProtocolDataMap pdmap_copy(pdmap); pdmap.clear(); for(ProtocolDataMap::const_iterator pdit=pdmap_copy.begin(); pdit!=pdmap_copy.end(); ++pdit) { if(pdit->first.printval(toks[0]).find(toks[1])!=STD_string::npos) pdmap[pdit->first].reference(pdit->second); } } } ODINLOG(odinlog,normalDebug) << "mem(result): " << Profiler::get_memory_usage() << STD_endl; return result; } ////////////////////////////////////////////////////////////////////////// struct ImageKey : public UniqueIndex { double acquisition_time; double slice_loc; STD_string filename; STD_string datatype; ImageKey(double tt, double sl, const STD_string& fn, const STD_string& dt) : acquisition_time(tt), slice_loc(sl), filename(fn), datatype(dt) {} bool operator < (const ImageKey& ik) const { if(slice_loc!=ik.slice_loc) return (slice_loc > KeyImageMap; int FileIO::read_dir(ProtocolDataMap& pdmap, const STD_string& dirname, const FileReadOpts& opts, const Protocol& protocol_template,ProgressMeter* progmeter) { Log odinlog("FileIO","read_dir"); ODINLOG(odinlog,normalDebug) << "mem(start): " << Profiler::get_memory_usage() << STD_endl; Range all=Range::all(); int result=0; svector dirfiles=browse_dir(dirname,false,true); unsigned int nfiles=dirfiles.size(); if(!nfiles) { ODINLOG(odinlog,errorLog) << "No files found in directory " << dirname << STD_endl; return -1; } STD_map oneimagemap; // Use local options to skip some of the global autoread options FileReadOpts opts_copy=opts; opts_copy.dset=""; if(progmeter) progmeter->new_task( nfiles,"FileIO::read_dir"); for(unsigned int i=0; iincrease_counter(dirfilename.c_str())) break;//cancel if the ProgressMeter says so if(readresult<0) { ODINLOG(odinlog,warningLog) << "Ignoring unrecognized file " << dirfiles[i] << " while reading dir" << STD_endl; } else if(readresult>0) { // ignore files unrecognized by the plugin (e.g. DICOMDIR) // Iterate over protocol-data pairs for(ProtocolDataMap::const_iterator pdit=onepdmap.begin(); pdit!=onepdmap.end(); ++pdit) { const Protocol& onefileprot=pdit->first; const Data& onefiledata=pdit->second; KeyImageMap& imgmap=oneimagemap[onefileprot]; // Get/insert key-image map for this protocol // Check x- and y-size KeyImageMap::const_iterator it=imgmap.begin(); if(it!=imgmap.end()) { // only check size if there already is an entry in the key-image map if(it->second.extent(0)!=onefiledata.extent(phaseDim)) { ODINLOG(odinlog,errorLog) << "Files in dir have different ysize" << STD_endl; return -1; } if(it->second.extent(1)!=onefiledata.extent(readDim)) { ODINLOG(odinlog,errorLog) << "Files in dir have different xsize" << STD_endl; return -1; } } STD_string dtype_prot=onefileprot.system.get_data_type(); // Insert repetitions and slices separately into map for(int irep=0; irep& dataref=imgmap[ImageKey(acqstart,sliceloc,dirfilename,dtype_prot)]; dataref.resize(onefiledata.extent(phaseDim),onefiledata.extent(readDim)); dataref=onefiledata(irep,islice,all,all); if(!progmeter) { ODINLOG(odinlog,loglevel()) << "Read slice from file " << dirfiles[i] << " " << onefiledata.shape() << " with acquisition_start/slice_location=" << acqstart << "/" << sliceloc << STD_endl; } } } } // end iterating over protocol-data pairs } } // end iterating over files ODINLOG(odinlog,loglevel()) << "Found " << oneimagemap.size() << " protocol(s) while reading files:" << STD_endl; ODINLOG(odinlog,normalDebug) << "mem(read): " << Profiler::get_memory_usage() << STD_endl; // Iterate over separate protocols to combine data int protindex=0; for(STD_map::iterator it=oneimagemap.begin(); it!=oneimagemap.end(); ++it) { KeyImageMap::const_iterator imgit; Protocol prot(it->first); KeyImageMap& imgmap=it->second; // non-const to be cleared after retrieving data from it TinyVector shape; imgit=imgmap.begin(); if(imgit==imgmap.end()) { ODINLOG(odinlog,errorLog) << "Empty imgmap" << STD_endl; return -1; } shape(readDim)=imgit->second.extent(1); shape(phaseDim)=imgit->second.extent(0); // Get slice offsets and min acq time by iterating over images STD_list slice_offsets; STD_list datatypes; double min_acqstart=imgit->first.acquisition_time; double max_acqstart=imgit->first.acquisition_time; for(imgit=imgmap.begin(); imgit!=imgmap.end(); ++imgit) { slice_offsets.push_back(imgit->first.slice_loc); datatypes.push_back(imgit->first.datatype); min_acqstart=STD_min(min_acqstart,imgit->first.acquisition_time); max_acqstart=STD_max(max_acqstart,imgit->first.acquisition_time); } // Find datatype with highest resolution in final dataset and use it for all datasets datatypes.sort(); datatypes.unique(); STD_string dtype=TypeTraits::type2label((float)0); // default if(find(datatypes.begin(),datatypes.end(),TypeTraits::type2label((u8bit) 0))!=datatypes.end()) dtype=TypeTraits::type2label((u8bit)0); if(find(datatypes.begin(),datatypes.end(),TypeTraits::type2label((s8bit) 0))!=datatypes.end()) dtype=TypeTraits::type2label((s8bit)0); if(find(datatypes.begin(),datatypes.end(),TypeTraits::type2label((u16bit)0))!=datatypes.end()) dtype=TypeTraits::type2label((u16bit)0); if(find(datatypes.begin(),datatypes.end(),TypeTraits::type2label((s16bit)0))!=datatypes.end()) dtype=TypeTraits::type2label((s16bit)0); if(find(datatypes.begin(),datatypes.end(),TypeTraits::type2label((u32bit)0))!=datatypes.end()) dtype=TypeTraits::type2label((u32bit)0); if(find(datatypes.begin(),datatypes.end(),TypeTraits::type2label((s32bit)0))!=datatypes.end()) dtype=TypeTraits::type2label((s32bit)0); if(datatypes.size()>1) { ODINLOG(odinlog,loglevel()) << "Using single datatype " << dtype << " for images with datatypes=" << svector(list2vector(datatypes)).printbody() << STD_endl; } prot.system.set_data_type(dtype); slice_offsets.sort(); slice_offsets.unique(); shape(sliceDim)=slice_offsets.size(); int ndatasets=imgmap.size(); shape(timeDim)=ndatasets/shape(sliceDim); // interpret remainder as time dimension ODINLOG(odinlog,loglevel()) << "ndatasets/shape(" << protindex << ")=" << ndatasets << "/" << shape << STD_endl; if(ndatasets!=(shape(timeDim)*shape(sliceDim))) { ODINLOG(odinlog,errorLog) << "Size mismatch, ndatasets(" << ndatasets << ")!=nreps(" << shape(timeDim) << ")*nslices(" << shape(sliceDim) << ")" << STD_endl; return -1; } // Insert slices into data according to their ordering Data data(shape); ODINLOG(odinlog,normalDebug) << "mem(data): " << Profiler::get_memory_usage() << STD_endl; int irep=0; int islice=0; STD_map sliceindexmap; // gets sorted according to temporal index for(imgit=imgmap.begin(); imgit!=imgmap.end(); ++imgit) { if(irep==0) sliceindexmap[imgit->first.acquisition_time]=islice; data(irep,islice,all,all)=imgit->second; result++; irep++; if(irep>=shape(timeDim)) { irep=0; islice++; if(islice>=shape(sliceDim)) islice=0; } } // set new acquisition start and duration prot.seqpars.set_AcquisitionStart(min_acqstart); ODINLOG(odinlog,normalDebug) << "min_acqstart: " << min_acqstart << " max_acqstart: " << max_acqstart << " dur: "<< max_acqstart - min_acqstart+ prot.seqpars.get_RepetitionTime()/1000 << STD_endl; prot.seqpars.set_ExpDuration( (max_acqstart - min_acqstart+ prot.seqpars.get_RepetitionTime()/1000 ) /60.0); // overwrite slice settings in protocol prot.geometry.set_nSlices(shape(sliceDim)); fvector slicevec=list2vector(slice_offsets); ODINLOG(odinlog,normalDebug) << "slicevec=" << slicevec.printbody() << STD_endl; if(slicevec.size()>1) { float slicedist=fabs(slicevec[1]-slicevec[0]); ODINLOG(odinlog,normalDebug) << "slicedist=" << slicedist << STD_endl; prot.geometry.set_sliceDistance(slicedist); } if(slicevec.size()>0) prot.geometry.set_offset(sliceDirection,0.5*(slicevec[0]+slicevec[slicevec.size()-1])); pdmap[prot].reference(data); // Finally, add data to protocol-data map imgmap.clear(); // save memory protindex++; } // end iterating over protocols ODINLOG(odinlog,normalDebug) << "mem(comb): " << Profiler::get_memory_usage() << STD_endl; return result; } ////////////////////////////////////////////////////////////////////////// int FileIO::autowrite(const ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts) { Log odinlog("FileIO","autowrite"); Range all=Range::all(); if(filename=="") { ODINLOG(odinlog,errorLog) << "Empty file name" << STD_endl; return -1; } FileFormatCreator ffc; FileFormat* ff=FileFormat::get_format(filename,opts.format); if(!ff) { FileFormat::format_error(filename); return -1; } if(opts.wprot!="") { svector protfnames=FileFormat::create_unique_filenames(opts.wprot, pdmap, opts.fnamepar); unsigned int ifile=0; for(ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) { ODINLOG(odinlog,loglevel()) << "Storing protocol in file " << protfnames[ifile] << STD_endl; pdit->first.write(protfnames[ifile]); ifile++; } } // local copy to avoid recursion FileWriteOpts opts_copy(opts); opts_copy.split=false; ODINLOG(odinlog,loglevel()) << "Writing format " << ff->description() << STD_endl; int result=0; if(opts.split) { svector splitfnames=FileFormat::create_unique_filenames(filename, pdmap, opts.fnamepar); unsigned int ifile=0; for(ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) { STD_string onefilename=splitfnames[ifile]; ODINLOG(odinlog,normalDebug) << "onefilename=" << onefilename << STD_endl; ProtocolDataMap mDummy; mDummy[pdit->first].reference(pdit->second); int writeresult=ff->write(mDummy, onefilename, opts_copy); if(writeresult<0) return -1; result+=writeresult; ODINLOG(odinlog,loglevel()) << "Wrote dataset to file " << onefilename << STD_endl; ifile++; } } else { result=ff->write(pdmap, filename, opts_copy); if(result<0) return -1; ODINLOG(odinlog,loglevel()) << "Wrote " << pdmap.size() << " dataset(s) to file " << filename << STD_endl; } return result; } ////////////////////////////////////////////////////////////// svector FileIO::autoformats() { Log odinlog("FileIO","autoread"); FileFormatCreator ffc; // for some reason, we needed a named object here instead of a plain constructor return FileFormat::possible_formats(); } ////////////////////////////////////////////////////////////// STD_string FileIO::autoformats_str(const STD_string& indent) { FileFormatCreator ffc; // for some reason, we needed a named object here instead of a plain constructor return FileFormat::formats_str(indent); } ////////////////////////////////////////////////////////////// bool FileIO::do_trace=true; STD_string FileFormat::selectDataType(const Protocol &prot,const FileWriteOpts& opts){ if(opts.datatype != AUTOTDATAYPESTR) return opts.datatype; else return prot.system.get_data_type(); } /////////////////////////////////////////////////////////////////////////////// // Unit Test #ifndef NO_UNIT_TEST ////////// General tests /////////////////////////////// class FileIOTest : public UnitTest { public: FileIOTest() : UnitTest("FileIO") {} private: bool check() const { Log odinlog(this,"check"); Range all=Range::all(); FileIO::set_trace_status(false); // disable logging to console // Testing whether files are sorted alphabetically according to their file name STD_string tmpdir(tempfile()); if(createdir(tmpdir.c_str())) return false; int testsize=16; Data testslice(1,1,testsize,testsize); int nfiles=22; for(int i=0; i testdirarr; if(testdirarr.autoread(tmpdir)<0) return false; TinyVector expected_shape(nfiles,1,testsize,testsize); if(testdirarr.shape()!=expected_shape) { ODINLOG(odinlog,errorLog) << "testdirarr.shape()=" << testdirarr.shape() << ", but expected " << expected_shape << STD_endl; return false; } for(int i=0; i1.0e-3) { ODINLOG(odinlog,errorLog) << "meanval(" << i << ")=" << meanval << ", but expected " << float(i) << STD_endl; return false; } } // Testing reading of complex data STD_string tmpfile(tempfile()+".float"); ComplexData<1> cdata(testsize); cdata=STD_complex(0.0,1.0); if(cdata.write(tmpfile)<0) return false; FileReadOpts opts; Data fdata; STD_map expected; expected["abs"]=1.0; expected["pha"]=0.5*PII; expected["real"]=0.0; expected["imag"]=1.0; for(STD_map::const_iterator it=expected.begin(); it!=expected.end(); ++it) { opts.cplx=it->first; if(fdata.autoread(tmpfile, opts)<0) return false; if(fdata.size()!=testsize) { ODINLOG(odinlog,errorLog) << "reading complex raw: size mismatch" << STD_endl; return false; } float meanval=mean(fdata); float expected=it->second; if(fabs(meanval-expected)>1.0e-3) { ODINLOG(odinlog,errorLog) << "reading complex raw: mean(" << opts.cplx.operator STD_string() << ")=" << meanval << ", but expected " << expected << STD_endl; return false; } } return true; } }; ////////// Format-specific tests /////////////////////////////// void create_fileio_testarr(Data& testarr, const TinyVector& shape) { testarr.resize(shape); testarr=0.0; for(int i=0; i indexvec=testarr.create_index(i); for(int j=0; j class FileIOFormatTest : public UnitTest { public: FileIOFormatTest(const STD_string& suff) : UnitTest(("FileIO "+suff).c_str()), suffix(suff) {} private: STD_string suffix; bool compare_arrays(const STD_string& test, const Data& a1, const Data& a2) const { Log odinlog(this,"compare_arrays"); if(a1.shape()!=a2.shape()) { ODINLOG(odinlog,errorLog) << test << " failed, shape mismatch:" << STD_endl; ODINLOG(odinlog,errorLog) << a1.shape() << " != " << a2.shape() << STD_endl; return false; } Data a1copy; a1.convert_to(a1copy); for(int i=0; i indexvec=a1.create_index(i); if(a1copy(indexvec)!=a2(indexvec)) { ODINLOG(odinlog,errorLog) << test << " failed, value mismatch at index " << indexvec << STD_endl; ODINLOG(odinlog,errorLog) << a1copy(indexvec) << " != " << a2(indexvec) << STD_endl; return false; } } return true; } bool check() const { Log odinlog(this,"check"); FileIO::set_trace_status(false); // disable logging to console STD_list > shapelst; shapelst.push_back(TinyVector(1,1,YSize,XSize)); if(!OnlyBitmap) { shapelst.push_back(TinyVector(3,4,YSize,XSize)); shapelst.push_back(TinyVector(1,4,YSize,XSize)); shapelst.push_back(TinyVector(3,1,YSize,XSize)); } for(STD_list >::const_iterator it=shapelst.begin(); it!=shapelst.end(); ++it) { FileReadOpts readopts; STD_string prefix(tempfile()); // separate name for each shape STD_string writefname=prefix+"."+suffix; STD_string readfname=writefname; if(ReadDir) { readfname=prefix+"_"+suffix; readopts.format=suffix; } Data testarr; create_fileio_testarr(testarr,*it); Data readdata; // simple write/read if(testarr.autowrite(writefname)<0) return false; if(readdata.autoread(readfname, readopts)<0) return false; if(!compare_arrays("autowrite/autoread("+readfname+")", testarr, readdata)) return false; // Testing whether geometry info is preserved if(!OnlyBitmap) { Protocol prot; Geometry& geo=prot.geometry; if(HasOrientation) { geo.set_orientation(-66.7, 78.2, -124.7); geo.set_offset(readDirection,22.7); geo.set_offset(phaseDirection,-5.9); geo.set_offset(sliceDirection,99.9); } geo.set_FOV(readDirection,192.6); geo.set_FOV(phaseDirection,200.2); geo.set_nSlices(testarr.extent(1)); geo.set_sliceDistance(6.1); if(HasSliceThick) { geo.set_sliceThickness(3.2); } else { geo.set_sliceThickness(6.1); // the same as slice distance } if(testarr.autowrite(writefname, FileWriteOpts(), &prot)<0) return false; Protocol readprot; if(readdata.autoread(readfname, readopts, &readprot)<0) return false; if(!compare_arrays("autowrite/autoread+geo("+readfname+")", testarr, readdata)) return false; Protocol protcopy(prot); // Create copy of protocol to use limited accuracy comparison of Protocol protcopy.geometry=readprot.geometry; // only geometry may differ if(!(prot==protcopy)) { // use limited accuracy comparison of Protocol ODINLOG(odinlog,errorLog) << "autowrite/autoread(geo)" << (*it) << " failed: prot.geometry=" << prot.geometry << "protcopy.geometry=" << protcopy.geometry << STD_endl; return false; } } } return true; } }; /////////////////////////////////////////////////////////////////////// void alloc_FileIOTest() { // create test instances new FileIOTest; new FileIOFormatTest<7, 13, double, false,false,true,true>("jdx"); #ifdef PNGSUPPORT new FileIOFormatTest<7, 13, u8bit, true,false,false,false>("png"); #endif #ifdef HAVE_LIBZ #ifndef STREAM_REPLACEMENT new FileIOFormatTest<7, 13, double, false,false,true,true>("jdx.gz"); #endif #endif #ifdef DICOMSUPPORT new FileIOFormatTest<16, 16, u16bit, false,true,true,true>("dcm"); // needs square matrix size #endif #ifdef NIFTISUPPORT new FileIOFormatTest<7, 13, double, false,false,true,false>("nii"); new FileIOFormatTest<7, 13, double, false,false,false,false>("hdr"); #ifdef HAVE_LIBZ #ifndef STREAM_REPLACEMENT new FileIOFormatTest<7, 13, double, false,false,true,false>("nii.gz"); #endif #endif #endif } #endif odin-1.8.5/odindata/filter_align.h0000644000175000017500000000271711322062337014000 00000000000000/*************************************************************************** filter_align.h - description ------------------- begin : Fri Jan 16 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_ALIGN_H #define FILTER_ALIGN_H #include class FilterAlign : public FilterStep { JDXfileName fname; JDXint blowup; STD_string label() const {return "align";} STD_string description() const {return "Align data to the geometry (voxel locations) of an external file";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterAlign();} void init(); }; #endif odin-1.8.5/odindata/filter_resize.cpp0000644000175000017500000000655711734622162014555 00000000000000#include "filter_resize.h" #include void FilterResize::init() { for(int i=0; i<3; i++) { newsize[i].set_description(STD_string(dataDimLabel[1+i])+"-size"); append_arg(newsize[i],"newsize"+itos(i)); } } bool FilterResize::process(Data& data, Protocol& prot) const { TinyVector oldshape(data.shape()); TinyVector newshape(data.shape()); for(int i=0; i<3; i++) newshape(1+i)=newsize[i]; data.congrid(newshape); // update stuff in the protocol after regridding prot.seqpars.set_MatrixSize(phaseDirection,newshape(phaseDim)); prot.seqpars.set_MatrixSize(readDirection,newshape(readDim)); if(prot.geometry.get_Mode()==slicepack) { prot.geometry.set_nSlices(newshape(sliceDim)); float distfactor=secureDivision(oldshape(sliceDim), newshape(sliceDim)); prot.geometry.set_sliceDistance(distfactor*prot.geometry.get_sliceDistance()); } else { prot.seqpars.set_MatrixSize(sliceDirection,newshape(sliceDim)); } return true; } //////////////////////////////////////////////////////////////////////////////// void FilterResample::init() { newsize.set_description("new size"); append_arg(newsize,"newsize"); } bool FilterResample::process(Data& data, Protocol& prot) const { TinyVector newshape(data.shape()); newshape(0)=newsize; data.congrid(newshape); // update stuff in the protocol after regridding prot.seqpars.set_NumOfRepetitions(newsize); return true; } //////////////////////////////////////////////////////////////////////////////// void FilterIsotrop::init() { size=0; size.set_description("voxelsize"); append_arg(size,"voxelsize"); } bool FilterIsotrop::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); Geometry &geo=prot.geometry; TinyVector shape(data.shape()),newshape=shape; TinyVector vox_mult; TinyVector vox_size( FileFormat::voxel_extent(geo,sliceDirection, shape(sliceDim)), FileFormat::voxel_extent(geo,phaseDirection, shape(phaseDim)), FileFormat::voxel_extent(geo,readDirection, shape(readDim)) ); float m; if(size!=0)m=size; else m=min(vox_size); vox_mult=vox_size/m; ODINLOG(odinlog,normalDebug) << "current voxel_size: " << vox_size << STD_endl; ODINLOG(odinlog,normalDebug) << "shape scaling vector: " << vox_mult << STD_endl; for(dataDim d=readDim;d>timeDim;d=dataDim(d-1)) newshape(d)=(int)(vox_mult(d-1)*shape(d)); ODINLOG(odinlog,normalDebug) << "new shape: " << newshape << STD_endl; data.congrid(newshape); //prevent update (called by set_nSlices) from overriding FOVslice switch(geo.get_Mode()){ case slicepack: geo.set_sliceThickness(m); geo.set_sliceDistance(m); break; case voxel_3d: geo.set_FOV(sliceDirection,m*newshape(sliceDim)); } // update stuff in the protocol after regridding geo.set_nSlices(newshape(sliceDim)); prot.seqpars.set_MatrixSize(phaseDirection,newshape(phaseDim)); prot.seqpars.set_MatrixSize(readDirection,newshape(readDim)); ODINLOG(odinlog,normalDebug) << "new voxel_size: " << TinyVector( FileFormat::voxel_extent(geo,sliceDirection, data.shape()(sliceDim)), FileFormat::voxel_extent(geo,phaseDirection, data.shape()(phaseDim)), FileFormat::voxel_extent(geo,readDirection, data.shape()(readDim))) << STD_endl; return true; } odin-1.8.5/odindata/data.h0000644000175000017500000010144011734622163012251 00000000000000/*************************************************************************** data.h - description ------------------- begin : Fri Apr 6 2001 copyright : (C) 2001 by Thies Jochimsen & Michael von Mengershausen email : jochimse@cns.mpg.de mengers@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef DATA_H #define DATA_H #ifndef TJUTILS_CONFIG_H #define TJUTILS_CONFIG_H #include #endif #include #ifdef ODIN_DEBUG #define BZ_DEBUG #endif #include // include 1st to overwrite mutex defines // undef mutex defines #ifdef BZ_MUTEX_DECLARE #undef BZ_MUTEX_DECLARE #endif #ifdef BZ_MUTEX_INIT #undef BZ_MUTEX_INIT #endif #ifdef BZ_MUTEX_LOCK #undef BZ_MUTEX_LOCK #endif #ifdef BZ_MUTEX_UNLOCK #undef BZ_MUTEX_UNLOCK #endif #ifdef BZ_MUTEX_DESTROY #undef BZ_MUTEX_DESTROY #endif // do not use mutex in Blitz, even if pthread is available // to get consistent behaviour across all platforms #define BZ_MUTEX_DECLARE(name) #define BZ_MUTEX_INIT(name) #define BZ_MUTEX_LOCK(name) #define BZ_MUTEX_UNLOCK(name) #define BZ_MUTEX_DESTROY(name) #include #include // to use arithmetics of TinyVectors using namespace blitz; #include #include #include #include #include // some additional macros for complex numbers BZ_DECLARE_FUNCTION_RET (float2real, STD_complex); BZ_DECLARE_FUNCTION_RET (float2imag, STD_complex); BZ_DECLARE_FUNCTION_RET (creal, float) BZ_DECLARE_FUNCTION_RET (cimag, float) BZ_DECLARE_FUNCTION_RET (cabs, float) BZ_DECLARE_FUNCTION_RET (phase, float) BZ_DECLARE_FUNCTION (logc) BZ_DECLARE_FUNCTION (expc) BZ_DECLARE_FUNCTION (conjc) // Other useful macros BZ_DECLARE_FUNCTION2(secureDivision) BZ_DECLARE_FUNCTION (secureInv) #ifdef STL_REPLACEMENT BZ_DECLARE_ARRAY_ET_SCALAR_OPS(tjstd_complex) #endif /** * @addtogroup odindata * @{ */ /////////////////////////////////////////////////////// struct FileMapHandle { FileMapHandle() : fd(-1), offset(0), refcount(1) {} int fd; LONGEST_INT offset; // in bytes int refcount; Mutex mutex; // protect refcount }; /////////////////////////////////////////////////////// /** * This template class holds multidimensional data. In addition to functionality * provided by the Blitz Array class, it offers methods to read/write raw data * and and other file formats (nifti, vtk, ...) to/from a file. * In addition, uing a special constructor, the array can be associated with a block * of data on disk using the UNIX mmap functionality. In this case, any changes made * to the array will be automatically tranfered to the file. Please note that any * attempt to resize such an array will most likely cause a segmentation fault. * */ template class Data : public Array { public: /** * Constructs an array with the given dimensionality and initial value */ Data(const TinyVector& dimvec, const T& val=0) : Array(dimvec), fmap(0) {(*this)=val;} // Variable extent constructors Data() : fmap(0) {} Data(int extent1) : Array(extent1), fmap(0) {} Data(int extent1, int extent2) : Array(extent1,extent2), fmap(0) {} Data(int extent1, int extent2,int extent3) : Array(extent1,extent2,extent3), fmap(0) {} Data(int extent1, int extent2,int extent3,int extent4) : Array(extent1,extent2,extent3,extent4), fmap(0) {} Data(int extent1, int extent2,int extent3,int extent4,int extent5) : Array(extent1,extent2,extent3,extent4,extent5), fmap(0) {} Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6) : Array(extent1,extent2,extent3,extent4,extent5,extent6), fmap(0) {} Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7) : Array(extent1,extent2,extent3,extent4,extent5,extent6,extent7), fmap(0) {} Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7,int extent8) : Array(extent1,extent2,extent3,extent4,extent5,extent6,extent7,extent8), fmap(0) {} Data(int extent1, int extent2,int extent3,int extent4,int extent5,int extent6,int extent7,int extent8,int extent9) : Array(extent1,extent2,extent3,extent4,extent5,extent6,extent7,extent8,extent9), fmap(0) {} /** * Maps the given file 'filename' into the newly created array via the the mmap function, * see the mmap man page for details. The mapping is abolish when the * array is destroyed (destructor). Other parameters: * - readonly : If true, file can only be read. If false, the file will be created if it does not exist * - shape : The extent in each dimension * - offset : Skip first 'offset' bytes */ Data(const STD_string& filename, bool readonly, const TinyVector& shape, LONGEST_INT offset=0 ); /** * Copy constructor */ Data(const Data& d) : fmap(0) {Data::reference(d);} /** * Copy constructor from Blitz::Array */ Data(const Array& a) : Array(a), fmap(0) {} /** * Constructor from an equivalent tjarray (\ref arrays). If rank of 'a' is smaller, extent will pe padded with 1 at front. */ Data(const tjarray,T>& a) : fmap(0) { (*this)=a;} /** * Constructor from expression template */ template Data(BZ_ETPARM(_bz_ArrayExpr) expr) : Array(expr), fmap(0) {} /** * Destructor */ ~Data(); /** * Assignment operator */ Data& operator = (const Data& d) {Array::operator=(d); return *this;} /** * Assignment operator from Blitz::Array */ Data& operator = (const Array& a) {Array::operator=(a); return *this;} /** * Fills all elements with 'val' */ Data& operator = (const T& val) {Array::operator=(val); return *this;} /** * Assignment operator for expression templates */ template inline Data& operator = (BZ_ETPARM(_bz_ArrayExpr) expr) { typedef _bz_typename T_expr::T_numtype T_numtype; evaluate(expr, _bz_update()); return *this; } /** * Assignment from an equivalent tjarray (\ref arrays). If rank of 'a' is smaller, extent will pe padded with 1 at front. */ Data& operator = (const tjarray,T>& a); // resolve ambiguities Array operator + (const Data& b) const {return Array(Array(*this)+Array(b));} Array operator - (const Data& b) const {return Array(Array(*this)-Array(b));} Array operator * (const Data& b) const {return Array(Array(*this)*Array(b));} Array operator / (const Data& b) const {return Array(Array(*this)/Array(b));} // resolve ambiguities Array operator + (const T& v) const {return Array(Array(*this)+v);} Array operator - (const T& v) const {return Array(Array(*this)-v);} Array operator * (const T& v) const {return Array(Array(*this)*v);} Array operator / (const T& v) const {return Array(Array(*this)/v);} /** * Reads the array from a raw data file 'filename' of type 'format' which can be one of * 's8bit, u8bit, s16bit, u16bit, s32bit, u32bit, float or double'. * No resizing is performed prior to reading. Skip the first 'offset' bytes. * - Return value: 0 if succesful, otherwise -1 */ int read(const STD_string& format,const STD_string& filename, LONGEST_INT offset=0); /** * Reads the array from a raw data file 'filename' of type 'T2'. * No resizing is performed prior to reading. Skip the first 'offset' bytes. * - Return value: 0 if succesful, otherwise -1 */ template int read(const STD_string& filename, LONGEST_INT offset=0); /** * Writes the array to a raw data file 'filename' of type 'format' which can be one of * 's8bit, u8bit, s16bit, u16bit, s32bit, u32bit, float or double'. * - Return value: 0 if succesful, otherwise -1 */ int write(const STD_string& format,const STD_string& filename, autoscaleOption scaleopt=autoscale) const; /** * Writes the array to a raw data file 'filename' of type 'T2'. * - Return value: 0 if succesful, otherwise -1 */ template int write(const STD_string& filename, autoscaleOption scaleopt=autoscale) const; /** * Writes the array to a raw data file 'filename' of type the same type as the array is. *The mode specifies whether an already existing file is overwritten, or the data is appended. * - Return value: 0 if succesful, otherwise -1 */ int write(const STD_string& filename, fopenMode mode=overwriteMode) const; /** * Writes the array as a formatted ASCII file to * 'filename', one value per line. If 'pre' is * of the same size as this, its values are * inserted before the value on each line, * and the values of 'post' are inserted after * the values of this array on each line. * Return value is -1 if an error occurs. */ int write_asc_file(const STD_string& filename, const Array& pre=defaultArray, const Array& post=defaultArray) const; /** * reads in white-space separated data from ASCII file, no resizing is performed prior to reading * Return value is -1 if an error occurs. */ int read_asc_file(const STD_string& filename); /** * Writes data set to file 'filename' in the format automatically detected by the given file extension. * Extra options can be given by 'opts' and protocol settings can be overwritten by 'prot'. * Returns number of slices, or -1 if it fails. */ int autowrite(const STD_string& filename, const FileWriteOpts& opts=FileWriteOpts(), const Protocol* prot=0) const; /** * Reads data set from file 'filename' assuming the format automatically detected by the given file extension. * Extra options can be given by 'opts' and protocol settings will be stored in 'prot'. * The progress meter 'progmeter' can be optionally specified to monitor the progress of the operation. * Returns number of slices sucessfully read, or -1 if it fails. */ int autoread(const STD_string& filename, const FileReadOpts& opts=FileReadOpts(), Protocol* prot=0, ProgressMeter* progmeter=0); /** * Returns true if the array is associated with a file on disk */ bool is_filemapped() const {return fmap;} /** * Exports this array into an equivalent tjarray (\ref arrays) */ operator tjarray,T> () const; /** * Creates an index vector according to a linear index for the whole array * by taking the shape into account. */ TinyVector create_index(unsigned long index) const; /** * Creates a linear index from an index vector */ unsigned long create_linear_index(const TinyVector& indexvec) const; /** * Shift the data by 'shift' pixels in dimension 'shift_dim'. The * data is shifted cyclically, i.e. the values which are shifted * out at one edge of the array will be shifted in on the other edge. */ void shift(unsigned int shift_dim, int shift); /** * Interpolate (or extrapolate) the data in the array to the new shape. * The interpolation is performed dimension-by-dimension using the GSL spline interpolation * routines. * Add extra shift 'subpixel_shift' in units of pixels on the destination grid if 'subpixel_shift' is non-null. * if 'left_to_right' is set to true, interpolation starts at the most left * dimension, i.e. at those with the highest index, down to the lowest index. * If set to false, interpolation is performed vice versa. */ void congrid(const TinyVector& newshape, const TinyVector* subpixel_shift=0, bool left_to_right=false); /** * Converts the array to type 'T2', with dimensionality 'N_rank2' and stores the result in 'dst'. * The scaling strategy can be specified by 'scaleopt'. * 'dst' will be unique, i.e. no other references to the array exist. * In addition to changing 'dst', a reference to the same array is returned for convenience. */ template Data& convert_to(Data& dst, autoscaleOption scaleopt=autoscale) const; // specialization which uses reference if type/rank are same and scale/offset==0.0 to reduce memory usage Data& convert_to(Data& dst, autoscaleOption scaleopt=autoscale) const; /** * Makes array unique and continuous and returns pointer to data */ T* c_array(); // Reimplemented Blitz::Array functions void reference(const Data& d); // dummy objects used for default arguments static Array defaultArray; private: void interpolate1dim(unsigned int dim, int newsize, float subpixel_shift); void detach_fmap(); FileMapHandle* fmap; }; template Array Data::defaultArray; /** @} */ /////////////////////////////////////////////////////////////////////////////// #ifdef STREAM_REPLACEMENT template inline STD_ostream& operator << (STD_ostream& s,const Array&) {return s;} template inline STD_ostream& operator << (STD_ostream& s,const TinyVector&) { return s;} inline STD_ostream& operator << (STD_ostream& s,const Range&) { return s;} #endif /////////////////////////////////////////////////////////////////////////////// /* * Create n-dim index from linear 'index' for a given 'shape' */ template TinyVector index2extent(const TinyVector& shape, unsigned int index) { TinyVector result; unsigned int temp=index; for(int i=N_rank-1;i>=0;i--){ result(i)=temp%shape(i); temp=temp/shape(i); } return result; } /////////////////////////////////////////////////////////////////////////////// // leave this function outside of class Data, otherwise it screws up // when using optimization template void convert_from_ptr(Data& dst, const T2* src, const TinyVector& shape, autoscaleOption scaleopt=autoscale) { Log odinlog("Data","convert_from_ptr"); int dstsize=product(shape); int srcsize=dstsize*Converter::get_elements((T)0)/Converter::get_elements((T2)0); ODINLOG(odinlog,normalDebug) << "dstsize/srcsize=" << dstsize << "/" << srcsize << STD_endl; dst.resize(shape); Converter::convert_array(src, dst.c_array(), srcsize, dstsize, scaleopt); } // specialization in case the type is the same template void convert_from_ptr(Data& dst, const T* src, const TinyVector& shape) { dst.reference(Array((T*)src, shape, duplicateData)); } //////////////////////////////////////////////////////////////////////////// template Data::Data(const STD_string& filename, bool readonly, const TinyVector& shape, LONGEST_INT offset ) : fmap(new FileMapHandle) { T* ptr=(T*)filemap(filename, (LONGEST_INT)product(shape)*sizeof(T), offset, readonly, fmap->fd); if(ptr && (fmap->fd)>=0) { // only negative file descriptor indicates filemap failure Array::reference(Array(ptr, shape, neverDeleteData)); fmap->offset=offset; } else { delete fmap; fmap=0; } } //////////////////////////////////////////////////////////////////////////// template void Data::detach_fmap() { Log odinlog("Data","detach_fmap"); if(fmap) { fmap->mutex.lock(); (fmap->refcount)--; ODINLOG(odinlog,normalDebug) << "fd/offset/refcount=" << fmap->fd << "/" << fmap->offset << "/" << fmap->refcount << STD_endl; if(!(fmap->refcount)) { fileunmap(fmap->fd, Array::data(), (LONGEST_INT)Array::size()*sizeof(T), fmap->offset); fmap->mutex.unlock(); delete fmap; fmap=0; } if(fmap) fmap->mutex.unlock(); } } //////////////////////////////////////////////////////////////////////////// template Data::~Data() { detach_fmap(); } //////////////////////////////////////////////////////////////////////////// template void Data::reference(const Data& d) { Log odinlog("Data","reference"); detach_fmap(); fmap=d.fmap; if(fmap) { MutexLock lock(fmap->mutex); (fmap->refcount)++; ODINLOG(odinlog,normalDebug) << "fmap->refcount=" << fmap->refcount << STD_endl; } Array::reference(d); } //////////////////////////////////////////////////////////////////////////// template Data& Data::operator = (const tjarray,T>& a) { Log odinlog("Data","="); if( a.dim() <= N_rank ) { ndim nn=a.get_extent(); int npad=N_rank-nn.dim(); ODINLOG(odinlog,normalDebug) << "npad=" << npad << STD_endl; for(int ipad=0; ipad tv; for(unsigned int i=0; i (filename); if(format==TypeTraits::type2label((s8bit)0)) return read (filename); if(format==TypeTraits::type2label((u16bit)0)) return read(filename); if(format==TypeTraits::type2label((s16bit)0)) return read(filename); if(format==TypeTraits::type2label((u32bit)0)) return read(filename); if(format==TypeTraits::type2label((s32bit)0)) return read(filename); if(format==TypeTraits::type2label((float)0)) return read (filename); if(format==TypeTraits::type2label((double)0)) return read(filename); ODINLOG(odinlog,errorLog) << "Unable to read file " << filename << " with data type " << format << STD_endl; return -1; } //////////////////////////////////////////////////////////////////////////// template template int Data::read(const STD_string& filename, LONGEST_INT offset) { Log odinlog("Data","read"); LONGEST_INT fsize=filesize(filename.c_str())-offset; LONGEST_INT nelements_file=fsize/sizeof(T2); LONGEST_INT length=product(Array::shape()); ODINLOG(odinlog,normalDebug) << "fsize / nelements_file / length = " << fsize << " / " << nelements_file << " / " << length << STD_endl; if(!length) return 0; if(nelements_file fileshape(Array::shape()); fileshape(N_rank-1) *= (Converter::get_elements((T)0)/Converter::get_elements((T2)0)); // Adjust extent of last dim for copmlex data Data filedata(filename, true, fileshape, offset); filedata.convert_to(*this); return 0; } //////////////////////////////////////////////////////////////////////////// template int Data::write(const STD_string& format, const STD_string& filename, autoscaleOption scaleopt) const { Log odinlog("Data","write"); if(format==TypeTraits::type2label((u8bit)0)) return write (filename,scaleopt); if(format==TypeTraits::type2label((s8bit)0)) return write (filename,scaleopt); if(format==TypeTraits::type2label((u16bit)0)) return write(filename,scaleopt); if(format==TypeTraits::type2label((s16bit)0)) return write(filename,scaleopt); if(format==TypeTraits::type2label((u32bit)0)) return write(filename,scaleopt); if(format==TypeTraits::type2label((s32bit)0)) return write(filename,scaleopt); if(format==TypeTraits::type2label((float)0)) return write (filename,scaleopt); if(format==TypeTraits::type2label((double)0)) return write(filename,scaleopt); ODINLOG(odinlog,errorLog) << "Unable to write file " << filename << " with data type " << format << STD_endl; return -1; } //////////////////////////////////////////////////////////////////////////// template int Data::write(const STD_string& filename, fopenMode mode) const { Log odinlog("Data","write"); if(filename=="") return 0; FILE* file_ptr=FOPEN(filename.c_str(),modestring(mode)); if(file_ptr==NULL) { ODINLOG(odinlog,errorLog) << "unable to create/open file >" << filename << "< - " << lasterr() << STD_endl; return -1; } Data data_copy(*this); // for contig memory LONGEST_INT nmemb=Array::numElements(); LONGEST_INT count=fwrite(data_copy.c_array(),sizeof(T),nmemb,file_ptr); if(count!=nmemb) { ODINLOG(odinlog,errorLog) << "unable to fwrite to file >" << filename << "< - " << lasterr() << STD_endl; return -1; } if(file_ptr!=NULL) fclose(file_ptr); return 0; } //////////////////////////////////////////////////////////////////////////// template template int Data::write(const STD_string& filename, autoscaleOption scaleopt) const { Log odinlog("Data","write"); rmfile(filename.c_str()); // remove old file to get new file size with mmap ODINLOG(odinlog,normalDebug) << "mem(pre): " << Profiler::get_memory_usage() << STD_endl; Data converted_data; convert_to(converted_data,scaleopt); ODINLOG(odinlog,normalDebug) << "mem(cnv): " << Profiler::get_memory_usage() << STD_endl; Data filedata(filename,false,converted_data.shape()); ODINLOG(odinlog,normalDebug) << "mem(map): " << Profiler::get_memory_usage() << STD_endl; filedata=converted_data; return 0; } //////////////////////////////////////////////////////////////////////////// template int Data::write_asc_file(const STD_string& filename, const Array& pre, const Array& post) const { bool have_pre=false; bool have_post=false; Data pre_data(pre); Data post_data(post); int n=Array::numElements(); if(pre_data.numElements()==n) have_pre=true; if(post_data.numElements()==n) have_post=true; STD_ofstream ofs(filename.c_str()); if(ofs.bad()) return -1; T val; for(int i=0; i int Data::read_asc_file(const STD_string& filename) { STD_ifstream ifs(filename.c_str()); if(ifs.bad()) return -1; STD_string valstr; for(int i=0; i::numElements(); i++) { if(ifs.bad()) return -1; ifs >> valstr; TypeTraits::string2type(valstr,(*this)(create_index(i))); } ifs.close(); return 0; } //////////////////////////////////////////////////////////////////////////// // Interface to FileIO functionality int fileio_autowrite(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol* prot); int fileio_autoread(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol* prot, ProgressMeter* progmeter); template int Data::autowrite(const STD_string& filename, const FileWriteOpts& opts, const Protocol* prot) const { Data filedata; convert_to(filedata); return fileio_autowrite(filedata, filename, opts, prot); } template int Data::autoread(const STD_string& filename, const FileReadOpts& opts, Protocol* prot, ProgressMeter* progmeter) { Data filedata; int result=fileio_autoread(filedata, filename, opts, prot, progmeter); if(result>0) filedata.convert_to(*this); return result; } //////////////////////////////////////////////////////////////////////////// template Data::operator tjarray,T> () const { tjarray,T> a; ndim nn(N_rank); for(unsigned int i=0; i::extent(i); a.redim(nn); for(unsigned int i=0;i template Data& Data::convert_to(Data& dst, autoscaleOption scaleopt) const { Log odinlog("Data","convert_to"); TinyVector newshape; newshape=1; for(int i=0; i<(N_rank-N_rank2+1); i++) { // collapse extra dims into first dim of new shape, including first dim int srcindex=i; if(srcindex>=0 && srcindex::extent(srcindex); } for(int i=0; i<(N_rank2-1); i++) { // Fill new shape with extents of original dim, except for the first dim int srcindex=N_rank-N_rank2+1+i; if(srcindex>=0 && srcindex::extent(srcindex); } // modify last dimension to account for different element sizes newshape(N_rank2-1)=newshape(N_rank2-1)*Converter::get_elements((T)0)/Converter::get_elements((T2)0); dst.resize(newshape); // dst will be unique now Data src_copy(*this); // make read/write copy of this Converter::convert_array(src_copy.c_array(), dst.c_array(), src_copy.numElements(), dst.numElements(), scaleopt); return dst; } // specialization which uses reference if type/rank are same and no scaling is necessary to reduce memory usage template Data& Data::convert_to(Data& dst, autoscaleOption scaleopt) const { Log odinlog("Data","convert_to"); if(scaleopt==noscale || !std::numeric_limits::is_integer) { ODINLOG(odinlog,normalDebug) << "Using reference" << STD_endl; dst.reference(*this); } else { Data src_copy(*this); // make read/write copy of this dst.resize(src_copy.shape()); // dst will be unique now Converter::convert_array(src_copy.c_array(), dst.c_array(), src_copy.numElements(), dst.numElements(), scaleopt); } return dst; } //////////////////////////////////////////////////////////////////////////// template TinyVector Data::create_index(unsigned long index) const { return index2extent(Array::shape(), index); } //////////////////////////////////////////////////////////////////////////// template unsigned long Data::create_linear_index(const TinyVector& indexvec) const { unsigned long totalIndex=0,subsize; TinyVector nn(Array::extent()); for(unsigned long i=0;i void Data::shift(unsigned int shift_dim, int shift) { Log odinlog("Data","shift"); if(!shift) return; if( shift_dim >= N_rank ){ ODINLOG(odinlog,errorLog) << "shift dimension(" << shift_dim << ") >= rank of data (" << N_rank << ") !\n"; return; } int shift_extent=Array::extent(shift_dim); int abs_shift=abs(shift); if(shift_extent < abs_shift){ ODINLOG(odinlog,errorLog) << "extent(" << shift_extent << ") less than shift(" << abs_shift << ") !\n"; return; } Data data_copy(Array::copy()); TinyVector index; for(int i=0; i::numElements(); i++) { index=create_index(i); T val=data_copy(index); int shiftindex=index(shift_dim)+shift; if(shiftindex>=shift_extent) shiftindex-=shift_extent; if(shiftindex<0) shiftindex+=shift_extent; index(shift_dim)=shiftindex; (*this)(index)=val; } } //////////////////////////////////////////////////////////////////////////// template void Data::congrid(const TinyVector& newshape, const TinyVector* subpixel_shift, bool left_to_right) { Log odinlog("Data","congrid"); for(int i=0;i::shape()(dim) && subpixel_shift==0.0) { ODINLOG(odinlog,normalDebug) << "interpolation not required" << STD_endl; return; } if(dim>=N_rank) { ODINLOG(odinlog,errorLog) << "dim is larger than N_rank" << STD_endl; return; } if(newsize<0) { ODINLOG(odinlog,errorLog) << "newsize is negative" << STD_endl; return; } Array olddata(*this); olddata.makeUnique(); TinyVector oldshape(olddata.shape()); int oldsize=oldshape(dim); TinyVector newshape(oldshape); newshape(dim)=newsize; resize(newshape); // This holds the the shape of the subspace which is orthogonal to direction 'dim' TinyVector ortho_shape(oldshape); ortho_shape(dim)=1; // The total number of elements in the orthogonal subspace unsigned long n_ortho=product(ortho_shape); ODINLOG(odinlog,normalDebug) << "n_ortho=" << n_ortho << STD_endl; TinyVector indexvec; T* oldoneline=new T[oldsize]; for(unsigned long iortho=0; iortho(ortho_shape,iortho); for(int j=0; j T* Data::c_array() { Log odinlog("Data","c_array"); bool need_copying=false; // check storage order TinyVectorord=Array::ordering(); for(int i=0; i::isRankStoredAscending(i)) need_copying=true; } // check for slicing if(!Array::isStorageContiguous()) need_copying=true; if(need_copying) { ODINLOG(odinlog,normalDebug) << "need_copying" << STD_endl; Data tmp(Array::shape()); tmp=(*this); // reference(copy()) would not be enough since it would preserve ordering reference(tmp); } return Array::data(); } #endif odin-1.8.5/odindata/fileio_gzip.cpp0000644000175000017500000001460411322062337014172 00000000000000#include "fileio.h" /* this based on the minigz-example by Jean-loup Gailly of the zlib distribution so hail him :-) (and see below for copyright notice) */ /* zlib.h -- interface of the 'zlib' general purpose compression library version 1.2.3, July 18th, 2005 Copyright (C) 1995-2005 Jean-loup Gailly and Mark Adler This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu The data format used by the zlib library is described by RFCs (Request for Comments) 1950 to 1952 in the files http://www.ietf.org/rfc/rfc1950.txt (zlib format), rfc1951.txt (deflate format) and rfc1952.txt (gzip format). */ #ifdef HAVE_LIBZ #ifndef STREAM_REPLACEMENT #include #include struct GzipFormat : public FileFormat { STD_string description() const {return "GNU-Zip container for other formats";} svector suffix() const { svector result; result.resize(1); result[0]="gz"; return result; } svector dialects() const {return svector();} bool gz_compress(STD_ifstream &in, gzFile out) { Log odinlog("GzipFormat","gz_compress"); char *buf = new char[2048*1024]; int len; int err; bool ret=true; try { for ( in.read(buf, 2048*1024); (len = in.gcount()); in.read(buf, 2048*1024) ) { if (gzwrite(out, buf, len) != len) { ODINLOG(odinlog,errorLog) << gzerror(out, &err) << STD_endl; return false; } } if (in.bad()) { ODINLOG(odinlog,errorLog) <<"file read" << STD_endl;return false; } } catch(...) { delete[] buf; throw; } delete buf; return ret; } bool file_compress(STD_string infile, STD_string outfile) { Log odinlog("GzipFormat","file_compress"); STD_ifstream in(infile.c_str(), ios::binary); if (in == NULL) { ODINLOG(odinlog,errorLog) << infile.c_str() << STD_endl; return false; } gzFile out = gzopen(outfile.c_str(), "wb"); if (out == NULL) { ODINLOG(odinlog,errorLog) << "gzopen " << outfile << " failed" << STD_endl; return false; } bool ret=gz_compress(in, out); if (gzclose(out) != Z_OK) { ODINLOG(odinlog,errorLog) << "gzclose " << outfile << " failed" << STD_endl; return false; } else return ret; } bool gz_uncompress(gzFile in, STD_ofstream &out) { Log odinlog("GzipFormat","gz_uncompress"); char *buf=new char[2048*1024]; int len; int err; try { for ( len = gzread(in, buf, 2048*1024); len; len = gzread(in, buf, 2048*1024) ) { if (len < 0){ODINLOG(odinlog,errorLog) << gzerror(in, &err) << STD_endl;return false;} else { out.write(buf,len); if (out.bad()) {ODINLOG(odinlog,errorLog) << "file write" << STD_endl;return false;} } } } catch(...) { delete[] buf; throw; } delete[] buf; return true; } bool file_uncompress(STD_string infile,STD_string outfile) { Log odinlog("GzipFormat","file_uncompress"); gzFile in = gzopen(infile.c_str(), "rb"); if (in == NULL) { ODINLOG(odinlog,errorLog) << "gzopen " << infile << " failed" << STD_endl; return false; } STD_ofstream out(outfile.c_str(), ios::binary); if (out.bad()) { ODINLOG(odinlog,errorLog) << infile.c_str() << STD_endl; return false; } bool ret=gz_uncompress(in, out); if (gzclose(in) != Z_OK) { ODINLOG(odinlog,errorLog) << "gclose " << outfile << " failed" << STD_endl; return false; } return ret; } static STD_string tempfilename(STD_string filename) { const STD_string unzipped_suffix=JDXfileName(JDXfileName(filename).get_basename_nosuffix()).get_suffix(); return tempfile()+"."+unzipped_suffix; } int read(FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template) { Log odinlog("GzipFormat","read"); const STD_string tmpfile=tempfilename(filename); ODINLOG(odinlog,normalDebug) << "tmpfile=" << tmpfile << STD_endl; if(file_uncompress(filename,tmpfile)) { bool tracestat_cache=FileIO::get_trace_status(); FileIO::set_trace_status(false); // disable temporarily int result=FileIO::autoread(pdmap, tmpfile, opts, protocol_template); FileIO::set_trace_status(tracestat_cache); rmfile(tmpfile.c_str()); return result; } else { return -1; } } int write(const FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts) { Log odinlog("GzipFormat","write"); const STD_string tmpfile=tempfilename(filename); ODINLOG(odinlog,normalDebug) << "tmpfile=" << tmpfile << STD_endl; bool tracestat_cache=FileIO::get_trace_status(); FileIO::set_trace_status(false); // disable temporarily int result=FileIO::autowrite(pdmap, tmpfile, opts); FileIO::set_trace_status(tracestat_cache); if(result>=0) { if(file_compress(tmpfile,filename)) { rmfile(tmpfile.c_str()); } else { const JDXfileName fname(filename); STD_string realname = fname.get_dirname() + SEPARATOR_STR +fname.get_basename_nosuffix(); ODINLOG(odinlog,infoLog) << " saving " << realname << STD_endl; movefile(tmpfile.c_str(), realname.c_str()); } } return result; } }; #endif #endif ////////////////////////////////////////////////////////////// void register_gzip_format() { #ifdef HAVE_LIBZ #ifndef STREAM_REPLACEMENT static GzipFormat gf; gf.register_format(); #endif #endif } odin-1.8.5/odindata/filter_splice.cpp0000644000175000017500000000556311725203122014516 00000000000000#include "filter_splice.h" #include "filter.h" void FilterSplice::init() { for(int i=0; i odinlog(c_label(),"process"); if(dir=="none") { ODINLOG(odinlog,errorLog) << "no dimension given for splice" << STD_endl; return false; } FileIO::ProtocolDataMap spliced_pdmap; for(FileIO::ProtocolDataMap::const_iterator it=pdmap.begin();it!=pdmap.end();it++) { const Protocol& prot=it->first; const Data& data=it->second; STD_string serDesc; int serNum; prot.study.get_Series(serDesc,serNum); if(serDesc!="") serDesc+="_"; TinyVector shape(data.shape()); int nsplice = shape(dir); TinyVector newshape(shape); newshape(dir)=1; direction protdir=direction(3-dir); dvector offsetvec; if(dir==sliceDim && prot.geometry.get_Mode()==slicepack) offsetvec=prot.geometry.get_sliceOffsetVector(); // better accuracy in slicepack mode float origoffset=0.0; float voxelsize=0.0; if(dir!=timeDim) { origoffset=prot.geometry.get_offset(protdir); voxelsize=FileFormat::voxel_extent(prot.geometry, protdir, nsplice); ODINLOG(odinlog,normalDebug) << "origoffset/voxelsize=" << origoffset << "/" << voxelsize << STD_endl; } for(int isplice=0; isplice spliced(newshape); TinyVector lowerBounds; TinyVector upperBounds; for(int i=0; i<4; i++) { lowerBounds(i)=0; upperBounds(i)=shape(i)-1; } lowerBounds(dir)=upperBounds(dir)=isplice; spliced=data(RectDomain<4>(lowerBounds, upperBounds)); // Adjust series description protcopy.study.set_Series(serDesc+dataDimLabel[dir]+itos(isplice,nsplice-1),serNum); // Adjusting protocol if(dir==timeDim) { protcopy.seqpars.set_NumOfRepetitions(1); protcopy.seqpars.set_AcquisitionStart(prot.seqpars.get_AcquisitionStart()+isplice*prot.seqpars.get_RepetitionTime()); } else { if(dir==sliceDim) protcopy.geometry.set_nSlices(1); protcopy.seqpars.set_MatrixSize(protdir,1); protcopy.geometry.set_FOV(protdir,voxelsize); if(offsetvec.size()) { protcopy.geometry.set_offset(protdir, offsetvec[isplice]); } else { float ioffset=float(isplice)-0.5*float(nsplice-1); protcopy.geometry.set_offset(protdir, origoffset+ioffset*voxelsize); } } spliced_pdmap[protcopy].reference(spliced); } } pdmap=spliced_pdmap; return true; } odin-1.8.5/odindata/fileio_nifti.cpp0000644000175000017500000003624011322062337014332 00000000000000#include "fileio.h" #include "filter.h" #ifdef NIFTISUPPORT #include ///////////////////////////////////////////////////////////// struct NiftiFormat : public FileFormat{ STD_string description() const {return "NIFTI/ANALYZE";} svector suffix() const{ svector result; result.resize(2); result[0]="nii"; result[1]="hdr"; return result; } svector dialects() const{ svector result; result.resize(1); result[0]="fsl"; return result; } float read_orientation(const nifti_image &ni,Geometry &geometry, const FileReadOpts& opts) { Log odinlog("NiftiFormat","read_orientation"); float spatscale=1.0; if(ni.xyz_units==NIFTI_UNITS_METER) spatscale=1.0e3; if(ni.xyz_units==NIFTI_UNITS_MICRON) spatscale=1.0e-3; //@todo check me geometry.set_FOV(readDirection,ni.dx*spatscale*ni.dim[1]); geometry.set_FOV(phaseDirection,ni.dy*spatscale*ni.dim[2]); geometry.set_sliceThickness(ni.dz*spatscale); geometry.set_sliceDistance(ni.dz*spatscale); //no interslice distance in nifti - so use thickness geometry.set_nSlices(ni.dim[3]); if(ni.nifti_type>0) { // only for non-ANALYZE dvector readvec(3),phasevec(3),slicevec(3),centervec(3); // RotMatrix scaleMat;//method 2 if(ni.qform_code>0) {// just tranform to the nominal space of the scanner ODINLOG(odinlog,normalDebug) << "Reading orientation from qform" << STD_endl; for(unsigned short i=0;i<3;i++) { readvec[i] =ni.qto_xyz.m[i][0]/ni.dx; phasevec[i] =ni.qto_xyz.m[i][1]/ni.dy; slicevec[i] =ni.qto_xyz.m[i][2]/ni.dz; centervec[i]=ni.qto_xyz.m[i][3]*spatscale; } } else if(ni.sform_code>0) { // method 3 ODINLOG(odinlog,normalDebug) << "Reading orientation from sform" << STD_endl; for(unsigned short i=0;i<3;i++) { readvec[i] =ni.sto_xyz.m[i][0]/ni.dx; phasevec[i] =ni.sto_xyz.m[i][1]/ni.dy; slicevec[i] =ni.sto_xyz.m[i][2]/ni.dz; centervec[i]=ni.sto_xyz.m[i][3]*spatscale; } } else { ODINLOG(odinlog,infoLog) << "can't read Orientation"<< STD_endl; } const dvector ivector =//diagonale trougth the image in "normal" space (geometry.get_FOV(readDirection)-ni.dx)*readvec+ (geometry.get_FOV(phaseDirection)-ni.dy)*phasevec+ (geometry.get_FOV(sliceDirection)-ni.dz)*slicevec; centervec+=ivector/2; ODINLOG(odinlog,normalDebug) << "FOV read/phase/slice:"<< geometry.get_FOV(readDirection) << "/" << geometry.get_FOV(phaseDirection) << "/" << geometry.get_FOV(sliceDirection) << STD_endl; ODINLOG(odinlog,normalDebug) << "readvec:" << readvec.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "phasevec:"<< phasevec.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "slicevec:"<< slicevec.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "image diagonale "<< ivector.printbody() <<"/" << sqrt(ivector[0]*ivector[0]+ivector[1]*ivector[1]+ivector[2]*ivector[2])<< STD_endl; ODINLOG(odinlog,normalDebug) << "center " << centervec.printbody() << STD_endl; // @todo should be set here // for(unsigned short i=0;i<3;i++) // scaleMat[i][i]=1/ni.pixdim[i+1]; geometry.set_orientation_and_offset(readvec,phasevec,slicevec,centervec); ODINLOG(odinlog,normalDebug) << "set up gradrot matrix " << geometry.get_gradrotmatrix().print() << STD_endl; ODINLOG(odinlog,normalDebug) << "set up center (offset) " << geometry.get_center().printbody() << STD_endl; return ni.scl_slope?:1; } return 1; } template void copy_from(const T* src,Data &dst, const FileReadOpts& opts) { convert_from_ptr(dst, src, dst.shape()); } int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("NiftiFormat","read"); nifti_image* ni=nifti_image_read(filename.c_str(), true); float scale=read_orientation(*ni,prot.geometry,opts); data.resize( ni->ndim>=4 ? ni->dim[4]:1, ni->ndim>=3 ? ni->dim[3]:1, ni->ndim>=2 ? ni->dim[2]:1, ni->dim[1] ); const TinyVector shape(data.shape()); ODINLOG(odinlog,normalDebug) << "shape/ndim=" << shape << "/" << ni->ndim << STD_endl; if(ni->nvox!=product(shape)) ODINLOG(odinlog,errorLog) << "ni->nvox=" << ni->nvox << " != product(shape)=" << product(shape) << STD_endl; STD_string type; //copy ni->data to data switch(ni->datatype) { case DT_UINT8: type=TypeTraits::type2label((u8bit)0); copy_from((u8bit*)ni->data, data,opts); break; case DT_INT8: type=TypeTraits::type2label((s8bit)0); copy_from((s8bit*)ni->data, data,opts); break; case DT_UINT16: type=TypeTraits::type2label((u16bit)0); copy_from((u16bit*)ni->data, data,opts); break; case DT_INT16: type=TypeTraits::type2label((s16bit)0); copy_from((s16bit*)ni->data, data,opts); break; case DT_UINT32: type=TypeTraits::type2label((u32bit)0); copy_from((u32bit*)ni->data, data,opts); break; case DT_INT32: type=TypeTraits::type2label((s32bit)0); copy_from((s32bit*)ni->data, data,opts); break; case DT_FLOAT32: type=TypeTraits::type2label((float)0); copy_from((float*)ni->data, data,opts); break; case DT_FLOAT64: type=TypeTraits::type2label((double)0); copy_from((double*)ni->data, data,opts); break; default: ODINLOG(odinlog,errorLog) << "Unsupported datatype " << ni->datatype << STD_endl; return -1; break; } ODINLOG(odinlog,normalDebug) << "type=" << type << STD_endl; if(type=="")return -1; //scale data data*=scale; //set some metadata prot.system.set_data_type(type); prot.seqpars.set_NumOfRepetitions(ni->dim[4]); float timescale=1.0; if(ni->time_units==NIFTI_UNITS_SEC) timescale=1.0e3; if(ni->time_units==NIFTI_UNITS_USEC) timescale=1.0e-3; prot.seqpars.set_RepetitionTime(timescale*ni->dt); nifti_image_free(ni); return shape(0)*shape(1); } void store_orientation(nifti_image &ni,const Data& data,const Geometry &geometry, const FileWriteOpts& opts) { Log odinlog("NiftiFormat","store_orientation"); ni.sform_code=ni.qform_code=NIFTI_XFORM_SCANNER_ANAT; //set scanner aligned space const RotMatrix rot(geometry.get_gradrotmatrix());//orientation of the image in "normal" space const TinyVector shape(data.shape());//size of the image in voxels const dvector center(geometry.get_center());//position of the image in "normal" space ni.dx=ni.pixdim[1]=voxel_extent(geometry,readDirection, shape(3)); ni.dy=ni.pixdim[2]=voxel_extent(geometry,phaseDirection, shape(2)); ni.dz=ni.pixdim[3]=voxel_extent(geometry,sliceDirection, shape(1)); const dvector ivector =//diagonale trougth the image (from first voxel, to the last) in "normal" space (geometry.get_FOV(readDirection)-ni.dx)*geometry.get_readVector()+ (geometry.get_FOV(phaseDirection)-ni.dy)*geometry.get_phaseVector()+ (geometry.get_FOV(sliceDirection)-ni.dz)*geometry.get_sliceVector(); // double heightAng,azimutAng,inplaneAng; // geometry.get_orientation(heightAng,azimutAng,inplaneAng); ODINLOG(odinlog,normalDebug) << "get_gradrotmatrix "<< rot.print() << STD_endl; ODINLOG(odinlog,normalDebug) << "get_readVector "<< geometry.get_readVector().printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "get_phaseVector "<< geometry.get_phaseVector().printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "get_sliceVector "<< geometry.get_sliceVector().printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "get_center "<< center.printbody() << STD_endl; ODINLOG(odinlog,normalDebug) << "FOV read/phase/slice "<< geometry.get_FOV(readDirection) << "/" << geometry.get_FOV(phaseDirection) << "/" << geometry.get_FOV(sliceDirection) << STD_endl; ODINLOG(odinlog,normalDebug) << "image diagonale "<< ivector.printbody() <<"/" << sqrt(ivector[0]*ivector[0]+ivector[1]*ivector[1]+ivector[2]*ivector[2])<< STD_endl; // ODINLOG(odinlog,normalDebug) << "heightAng,azimutAng,inplaneAng " << heightAng << "," << azimutAng << "," << inplaneAng << STD_endl; //create space tranformation matrices - transforms the space when reading _NOT_ the data //@todo maybe we can get the quaternions directly from the given rotation angles for(int y =0;y<3;y++) { ni.qto_xyz.m[0][y]=rot[0][y]; ni.qto_xyz.m[1][y]=rot[1][y]; ni.qto_xyz.m[2][y]=rot[2][y]; ni.qto_xyz.m[y][3]=center[y]-ivector[y]/2; } memcpy(ni.sto_xyz.m,ni.qto_xyz.m,sizeof(ni.sto_xyz.m)); //add scaling to the sform for(int y =0;y<3;y++){ ni.sto_xyz.m[0][y]*=ni.pixdim[1+y]; ni.sto_xyz.m[1][y]*=ni.pixdim[1+y]; ni.sto_xyz.m[2][y]*=ni.pixdim[1+y]; } ni.dx=ni.pixdim[1]; ni.dy=ni.pixdim[2]; ni.dz=ni.pixdim[3]; //generate matching quaternions nifti_mat44_to_quatern( ni.qto_xyz, &ni.quatern_b,&ni.quatern_c,&ni.quatern_d, &ni.qoffset_x,&ni.qoffset_y,&ni.qoffset_z, NULL,NULL,NULL, &ni.qfac); } template void* copy_to(Data &src,Data &dst,nifti_image &ni, Geometry& geo,const FileWriteOpts& opts) { Log odinlog("NiftiFormat","copy_to"); src.convert_to(dst,noupscale); const TinyVector shape(src.shape()); ni.ndim=ni.dim[0]=shape(0)>1 ? 4:3; ni.nx=ni.dim[1]=shape(3); ni.ny=ni.dim[2]=shape(2); ni.nz=ni.dim[3]=shape(1); ni.nt=ni.dim[4]=shape(0); //@todo - is already done in autoscaled conversion - waste of time ni.cal_max = max(dst); ni.cal_min = min(dst); ni.nvox=product(shape); //and return pointer to the converted data return dst.c_array(); } int write(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) { Log odinlog("NiftiFormat","write"); STD_string type=selectDataType(prot,opts); JDXfileName fname(filename); Protocol protcopy(prot); Geometry& geo=protcopy.geometry; Data src(data); nifti_image ni; memset(&ni,0, sizeof(nifti_image)); //set everything to zero - default value for "not used" ni.nu=ni.nv=ni.nw=1; if(tolowerstr(opts.dialect)=="fsl") { bool do_transform=false; STD_string sppart="s,p"; if(geo.get_orientation()==sagittal || geo.get_orientation()==coronal) { ODINLOG(odinlog,infoLog) << "Rotating around read axis for fsl dialect" << STD_endl; sppart="p-,s"; do_transform=true; } STD_string rsign; double heightAng, azimutAng, inplaneAng; bool revSlice; geo.get_orientation(heightAng, azimutAng, inplaneAng, revSlice); if(!revSlice) { // FSL needs 'radiological' handness ODINLOG(odinlog,infoLog) << "Reversing handness for fsl dialect" << STD_endl; rsign="-"; do_transform=true; } if(do_transform) FilterChain("-swapdim "+sppart+",r"+rsign+"").apply(protcopy,src); } // Compatabilty with FSL STD_string newtype; if(IS_TYPE(s8bit,type)) newtype=TypeTraits::type2label((u8bit)0); else if(IS_TYPE(u16bit,type)) newtype=TypeTraits::type2label((s16bit)0); else if(IS_TYPE(u32bit,type)) newtype=TypeTraits::type2label((s32bit)0); if(newtype!="") { if(tolowerstr(opts.dialect)=="fsl" || fname.get_suffix()=="hdr") { ODINLOG(odinlog,infoLog) << "data type " << type << " is not supported, falling back to " << newtype << STD_endl; type=newtype; } else { ODINLOG(odinlog,warningLog) << "data type " << type << " is not supported in FSL, use '-wdialect fsl' to correct this" << STD_endl; } } store_orientation(ni,src,geo,opts); //dummies to keep the data ni.data points to Data< u8bit,4> u8bit_data; Data< s8bit,4> s8bit_data; Data u16bit_data; Data s16bit_data; Data u32bit_data; Data s32bit_data; Data< float,4> float_data; Data double_data; ni.datatype=DT_UNKNOWN; if( IS_TYPE( u8bit,type)) {ni.datatype=DT_UINT8; ni.data=copy_to(src, u8bit_data,ni,geo,opts);} else if(IS_TYPE( s8bit,type)) {ni.datatype=DT_INT8; ni.data=copy_to(src, s8bit_data,ni,geo,opts);} else if(IS_TYPE(u16bit,type)) {ni.datatype=DT_UINT16; ni.data=copy_to(src,u16bit_data,ni,geo,opts);} else if(IS_TYPE(s16bit,type)) {ni.datatype=DT_INT16; ni.data=copy_to(src,s16bit_data,ni,geo,opts);} else if(IS_TYPE(u32bit,type)) {ni.datatype=DT_UINT32; ni.data=copy_to(src,u32bit_data,ni,geo,opts);} else if(IS_TYPE(s32bit,type)) {ni.datatype=DT_INT32; ni.data=copy_to(src,s32bit_data,ni,geo,opts);} else if(IS_TYPE(float,type)) {ni.datatype=DT_FLOAT32;ni.data=copy_to(src, float_data,ni,geo,opts);} else if(IS_TYPE(double,type)) {ni.datatype=DT_FLOAT64;ni.data=copy_to(src,double_data,ni,geo,opts);} ni.nbyper=TypeTraits::typesize(type); ODINLOG(odinlog,normalDebug) << "nbyper/datatype=" << ni.nbyper << "/" << ni.datatype << STD_endl; ODINLOG(odinlog,normalDebug) << "ni.pixdim[1/2/3]=" << ni.pixdim[1] << "/" << ni.pixdim[2] << "/" << ni.pixdim[3] << STD_endl; if(src.extent(0)) ni.dt=ni.pixdim[4] = prot.seqpars.get_RepetitionTime(); //@todo we could save scale and offset here - intead of autoscale ni.scl_slope=1; ni.scl_inter=0.0;// http://209.85.135.104/search?q=cache:AxBp5gn9GzoJ:nifti.nimh.nih.gov/board/read.php%3Ff%3D1%26i%3D57%26t%3D57+nifti-1+scl_slope&hl=en&ct=clnk&cd=1&client=iceweasel-a ni.freq_dim=1; ni.phase_dim=2; ni.slice_dim=3; ni.xyz_units=NIFTI_UNITS_MM; ni.time_units=NIFTI_UNITS_MSEC; ni.fname=(char*)filename.c_str(); STD_string imgfile; // Keep in scope for valid char* pointer if(fname.get_suffix()=="hdr") { ni.nifti_type=0; // ANALYZE imgfile=fname.get_dirname()+SEPARATOR_STR+fname.get_basename_nosuffix()+".img"; ODINLOG(odinlog,normalDebug) << "imgfile=" << imgfile << STD_endl; ni.iname=(char*)imgfile.c_str(); } else { ni.nifti_type=1; // NIFTI ni.iname=(char*)filename.c_str(); } STD_string studydescr; STD_string physician; prot.study.get_Context(studydescr, physician); snprintf(ni.descrip, 80, "%s", studydescr.c_str()); STD_string seriesdescr; int seriesnr; prot.study.get_Series(seriesdescr, seriesnr); snprintf(ni.intent_name, 16, "%s", seriesdescr.c_str()); errno=0; //reset errno nifti_image_write(&ni); //write the image - in case of a failure errno should be set if(errno) { //if so, tell the user, clean up and return -1 ODINLOG(odinlog,errorLog) << "Could not write to "<< filename << "(" <, (C) 2008 // // Copyright: See COPYING file that comes with this distribution // // #ifndef FILTER_RESLICE_H #define FILTER_RESLICE_H #include class FilterReSlice : public FilterStep { JDXenum orient; STD_string label() const {return "reslice";} STD_string description() const {return "reslices the image to a given orientation";} bool process(Data& data, Protocol& prot)const; FilterStep* allocate() const {return new FilterReSlice();} void init(); }; ///////////////////////////////////////////////////////////////////////////// class FilterSwapdim : public FilterStep { JDXstring newread,newphase,newslice; STD_string label() const {return "swapdim";} STD_string description() const {return "swap/reflect dimensions by specifying a direction triple with optional reflection sign appended";} bool process(Data& data, Protocol& prot)const; FilterStep* allocate() const {return new FilterSwapdim();} static bool selChannel(STD_string name, direction &dir, int& sign); void init(); }; #endif odin-1.8.5/odindata/filter_reduction.h0000644000175000017500000000613211725203122014671 00000000000000/*************************************************************************** filter_reduction.h - description ------------------- begin : Fri Feb 26 2010 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_REDUCTION_H #define FILTER_REDUCTION_H enum reductionOp { minip=0, maxip, proj }; static const char* reductionOpLabel[]={"minip", "maxip", "proj"}; #include template class FilterReduction : public FilterStep { JDXenum dir; STD_string label() const {return reductionOpLabel[Op];} STD_string description() const { STD_string opstr; if(Op==minip) opstr="minimum intensity "; if(Op==maxip) opstr="maximum intensity "; return "Perform "+opstr+"projection over given direction"; } void init() { for(int i=0; i& data, Protocol& prot) const { Log odinlog(c_label(),"process"); if(dir=="none"){ ODINLOG(odinlog,errorLog) << "no valid dimension given" << STD_endl; return false; } TinyVector inshape=data.shape(); TinyVector outshape=data.shape(); outshape(dir)=1; Data outdata(outshape); for(int i=0; i index=outdata.create_index(i); TinyVector lowerBounds=index; TinyVector upperBounds=index; upperBounds(dir)=inshape(dir)-1; if(Op==minip) outdata(index)=min(data(RectDomain<4>(lowerBounds, upperBounds))); if(Op==maxip) outdata(index)=max(data(RectDomain<4>(lowerBounds, upperBounds))); if(Op==proj) outdata(index)=sum(data(RectDomain<4>(lowerBounds, upperBounds))); } data.reference(outdata); // Adjusting protocol, center of slicepack and FOV remains the same if(dir==timeDim) { prot.seqpars.set_NumOfRepetitions(1); } else { if(dir==sliceDim) prot.geometry.set_nSlices(1); prot.seqpars.set_MatrixSize(direction(3-dir),1); } return true; } FilterStep* allocate() const {return new FilterReduction();} }; #endif odin-1.8.5/odindata/integration.h0000644000175000017500000000512611322062337013661 00000000000000/*************************************************************************** integration.h - description ------------------- begin : Fri Apr 6 2001 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef INTEGRATION_H #define INTEGRATION_H #include /** * @addtogroup odindata * @{ */ /** * Base class of all function classes which should be integrated. * To use this class, derive from it and overload the virtual * function 'evaluate'. */ class Integrand { public: /** * Returns the function value at position 'x'. */ virtual double evaluate(double x) const = 0; /** * Returns the integral from 'xmin' to 'xmax'. * Integration is performed with 'max_subintervals' at which the function * will be calculated and the specified relative 'error_limit'. */ double get_integral(double xmin, double xmax, unsigned int max_subintervals=1000, double error_limit=1e-7) const; protected: Integrand() {} virtual ~Integrand() {} }; //////////////////////////////////////////////////////////// class GslData4Integr; // forward declaration /** * Class which is used for integration of functions. */ class FunctionIntegral { public: /** * Prepare an integration of function 'func' * with 'max_subintervals' at which the function * will be calculated and the specified relative 'error_limit'. */ FunctionIntegral(const Integrand& func, unsigned int max_subintervals=1000, double error_limit=1e-7); /** * Destructor */ ~FunctionIntegral(); /** * Returns the integral from 'xmin' to 'xmax'. */ double get_integral(double xmin, double xmax) const; private: static double integrand(double x, void *params); const Integrand& f; unsigned int n_intervals; double errlimit; GslData4Integr* gsldata; }; /** @} */ #endif odin-1.8.5/odindata/image.cpp0000644000175000017500000001553111363773554012773 00000000000000#include "image.h" #include "data.h" #include Image::Image(const STD_string& label) : JcampDxBlock(label) { magnitude.set_label("magnitude"); magnitude.set_filemode(compressed); append_all_members(); } Image& Image::operator = (const Image& i) { JcampDxBlock::operator = (i); geo=i.geo; magnitude=i.magnitude; append_all_members(); return *this; } unsigned int Image::size(axis ax) const { ndim nn=get_magnitude().get_extent(); int index=nn.size()-1-ax; if(index>=0) return nn[index]; return 1; } Image& Image::transpose_inplane(bool reverse_read, bool reverse_phase) { unsigned int d=magnitude.dim(); if(d<2) return *this; geo.transpose_inplane(reverse_read,reverse_phase); // transpose image data farray magnitude_copy(magnitude); ndim shape=magnitude.get_extent(); STD_swap(shape[d-1],shape[d-2]); magnitude.redim(shape); for(unsigned int i=0; i odinlog(this,"ImageSet(Sample)"); float min_fov=100.0; int min_size=64; farray sddata(smp.get_spinDensity()); STD_string maplabel="Spin Density"; sddata.normalize(); ODINLOG(odinlog,normalDebug) << "sddata.get_extent()=" << sddata.get_extent() << STD_endl; float xFOV=smp.get_FOV(xAxis); float yFOV=smp.get_FOV(yAxis); float zFOV=smp.get_FOV(zAxis); float maxFOV=maxof3(xFOV,yFOV,zFOV); if(maxFOV odinlog(this,"append_image"); bool rename=false; if(img.get_label()=="" || JcampDxBlock::parameter_exists(img.get_label())) rename=true; images.push_back(img); STD_list::iterator it=images.end(); --it; if(rename) it->set_label("Image"+itos(images.size()-1)); JcampDxBlock::append(*it); unsigned int nimages=images.size(); ODINLOG(odinlog,normalDebug) << "nimages=" << nimages << STD_endl; Content.resize(nimages); int index=0; for(it=images.begin(); it!=images.end(); ++it) { ODINLOG(odinlog,normalDebug) << "index/label=" << index << "/" << it->get_label() << STD_endl; Content[index]=it->get_label(); index++; } return *this; } ImageSet& ImageSet::clear_images() { images.clear(); Content.resize(0); return *this; } Image& ImageSet::get_image(unsigned int index) { Log odinlog(this,"get_image"); unsigned int nimages=images.size(); ODINLOG(odinlog,normalDebug) << "index/nimages=" << index << "/" << nimages << STD_endl; if(index>=nimages) return dummy; STD_list::iterator it=images.begin(); for(unsigned int i=0; i odinlog(this,"load"); clear_images(); // check whether we have a whole set of images and determine the total num of images first int noiresult=Content.load(filename); svector contcopy=Content; // create copy because append_image will modify Content unsigned int nimages=contcopy.size(); ODINLOG(odinlog,normalDebug) << "noiresult/nimages/Content=" << noiresult << "/" << nimages << "/" << contcopy.printbody() << STD_endl; int result=0; if(noiresult>0) { // create placeholders Image img; for(unsigned int i=0; i0) { clear_images(); append_image(img); } } return result; } void ImageSet::append_all_members() { JcampDxBlock::clear(); append_member(Content); } odin-1.8.5/odindata/filter_mask.cpp0000644000175000017500000001065011725203122014163 00000000000000#include "filter_mask.h" #include "utils.h" // for TinyVector comparison void FilterGenMask::init(){ min.set_description("lower threshold"); append_arg(min,"min"); max.set_description("upper threshold"); append_arg(max,"max"); } bool FilterGenMask::process(Data& data, Protocol& prot) const { /* TinyVector datashape=data.shape(); TinyVector maskshape=data.shape(); maskshape(timeDim)=1; Data mask(maskshape); mask=1.0; TinyVector maskindex; TinyVector dataindex; for(int i=0; imax) mask(maskindex)=0.0; } } data.reference(mask); */ data=where(Array(data)>=min && Array(data)<=max, float(1.0), float(0.0)); return true; } /////////////////////////////////////////////////////////////////////////// bool FilterAutoMask::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); int nslots=100; float step=secureDivision(max(data),nslots); ODINLOG(odinlog,normalDebug) << "nslots/step=" << nslots << "/" << step << STD_endl; Data hist(nslots); hist=0.0; // create histogram for(int i=0; i=0 && slothist(islot)) { thresh=islot*step; break; } } ODINLOG(odinlog,normalDebug) << "thresh=" << thresh << STD_endl; data=where(Array(data)>thresh, float(1.0), float(0.0)); return true; } /////////////////////////////////////////////////////////////////////////// typedef STD_list > QuantilIndexList; typedef STD_map QuantilIndexMap; void FilterQuantilMask::init(){ fraction.set_minmaxval(0.0,1.0).set_description("quantil"); append_arg(fraction,"fraction"); } bool FilterQuantilMask::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); int ntotal=data.size(); float frac=fraction; check_range(frac,0.0,1.0); int nmask=int((1.0-frac)*ntotal+0.5); ODINLOG(odinlog,normalDebug) << "ntotal/nmask=" << ntotal << "/" << nmask << STD_endl; Data mask(data.shape()); mask=0.0; QuantilIndexMap indexmap; for(int i=0; i index=data.create_index(i); indexmap[data(index)].push_back(index); } int nmap=indexmap.size(); ODINLOG(odinlog,normalDebug) << "ntotal/nmap=" << ntotal << "/" << nmap << STD_endl; QuantilIndexMap::const_iterator mapiter=indexmap.end(); int j=0; while(jsecond; ODINLOG(odinlog,normalDebug) << "indexmap(" << mapiter->first << ")=" << indexlist.size() << STD_endl; for(QuantilIndexList::const_iterator listiter=indexlist.begin(); listiter!=indexlist.end(); ++listiter) { mask(*listiter)=1.0; j++; } } data.reference(mask); return true; } /////////////////////////////////////////////////////////////////////////// void FilterUseMask::init() { fname.set_description("filename"); append_arg(fname,"fname"); } bool FilterUseMask::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); // Load external file Data maskdata; if(maskdata.autoread(fname)<0) return false; TinyVector maskshape=maskdata.shape(); TinyVector datashape=data.shape(); maskshape(timeDim)=datashape(timeDim)=1; if(maskshape!=datashape) { ODINLOG(odinlog,errorLog) << "shape mismatch: " << maskshape << "!=" << datashape << STD_endl; return false; } fvector vals; for(int i=0; i index=data.create_index(i); float val=data(index); index(timeDim)=0; if(maskdata(index)) vals.push_back(val); } data.resize(1,vals.size(),1,1); data(0,Range::all(),0,0)=Data(vals); return true; } odin-1.8.5/odindata/linalg.cpp0000644000175000017500000004032411322062337013136 00000000000000#include "linalg.h" #include "utils.h" #include #include #ifdef HAVE_LIBGSL #include #include #include #endif #ifdef HAVE_LAPACK // The lapack functions extern "C" void cgelss_( int* M, int* N, int* NRHS, STD_complex* A, int* LDA, STD_complex* B, int* LDB, float* S, float* RCOND, int* RANK, STD_complex* WORK, int* LWORK, float* RWORK, int* INFO ); extern "C" void sgelss_( int* M, int* N, int* NRHS, float* A, int* LDA, float* B, int* LDB, float* S, float* RCOND, int* RANK, float* WORK, int* LWORK, int* INFO ); //extern "C" void cgesvd_( char* JOBU, char* JOBVT, int* M, int* N, STD_complex* A, int* LDA, float* S, STD_complex* U, int* LDU, STD_complex* VT, int* LDVT, STD_complex* WORK, int* LWORK, float* RWORK, int* INFO ); //extern "C" void sgesvd_( char* JOBU, char* JOBVT, int* M, int* N, float* A, int* LDA, float* S, float* U, int* LDU, float* VT, int* LDVT, float* WORK, int* LWORK, int* INFO ); extern "C" void ssyev_( char* JOBZ, char* UPLO, int* N, float* A, int* LDA, float* W, float* WORK, int* LWORK, int* INFO); // Chose appropriate LAPACK function by function overloading int gelss( int* M, int* N, int* NRHS, STD_complex* A, int* LDA, STD_complex* B, int* LDB, float* S, float* RCOND, int* RANK, STD_complex* WORK, int* LWORK, float* RWORK, int* INFO ) { cgelss_( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, WORK, LWORK, RWORK, INFO ); return int(WORK[0].real()); } int gelss( int* M, int* N, int* NRHS, float* A, int* LDA, float* B, int* LDB, float* S, float* RCOND, int* RANK, float* WORK, int* LWORK, float* RWORK, int* INFO ) { sgelss_( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, WORK, LWORK, INFO ); return int(WORK[0]); } /* int gesvd( char* JOBU, char* JOBVT, int* M, int* N, STD_complex* A, int* LDA, float* S, STD_complex* U, int* LDU, STD_complex* VT, int* LDVT, STD_complex* WORK, int* LWORK, float* RWORK, int* INFO) { cgesvd_( JOBU, JOBVT, M, N, A, LDA, S, U, LDU, VT, LDVT, WORK, LWORK, RWORK, INFO ); return int(WORK[0].real()); } int gesvd( char* JOBU, char* JOBVT, int* M, int* N, float* A, int* LDA, float* S, float* U, int* LDU, float* VT, int* LDVT, float* WORK, int* LWORK, float* RWORK, int* INFO) { sgesvd_( JOBU, JOBVT, M, N, A, LDA, S, U, LDU, VT, LDVT, WORK, LWORK, INFO ); return int(WORK[0]); } */ //////////////////////////////////// bool report_error(int INFO, const char* caller) { Log odinlog("",caller); if(INFO<0) { ODINLOG(odinlog,errorLog) << "the " << -INFO << "-th argument had an illegal value." << STD_endl; return true; } if(INFO>0) { ODINLOG(odinlog,errorLog) << "the algorithm failed to converge." << STD_endl; return true; } return false; } //////////////////////////////////// static Mutex lapack_mutex; //////////////////////////////////// /* Array conjugate_transpose_matrix(Array& M) {return Array(conj(M.transpose(1,0)));} Array conjugate_transpose_matrix(Array& M) {return M.transpose(1,0);} template bool svd_lapack(const Data& A, Data& U, Data& sigma, Data& V) { Log odinlog("","svd_lapack"); int M=A.extent(0); // rows int N=A.extent(1); // cols ODINLOG(odinlog,normalDebug) << "M/N=" << M << "/" << N << STD_endl; Array A_fortran(A.shape(), ColumnMajorArray<2>()); // Array with Fortran storage order A_fortran=A; // creates unique copy sigma.resize(N); Array U_fortran(A.shape(), ColumnMajorArray<2>()); // Array with Fortran storage order Array VT_fortran(TinyVector(N,N), ColumnMajorArray<2>()); // Array with Fortran storage order Array WORK(1); int LWORK=-1; // get optimal workspace size Array RWORK(5*STD_min(M,N)); int NRHS=1; int RANK; int INFO; char JOBU='A'; char JOBVT='A'; #ifndef HAVE_THREADSAFE_LAPACK MutexLock lock(lapack_mutex); //LAPACK is generally not thread safe, so we will serialize use of LAPACK #endif // call once to get optimal size of the WORK array LWORK=gesvd( &JOBU, &JOBVT, &M, &N, A_fortran.data(), &M, sigma.data(), U_fortran.data(), &M, VT_fortran.data(), &N, WORK.data(), &LWORK, RWORK.data(), &INFO); ODINLOG(odinlog,normalDebug) << "INFO/LWORK=" << INFO << "/" << LWORK << STD_endl; if(report_error(INFO,"svd_lapack(worksize)")) return false; WORK.resize(LWORK); // perform SVD gesvd( &JOBU, &JOBVT, &M, &N, A_fortran.data(), &M, sigma.data(), U_fortran.data(), &M, VT_fortran.data(), &N, WORK.data(), &LWORK, RWORK.data(), &INFO); ODINLOG(odinlog,normalDebug) << "INFO=" << INFO << STD_endl; if(report_error(INFO,"svd_lapack(svd)")) return false; U.resize(M,N); U=U_fortran; V.resize(N,N); V=conjugate_transpose_matrix(VT_fortran); return true; } */ //////////////////////////////////// template bool solve_linear_lapack(Data& result, const Data& A, const Data& b, float sv_truncation) { Log odinlog("","solve_linear_lapack"); int M=A.extent(0); // rows int N=A.extent(1); // cols ODINLOG(odinlog,normalDebug) << "M/N=" << M << "/" << N << STD_endl; Array A_fortran(A.shape(), ColumnMajorArray<2>()); // Array with Fortran storage order A_fortran=A; // creates unique copy Array B_X(M); // Use Copy because it is used for in- and output B_X=b; Array S(N); Array WORK(1); int LWORK=-1; // get optimal workspace size Array RWORK(5*STD_min(M,N)); int NRHS=1; int RANK; int INFO; #ifndef HAVE_THREADSAFE_LAPACK MutexLock lock(lapack_mutex); //LAPACK is generally not thread safe, so we will serialize use of LAPACK #endif // call once to get optimal size of the WORK array LWORK=gelss( &M, &N, &NRHS, A_fortran.data(), &M, B_X.data(), &M, S.data(), &sv_truncation, &RANK, WORK.data(), &LWORK, RWORK.data(), &INFO ); ODINLOG(odinlog,normalDebug) << "INFO/LWORK=" << INFO << "/" << LWORK << STD_endl; if(report_error(INFO,"solve_linear_lapack(worksize)")) return false; WORK.resize(LWORK); // perform SVD gelss( &M, &N, &NRHS, A_fortran.data(), &M, B_X.data(), &M, S.data(), &sv_truncation, &RANK, WORK.data(), &LWORK, RWORK.data(), &INFO ); ODINLOG(odinlog,normalDebug) << "INFO=" << INFO << STD_endl; if(report_error(INFO,"solve_linear_lapack(svd)")) return false; result.resize(N); result=B_X(Range(0,N-1)); return true; } #endif /////////////////////////////////////////////////////////////////////////////////////////////////////// bool shape_error(const TinyVector& A_shape, int b_extent) { Log odinlog("solve_linear","shape_error"); int A_nrows=A_shape(0); int A_ncols=A_shape(1); if(A_nrows==0 || A_ncols==0) { ODINLOG(odinlog,errorLog) << "Zero-size matrix" << STD_endl; return true; } if(A_ncols>A_nrows) { ODINLOG(odinlog,errorLog) << "cols>rows matrices not supported" << STD_endl; return true; } if(b_extent!=A_nrows) { ODINLOG(odinlog,errorLog) << "size mismatch (b_extent=" << b_extent << ") != (A_nrows=" << A_nrows << ")" << STD_endl; return true; } return false; } ////////////////////////////////////////////////// /* ComplexData<2> matrix_inverse(const ComplexData<2>& A, float sv_truncation) { Log odinlog("","matrix_inverse(complex)"); Range all=Range::all(); ComplexData<2> result; bool svdresult=false; ComplexData<2> U; Data sigma; ComplexData<2> V; #ifdef HAVE_LAPACK svdresult=svd_lapack(A, U, sigma, V); #endif if(!svdresult) { ODINLOG(odinlog,errorLog) << "SVD failed" << STD_endl; } // Regularization int ncol=sigma.size(); float threshold=sv_truncation*sigma(0); ComplexData<1> Sinv(ncol); for(int icol=0; icol solve_linear(const Data& A, const Data& b, float sv_truncation) { Log odinlog("","solve_linear(float)"); Data result; if(shape_error(A.shape(),b.extent(0))) return result; #ifdef HAVE_LAPACK solve_linear_lapack(result,A, b, sv_truncation); #else #ifdef HAVE_LIBGSL Range all=Range::all(); int nrows=A.extent(0); int ncols=A.extent(1); ODINLOG(odinlog,normalDebug) << "nrows/ncols=" << nrows << "/" << ncols << STD_endl; gsl_matrix *A_gsl=gsl_matrix_alloc (nrows, ncols); gsl_matrix *V_gsl=gsl_matrix_alloc (ncols, ncols); gsl_vector *S_gsl=gsl_vector_alloc (ncols); gsl_vector *work =gsl_vector_alloc (ncols); gsl_matrix *X_gsl=0; // additional workspace if( nrows > (2*ncols) ) X_gsl=gsl_matrix_alloc (ncols, ncols); // Use modified SVD for massively over-determined matrices for(int irow=0; irow U(nrows,ncols); for(int irow=0; irow S(ncols); for(int icol=0; icol solve_linear(const ComplexData<2>& A, const ComplexData<1>& b, float sv_truncation) { Log odinlog("","solve_linear(complex)"); ComplexData<1> result; if(shape_error(A.shape(),b.extent(0))) return result; #ifdef HAVE_LAPACK solve_linear_lapack(result, A, b, sv_truncation); #else // create real matrix according to NRC, section 2.3 int A_nrows=A.extent(0); int A_ncols=A.extent(1); Data Af(2*A_nrows,2*A_ncols); for(int irow=0; irow bf(2*nb); for(int i=0; i xf=solve_linear(Af,bf,sv_truncation); int nx=xf.extent(0)/2; result.resize(nx); for(int i=0; i eigenvalues(const Data& A) { Log odinlog("","eigenvalues"); Data result; int N=A.extent(0); if(A.extent(1)!=N) { ODINLOG(odinlog,errorLog) << "Matrix not quadratic" << STD_endl; return result; } ODINLOG(odinlog,normalDebug) << "N=" << N << STD_endl; result.resize(N); result=0.0; #ifdef HAVE_LAPACK Array A_fortran(A.shape(), ColumnMajorArray<2>()); // Array with Fortran storage order A_fortran=A; // creates unique copy char JOBZ='N'; char UPLO='U'; Array WORK(1); int LWORK=-1; // get optimal workspace size int INFO; #ifndef HAVE_THREADSAFE_LAPACK MutexLock lock(lapack_mutex); //LAPACK is generally not thread safe, so we will serialize use of LAPACK #endif // call once to get optimal size of the WORK array ssyev_(&JOBZ, &UPLO, &N, A_fortran.data(), &N, result.data(), WORK.data(), &LWORK, &INFO); LWORK=int(WORK(0)); if(report_error(INFO,"eigenvalues(worksize)")) return result; WORK.resize(LWORK); // perform actual diagonalization ssyev_(&JOBZ, &UPLO, &N, A_fortran.data(), &N, result.data(), WORK.data(), &LWORK, &INFO); ODINLOG(odinlog,normalDebug) << "INFO=" << INFO << STD_endl; if(report_error(INFO,"eigenvalues(diagonalization)")) return result; #else #ifdef HAVE_LIBGSL gsl_matrix* m=gsl_matrix_alloc(N, N); for(int j=0; j odinlog(this,"check"); // Self-consistency check ComplexData<2> A(3,3); for(int i=0; i<9; i++) A(A.create_index(i))=STD_complex(float(i),sqrt(float(i))); ComplexData<1> b(3); b(0)=STD_complex(0.1,4.5); b(1)=STD_complex(4.1,0.2); b(2)=STD_complex(-3.4,-7.5); ComplexData<1> x=solve_linear(A,b); ComplexData<1> b_test(3); b_test=matrix_product(A,x); if(cabs(sum(b_test-b))>1.0e-3) { ODINLOG(odinlog,errorLog) << "A=" << A << STD_endl; ODINLOG(odinlog,errorLog) << "x=" << x << STD_endl; ODINLOG(odinlog,errorLog) << "b=" << b << STD_endl; ODINLOG(odinlog,errorLog) << "b_test=" << b_test << STD_endl; ODINLOG(odinlog,errorLog) << "test failed" << STD_endl; return false; } // Test overdetermined system and its errors int nrows=100; int ncols=4; int errcol=1; A.resize(nrows,ncols); b.resize(nrows); ComplexData<1> x_expected(ncols); for(int i=0; i x_solved=solve_linear(A,b,0.02); // Actual solution by GSL x_expected(0)=STD_complex(0.941546,-6.1919); x_expected(1)=STD_complex(1.4224,-6.87925); x_expected(2)=STD_complex(1.03419,-6.38178); x_expected(3)=STD_complex(1.07938,-6.4723); if(cabs(sum(x_solved-x_expected))>1.0e-3) { ODINLOG(odinlog,errorLog) << "A=" << A << STD_endl; ODINLOG(odinlog,errorLog) << "b=" << b << STD_endl; ODINLOG(odinlog,errorLog) << "x_expected=" << x_expected << STD_endl; ODINLOG(odinlog,errorLog) << "x_solved=" << x_solved << STD_endl; return false; } // Testing eigenvalues Data Asimple(2,2); Asimple(0,0)=13; Asimple(1,1)=7; Asimple(1,0)=Asimple(0,1)=-4; // symmetric Data eig_calculated(eigenvalues(Asimple)); Data eig_expected(2); eig_expected(0)=5; eig_expected(1)=15; if(sum(fabs(eig_calculated-eig_expected))) { ODINLOG(odinlog,errorLog) << "eig_calculated=" << eig_calculated << STD_endl; ODINLOG(odinlog,errorLog) << "eig_expected=" << eig_expected << STD_endl; return false; } return true; } }; void alloc_LinAlgTest() {new LinAlgTest();} // create test instance #endif odin-1.8.5/odindata/filter.cpp0000644000175000017500000000341411322062337013154 00000000000000#include "filter.h" bool FilterChain::create(const svector& args) { Log odinlog("FilterChain","create"); filters.clear(); ODINLOG(odinlog,normalDebug) << "args=" << args.printbody() << STD_endl; unsigned int nargs=args.size(); for(unsigned int i=0; inumof_args()) { STD_string argstr=args[i+1]; ODINLOG(odinlog,normalDebug) << "argstr=" << argstr << STD_endl; if(argstr.length()) filter->set_args(argstr); i++; } filters.push_back(filter); } } } return true; } FilterChain::FilterChain(int argc,char *argv[]) { Log odinlog("FilterChain","FilterChain"); int nargs=argc-1; if(nargs<=0) return; svector args; args.resize(nargs); for(int i=0; i odinlog("FilterChain","apply"); for(STD_list::const_iterator fit=filters.begin();fit!=filters.end();fit++){ ODINLOG(odinlog,normalDebug) << "Applying " << (*fit)->label() << " to the whole Dataset" << STD_endl; FilterStep *step=*fit; if(!step->process(pdmap)) return false; } return true; } bool FilterChain::apply(Protocol& prot, Data& data) const { Log odinlog("FilterChain","apply"); for(STD_list::const_iterator fit=filters.begin();fit!=filters.end();fit++){ ODINLOG(odinlog,normalDebug) << "Applying " << (*fit)->label() << STD_endl; if(!(*fit)->process(data, prot)) return false; } return true; } odin-1.8.5/odindata/integration.cpp0000644000175000017500000000457011322062337014216 00000000000000#include "integration.h" #include #ifdef HAVE_LIBGSL #include double Integrand::get_integral(double xmin, double xmax, unsigned int max_subintervals, double error_limit) const { FunctionIntegral fi(*this,max_subintervals,error_limit); return fi.get_integral(xmin,xmax); } ////////////////////////////////////////////////////////////// struct GslData4Integr { gsl_integration_workspace* w; }; ////////////////////////////////////////////////////////////// FunctionIntegral::FunctionIntegral(const Integrand& func, unsigned int max_subintervals, double error_limit) : f(func), n_intervals(max_subintervals), errlimit(error_limit) { gsldata=new GslData4Integr; gsldata->w = gsl_integration_workspace_alloc(n_intervals); } FunctionIntegral::~FunctionIntegral() { gsl_integration_workspace_free(gsldata->w); delete gsldata; } double FunctionIntegral::get_integral(double xmin, double xmax) const { double result, error; gsl_function gsl_F; gsl_F.function = &integrand; gsl_F.params = (void*)&f; gsl_integration_qags (&gsl_F, xmin, xmax, 0, errlimit, n_intervals, gsldata->w, &result, &error); return result; } double FunctionIntegral::integrand(double x, void *params) { const Integrand* integr=(const Integrand*)params; return integr->evaluate(x); } ////////////////////////////////////////////////////////////// // Unit test #ifndef NO_UNIT_TEST class FunctionIntegralTest : public UnitTest { struct QuadrFunction : public Integrand { double evaluate(double x) const {return x*x;} }; struct QuadrIntFunction : public Integrand { double evaluate(double x) const {return qf.get_integral(0.0,x);} QuadrFunction qf; }; public: FunctionIntegralTest() : UnitTest("FunctionIntegral") {} private: bool check() const { Log odinlog(this,"check"); // testing quadratic integral function QuadrIntFunction func; STD_string expected_str=ftos(1.0/12.0); STD_string calculated_str=ftos(func.get_integral(0.0,1.0)); if(calculated_str!=expected_str) { ODINLOG(odinlog,errorLog) << "integral=" << calculated_str << ", but expected integral=" << expected_str << STD_endl; return false; } return true; } }; void alloc_FunctionIntegralTest() {new FunctionIntegralTest();} // create test instance #endif #else #error "GNU Scientific library is missing!" #endif odin-1.8.5/odindata/filter_lowpass.h0000644000175000017500000000262311455553535014406 00000000000000/*************************************************************************** filter_lowpass.h - description ------------------- begin : Thu Apr 22 2010 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_LOWPASS_H #define FILTER_LOWPASS_H #include class FilterLowPass : public FilterStep { JDXfloat freq; STD_string label() const {return "lowpass";} STD_string description() const {return "Lowpass filtering";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterLowPass();} void init(); }; #endif odin-1.8.5/odindata/filter_clip.h0000644000175000017500000000513011322062337013625 00000000000000/*************************************************************************** filter_scale.h - description ------------------- begin : Thu Jan 31 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_CLIP_H #define FILTER_CLIP_H #include class FilterMin : public FilterStep { JDXfloat thresh; STD_string label() const {return "min";} STD_string description() const {return "Clip all values below mininum value";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterMin();} void init(); }; //////////////////////////////////////////////////////////////////////////// class FilterMax : public FilterStep { JDXfloat thresh; STD_string label() const {return "max";} STD_string description() const {return "Clip all values above maximum value";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterMax();} void init(); }; //////////////////////////////////////////////////////////////////////////// class FilterType : public FilterStep { protected: JDXstring type; float getThresh(bool upper)const; void init(); }; class FilterTypeMin : public FilterType { STD_string label() const {return "typemin";} STD_string description() const {return "Clip all values below mininum of a specific datatype";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterTypeMin();} }; class FilterTypeMax : public FilterType { STD_string label() const {return "typemax";} STD_string description() const {return "Clip all values above maximum of a specific datatype";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterTypeMax();} }; #endif odin-1.8.5/odindata/converter.cpp0000644000175000017500000000020711712547770013707 00000000000000#include "converter.h" #include const char* OdinData::get_compName() {return "Data";} LOGGROUNDWORK(OdinData) odin-1.8.5/odindata/statistics.cpp0000644000175000017500000000400411322062337014055 00000000000000#include "statistics.h" #include STD_ostream& operator << (STD_ostream& s, statisticResult stats) { s << stats.mean << " +/- " << stats.meandev << " (min=" << stats.min << ", max=" << stats.max << ", stdev=" << stats.stdev << ")"; return s; } ///////////////////////////////////////////////////// // instantiate one special template for checking at compile time #ifdef ODIN_DEBUG template statisticResult statistics(const Array&, const Array*); template float median(const Array&); template double weightmean(const Array& , const Array&); #endif ///////////////////////////////////////////////////// // unit test #ifndef NO_UNIT_TEST class StatisticsTest : public UnitTest { public: StatisticsTest() : UnitTest("statistics") {} private: bool check() const { Log odinlog(this,"check"); int testsize=10; Data testarray(testsize,testsize); TinyVector index; for(int i=0; i template class FilterFlip : public FilterStep { STD_string label() const {return STD_string(1,STD_string(dataDimLabel[Dir])[0])+"flip";} // Use only 1st letter STD_string description() const {return "Flip data in "+STD_string(dataDimLabel[Dir])+" direction";} bool process(Data& data, Protocol& prot) const { data.reverseSelf(Dir); // Adjust protocol dvector sign(3); sign=1.0; sign[3-Dir]=-1.0; prot.geometry.set_orientation_and_offset( sign[0]*prot.geometry.get_readVector(), sign[1]*prot.geometry.get_phaseVector(), sign[2]*prot.geometry.get_sliceVector(), prot.geometry.get_center()); return true; } FilterStep* allocate() const {return new FilterFlip

    ();} void init() {} }; #endif odin-1.8.5/odindata/gridding.cpp0000644000175000017500000000433311322062337013457 00000000000000#include "gridding.h" #include // instantiate one special template for checking at compile time #ifdef ODIN_DEBUG template class Gridding; template class CoordTransformation; #endif ///////////////////////////////////////////////////// // unit test #ifndef NO_UNIT_TEST #include "statistics.h" class GriddingTest : public UnitTest { public: GriddingTest() : UnitTest("Gridding") {} private: bool check() const { Log odinlog(this,"check"); // Test using a 3*FOV/4 (filled with 1) and FOV/2 (filled with 2) box int testsize=128; Data testbox(testsize,testsize); testbox=0.0; Range inner(testsize/8, 7*testsize/8-1); testbox(inner,inner)=1.0; inner=Range(testsize/4, 3*testsize/4-1); testbox(inner,inner)=2.0; // testbox.autowrite("testbox.jdx"); float radialfactor=1.2; // so that sampling disk covers the whole box int ncycles=int(radialfactor*testsize/2+0.5); // suffucient sampling in radial direction int spirsize=int(radialfactor*int(2.0*PII*ncycles*testsize)+0.5); // suffucient along spiral STD_vector > src_coords(spirsize); Data src(spirsize); src=0.0; for(int i=0; i dst(testbox.shape()); JDXfilter gridkernel; gridkernel.set_function("Gauss"); Gridding gridder; gridder.init(dst.shape(), 2.0, src_coords, gridkernel, sqrt(2.0)*2.0/float(testsize)); Data griddedbox(gridder(src)); // griddedbox.autowrite("griddedbox.jdx"); Data diff(testbox-griddedbox); // diff.autowrite("diff.jdx"); float absdiff=sum(fabs(diff)); if(absdiff>30.0) { ODINLOG(odinlog,errorLog) << "absdiff=" << absdiff << STD_endl; return false; } return true; } }; void alloc_GriddingTest() {new GriddingTest();} // create test instance #endif odin-1.8.5/odindata/statistics.h0000644000175000017500000001135311322062337013527 00000000000000/*************************************************************************** statistics.h - description ------------------- begin : Fri Apr 6 2001 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef STATISTICS_H #define STATISTICS_H #include #include /** * @addtogroup odindata * @{ */ /////////////////////////////////////////////////////////// /** * Results of a statistical analysis * */ struct statisticResult { /** * The minimum value */ double min; /** * The minimum value */ double max; /** * The mean value */ double mean; /** * The standard deviation */ double stdev; /** * The standard deviation of the mean value */ double meandev; /** * Prints statistics to ostream */ friend STD_ostream& operator << (STD_ostream& s, statisticResult stats); }; /////////////////////////////////////////////////////////// /** * Returns a statistical description of 'ensemble'. If mask is non-zero, * only values with mask!=0 are considered. * */ template statisticResult statistics(const Array& ensemble, const Array* mask=0) { Log odinlog("","statistics"); statisticResult result; result.min=0.0; result.max=0.0; result.mean=0.0; result.stdev=0.0; result.meandev=0.0; if(mask && !same_shape(ensemble,*mask)) { ODINLOG(odinlog,errorLog) << "size mismatch (ensemble.shape()=" << ensemble.shape() << ") != (mask.shape()=" << mask->shape() << ")" << STD_endl; return result; } int n=ensemble.numElements(); Data ensemble_copy(ensemble); int nvals=0; TinyVector index; for(int i=0; iresult.max) result.max=val; } } } result.mean=secureDivision(result.mean,double(nvals)); nvals=0; for(int i=0; i1) result.stdev=sqrt(result.stdev/double(nvals-1)); else result.stdev=0.0; result.meandev=result.stdev/sqrt(double(nvals)); return result; } /////////////////////////////////////////////////////////// /** * Returns the median of 'ensemble'. * */ template T median(const Array& ensemble) { Data ensemble_copy(ensemble); Array diff(ensemble.shape()); TinyVector index; for(int i=0; i T weightmean(const Array& ensemble, const Array& weight) { Log odinlog("","weightmean"); T result; result=0; // double-stage init for TinyVector Data ensemble_copy(ensemble); if(ensemble.shape()!=weight.shape()) { ODINLOG(odinlog,errorLog) << "size mismatch (ensemble.shape()=" << ensemble.shape() << ") != (weight.shape()=" << weight.shape() << ")" << STD_endl; return result; } float weightsum=0.0; TinyVector index; for(int i=0; i /** * @addtogroup odindata * @{ */ /////////////////////////////////////////////////////////////////////////////////// /** * Base class for all steps (functors). * The template argument is the type of the specialized, derived class. */ template class Step { public: virtual ~Step() {} /** * Overload this function to return a unique label for the functor. */ virtual STD_string label() const = 0; /** * Overload this function to return a brief description of the functor. */ virtual STD_string description() const = 0; /** * Overload this function to allocate an empty object of the step. */ virtual T* allocate() const = 0; /** * Initialize the step, i.e. initiliaze its parameters and append them by 'append_arg'. */ virtual void init() = 0; /** * Clone this step (including its arguments). */ T* clone() const; /** * Overrides the arguments of the functor using a string with comma-separated argument values. */ void set_args(const STD_string& argstr); /** * Returns description of arguments as comma-separated list. */ STD_string args_description() const; /** * Returns the number of arguments. */ unsigned int numof_args() const {return args.numof_pars();} /** * Append arguments of the functor to parblock. */ void append_opts(JcampDxBlock& parblock); protected: /** * Append step argument, to be used in init() of each step. */ void append_arg(JcampDxClass& arg, const STD_string& arglabel); const char* c_label() const {if(!label_cache.size()) label_cache=label(); return label_cache.c_str();} // For Debug private: JcampDxBlock args; mutable STD_string label_cache; }; /////////////////////////////////////////////////////////////////////////////////// /** * Factory for steps (functors). * The template argument is the type of the step to be created by the factory. */ template class StepFactory { public: /** * Set up factory (creates template objects). Appends parameters of all steps to 'parblock'. */ StepFactory(JcampDxBlock* parblock=0); ~StepFactory(); /** * Returns allocated step functor which matches given 'label'. */ T* create(const STD_string& label) const; /** * Returns documention 'code' for doxygen. */ STD_string manual() const; /** * Returns documention for command line. */ STD_string get_cmdline_usage(const STD_string& lineprefix) const; private: typedef STD_map StepMap; StepMap templates; mutable STD_list garbage; }; /** @} */ #endif odin-1.8.5/odindata/filter_detrend.h0000644000175000017500000000265611712547771014352 00000000000000/*************************************************************************** filter_detrend.h - description ------------------- begin : Sun May 17 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_DETREND_H #define FILTER_DETREND_H #include class FilterDeTrend : public FilterStep { JDXint nlow; JDXbool zeromean; STD_string label() const {return "detrend";} STD_string description() const {return "Remove slow drift over time";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterDeTrend();} void init(); }; #endif odin-1.8.5/odindata/filter_nan.h0000644000175000017500000000113211322062337013450 00000000000000// // C++ Interface: filter_nan // // Description: // // // Author: , (C) 2007 // // Copyright: See COPYING file that comes with this distribution // // #ifndef FILTER_NAN_H #define FILTER_NAN_H #include /** @author Enrico Reimer */ class FilterNaN : public FilterStep { JDXfloat replace; STD_string label() const {return "noNaN";} STD_string description() const {return "Replaces every NaN by the given value";} bool process(Data& data, Protocol& prot)const; FilterStep* allocate() const {return new FilterNaN();} void init(); }; #endif odin-1.8.5/odindata/filter_rot.h0000644000175000017500000000262011322062337013503 00000000000000/*************************************************************************** filter_rot.h - description ------------------- begin : Sun Jan 20 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_ROT_H #define FILTER_ROT_H #include class FilterRot : public FilterStep { JDXdouble angle; JDXdouble kernel; STD_string label() const {return "rot";} STD_string description() const {return "In-plane rotation";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterRot();} void init(); }; #endif odin-1.8.5/odindata/utils.h0000644000175000017500000001135411734622162012503 00000000000000/*************************************************************************** mri_utils.h - description ------------------- begin : Wed Feb 9 2005 copyright : (C) 2005 by Thies H. Jochimsen email : ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef UTILS_H #define UTILS_H #include /** * @addtogroup odindata * @{ */ /** * unwrap phase in one dimension, starting at position 'startindex' */ Data unwrap_phase(const Data& phase, int startindex=0); ////////////////////////////////////////////////////////// /** * matrix-vector product */ template Array matrix_product(const Array& matrix, const Array& vector) { Log odinlog("","matrix_product"); int nrows=matrix.extent()(0); int ncols=matrix.extent()(1); Array result(nrows); result=0; int vector_extent=vector.extent(0); if(vector.extent(0)!=ncols) { ODINLOG(odinlog,errorLog) << "size mismatch (vector_extent=" << vector_extent << ") != (ncols=" << ncols << ")" << STD_endl; return result; } for(int icol=0; icol Array matrix_product(const Array& matrix1, const Array& matrix2) { Log odinlog("","matrix_product"); int nrows=matrix1.extent()(0); int ncols=matrix2.extent()(1); ODINLOG(odinlog,normalDebug) << "nrows/ncols=" << nrows << "/" << ncols << STD_endl; Array result(nrows,ncols); result=0; if(matrix1.extent(1)!=matrix2.extent(0)) { ODINLOG(odinlog,errorLog) << "size mismatch (matrix1=" << matrix1.shape() << ", matrix2=" << matrix2.shape() << ")" << STD_endl; return result; } int nprod=matrix1.extent(1); ODINLOG(odinlog,normalDebug) << "nprod=" << nprod << STD_endl; for(int irow=0; irow Array vector_product(const Array& u, const Array& v) { Log odinlog("","vector_product"); Array result(3); if(u.extent(0)!=3 || v.extent(0)!=3) { ODINLOG(odinlog,errorLog) << "input size != 3" << STD_endl; return result; } result(0)=u(1)*v(2)-u(2)*v(1); result(1)=u(2)*v(0)-u(0)*v(2); result(2)=u(0)*v(1)-u(1)*v(0); return result; } ////////////////////////////////////////////////////////// /** * Equal-comparison operator for TinyVectors */ template bool operator == (const TinyVector& t1, const TinyVector& t2) { return sum(abs(t1-t2))==0; } ////////////////////////////////////////////////////////// /** * Unequal-comparison operator for TinyVectors */ template bool operator != (const TinyVector& t1, const TinyVector& t2) { return !(t1==t2); } ////////////////////////////////////////////////////////// /** * Compares array shapes while discarding dimensions with zero value in dimmask. Returns true if equal. */ template bool same_shape(const Array& a1, const Array& a2, const TinyVector& dimmask=1) { for(int i=0; i bool check_range(T& val, T min, T max) { bool in_range=true; if(valmax) {val=max; in_range=false;} return in_range; } /** @} */ #endif odin-1.8.5/odindata/filter_mask.h0000644000175000017500000000533211725203122013631 00000000000000/*************************************************************************** filter_mask.h - description ------------------- begin : Wed Nov 5 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_MASK_H #define FILTER_MASK_H #include class FilterGenMask : public FilterStep { JDXfloat min; JDXfloat max; STD_string label() const {return "genmask";} STD_string description() const {return "Create mask including all voxels with value in given range";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterGenMask();} void init(); }; /////////////////////////////////////////////////////////////////////////// class FilterAutoMask : public FilterStep { STD_string label() const {return "automask";} STD_string description() const {return "Create mask using automatic histogram-based threshold";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterAutoMask();} void init() {} }; /////////////////////////////////////////////////////////////////////////// class FilterQuantilMask : public FilterStep { JDXfloat fraction; STD_string label() const {return "quantilmask";} STD_string description() const {return "Create mask including all voxels above the given fractional threshold";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterQuantilMask();} void init(); }; /////////////////////////////////////////////////////////////////////////// class FilterUseMask : public FilterStep { JDXfileName fname; STD_string label() const {return "usemask";} STD_string description() const {return "Create 1D dataset including all values within mask from file";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterUseMask();} void init(); }; #endif odin-1.8.5/odindata/correlation.cpp0000644000175000017500000000323211455553535014222 00000000000000#include "correlation.h" fmriResult fmri_eval(const Data& timecourse, const Data& designvec) { Log odinlog("","fmri_eval"); fmriResult result; if( !same_shape(timecourse, designvec) ) { ODINLOG(odinlog,errorLog) << "design file size mismatch" << STD_endl; return result; } int nrep=timecourse.numElements(); float maxdesign=max(designvec); float mindesign=min(designvec); // Calculate baseline int nbaseline=0; for(int i=0; i restdata(nrest); Array stimdata(nstim); int irest=0; int istim=0; for(int i=0; i&, const Array&); #endif odin-1.8.5/odindata/step.cpp0000644000175000017500000000002211322062337012632 00000000000000#include "step.h" odin-1.8.5/odindata/filter_range.h0000644000175000017500000000624211322062337013777 00000000000000/*************************************************************************** filter_range.h - description ------------------- begin : Tue Jan 29 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_RANGE_H #define FILTER_RANGE_H #include bool str2range(const STD_string& str, Range& range, int srcsize); template class FilterRange : public FilterStep { JDXstring range; STD_string label() const {return STD_string(1,STD_string(dataDimLabel[Dir])[0])+"range";} // Use only 1st letter STD_string description() const {return "Select range in "+STD_string(dataDimLabel[Dir])+" direction";} bool process(Data& data, Protocol& prot) const { Range all=Range::all(); Range rng[4]; for(int i=0; i<4; i++) rng[i]=Range::all(); if(!str2range(range,rng[Dir],data.extent(Dir))) return false; TinyVector newshape=data.shape(); newshape(Dir)=rng[Dir].length(); float fovfraction=secureDivision(rng[Dir].last()-rng[Dir].first()+1, data.shape()[Dir]); float offsetfactor=secureDivision(0.5*(rng[Dir].first()+rng[Dir].last()), data.shape()[Dir])-0.5; Data data_copy(data.copy()); data.resize(newshape); data(all,all,all,all)=data_copy(rng[timeDim],rng[sliceDim],rng[phaseDim],rng[readDim]); // adapt protocol int stride=rng[Dir].stride(); if(Dir==timeDim) { prot.seqpars.set_NumOfRepetitions(newshape(timeDim)); if(stride>1) prot.seqpars.set_RepetitionTime(prot.seqpars.get_RepetitionTime()*stride); } else { direction geodir=direction(3-Dir); prot.geometry.set_offset(geodir,prot.geometry.get_offset(geodir)+offsetfactor*prot.geometry.get_FOV(geodir)); prot.geometry.set_FOV(geodir,fovfraction*prot.geometry.get_FOV(geodir)); prot.seqpars.set_MatrixSize(geodir,newshape(Dir)); if(Dir==sliceDim) { if(prot.geometry.get_Mode()==slicepack) { prot.geometry.set_nSlices(newshape(sliceDim)); if(stride>1) prot.geometry.set_sliceDistance(prot.geometry.get_sliceDistance()*stride); prot.seqpars.set_MatrixSize(sliceDirection,1); } } } return true; } FilterStep* allocate() const {return new FilterRange();} void init() { range.set_description("Single value or range, optionally with increment (e.g. 1-10:3)"); append_arg(range,"range"); } }; #endif odin-1.8.5/odindata/fileio_asc.cpp0000644000175000017500000001105511712547771014001 00000000000000#include "fileio.h" ////////////////////////////////////////////////////////////// struct AsciiFormat : public FileFormat { STD_string description() const {return "ASCII";} svector suffix() const { svector result; result.resize(1); result[0]="asc"; return result; } svector dialects() const { svector result; result.resize(1); result[0]="tcourse"; return result; } int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { STD_string ascfile; ::load(ascfile,filename); unsigned int nelements=tokens(ascfile).size(); if(tolowerstr(opts.dialect)=="tcourse") data.resize(nelements,1,1,1); else data.resize(1,nelements,1,1); if(data.read_asc_file(filename)<0) return -1; return nelements; } int write(const Data& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) { return data.write_asc_file(filename); } }; ////////////////////////////////////////////////////////////// struct MatlabAsciiFormat : public FileFormat { STD_string description() const {return "Matlab ascii 2D data matrix";} svector suffix() const { svector result; result.resize(1); result[0]="dat"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { STD_string str; if(::load(str, filename)<0) return -1; sarray table(parse_table(str)); int nrows=table.size(0); int ncols=table.size(1); data.resize(1,1,nrows,ncols); for(int irow=0; irow& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) { int nrows=data.extent(2); int ncols=data.extent(3); sarray table(nrows,ncols); for(int irow=0; irow& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("PosFormat","read"); ODINLOG(odinlog,errorLog) << "Implement me" << STD_endl; return -1; } int write(const Data& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) { int nx=data.extent(3); int ny=data.extent(2); STD_ofstream ofs(filename.c_str()); if(ofs.bad()) return -1; for(int i=0; i index=data.create_index(i); if(data(index)>0.0) { int ix=index(3); int iy=index(2); ofs << ftos(float(ix)/float(nx)-0.5) << " " << ftos(float(iy)/float(ny)-0.5) << STD_endl; } } return 1; } }; ////////////////////////////////////////////////////////////// struct IndexFormat : public FileFormat { STD_string description() const {return "3D-indices of non-zeroes in ASCII";} svector suffix() const { svector result; result.resize(1); result[0]="idx"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("IndexFormat","read"); ODINLOG(odinlog,errorLog) << "Implement me" << STD_endl; return -1; } int write(const Data& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) { STD_ofstream ofs(filename.c_str()); if(ofs.bad()) return -1; for(int i=0; i index=data.create_index(i); if(data(index)) ofs << index(sliceDim) << " " << index(phaseDim) << " " << index(readDim) << STD_endl; } return 1; } }; ////////////////////////////////////////////////////////////// void register_asc_format() { static AsciiFormat af; static PosFormat pf; static IndexFormat idf; static MatlabAsciiFormat mf; af.register_format(); pf.register_format(); idf.register_format(); mf.register_format(); } odin-1.8.5/odindata/filter_step.cpp0000644000175000017500000000624611734622163014223 00000000000000#include "filter.h" #include "filter_step.h" #include "filter_align.h" #include "filter_clip.h" #include "filter_detrend.h" #include "filter_lowpass.h" #include "filter_mask.h" #include "filter_merge.h" #include "filter_nan.h" #include "filter_resize.h" #include "filter_rot.h" #include "filter_flip.h" #include "filter_range.h" #include "filter_reduction.h" #include "filter_reslice.h" #include "filter_scale.h" #include "filter_shift.h" #include "filter_tile.h" #include "filter_splice.h" #include #include // Instantiate template classes template class Step; template class StepFactory; const char* Filter::get_compName() {return "Filter";} LOGGROUNDWORK(Filter); void FilterStep::create_templates(STD_list& result) { result.push_back(new FilterAlign()); result.push_back(new FilterMin()); result.push_back(new FilterMax()); result.push_back(new FilterTypeMax()); result.push_back(new FilterTypeMin()); result.push_back(new FilterDeTrend()); result.push_back(new FilterLowPass()); result.push_back(new FilterGenMask()); result.push_back(new FilterAutoMask()); result.push_back(new FilterQuantilMask()); result.push_back(new FilterUseMask()); result.push_back(new FilterNaN()); result.push_back(new FilterRot()); result.push_back(new FilterFlip()); result.push_back(new FilterFlip()); result.push_back(new FilterFlip()); result.push_back(new FilterRange()); result.push_back(new FilterRange()); result.push_back(new FilterRange()); result.push_back(new FilterRange()); result.push_back(new FilterScale()); result.push_back(new FilterShift()); result.push_back(new FilterReSlice()); result.push_back(new FilterSwapdim()); result.push_back(new FilterResize()); result.push_back(new FilterResample()); result.push_back(new FilterIsotrop()); result.push_back(new FilterTile()); result.push_back(new FilterMerge()); result.push_back(new FilterSplice()); result.push_back(new FilterReduction()); result.push_back(new FilterReduction()); result.push_back(new FilterReduction()); } bool FilterStep::process(Data& data, Protocol& prot)const{ Log odinlog("FilterStep","process"); ODINLOG(odinlog,errorLog) << "process seems not to be implemented for " << label() << STD_endl; return false; } bool FilterStep::process(FileIO::ProtocolDataMap& pdmap)const{ Log odinlog("FilterStep","process"); bool ret=true; FileIO::ProtocolDataMap pdmap_out; while(!pdmap.empty()){ STD_pair > pdpair=*pdmap.begin(); pdmap.erase(pdmap.begin());//in case we modify the protocol it is better to completly remove the pd-pair and insert it cleanly afterwards if(process(pdpair.second,pdpair.first)){ pdmap_out.insert(pdpair);//.. and insert it into the result-map } else { int number;STD_string desc; pdpair.first.study.get_Series(desc,number); ODINLOG(odinlog,errorLog) << "processing " << label() << " on S" << number << " failed"<< STD_endl; ret=false; } } pdmap=pdmap_out; return ret; } odin-1.8.5/odindata/filter_step.h0000644000175000017500000000206411322062337013654 00000000000000// // C++ Interface: filterstep // // Description: // // // Author: , (C) 2007 // // Copyright: See COPYING file that comes with this distribution // // #ifndef FILTERSTEP_H #define FILTERSTEP_H #include #include #include /** @author Enrico Reimer */ class FilterStep : public Step { public: virtual ~FilterStep() {} /** * Apply filter to protocol-data pair. */ virtual bool process(Data& data, Protocol& prot)const; /** * Apply filter to a 'pdmap'. */ virtual bool process(FileIO::ProtocolDataMap& pdmap)const; // To be used by factory via duck typing static void create_templates(STD_list& result); static STD_string manual_group() {return "filter_steps";} static void interface_description(const FilterStep* step, STD_string& in, STD_string& out) {} }; /////////////////////////////////////////////////////////////////////////////////// typedef StepFactory FilterFactory; // The factory for filter steps #endif odin-1.8.5/odindata/filter_tile.h0000644000175000017500000000262111322062337013635 00000000000000/*************************************************************************** filter_tile.h - description ------------------- begin : Wed Nov 5 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef FILTER_TILE_H #define FILTER_TILE_H #include class FilterTile : public FilterStep { JDXint cols; STD_string label() const {return "tile";} STD_string description() const {return "Combine slices into a square 2D image";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterTile();} void init(); }; #endif odin-1.8.5/odindata/filter_flip.cpp0000644000175000017500000000003111322062337014156 00000000000000#include "filter_flip.h" odin-1.8.5/odindata/image.h0000644000175000017500000000746711322062337012432 00000000000000/*************************************************************************** image.h - description ------------------- begin : Fr Feb 25 2005 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef IMAGE_H #define IMAGE_H #include //#include class Sample; // forward declaration /** * @addtogroup odindata * @{ */ ///////////////////////////////////////////////////////////////// /** * Class to hold reconstructed images of one Geometry */ class Image : public JcampDxBlock { public: /** * Default constructor */ Image(const STD_string& label="unnamedImage"); /** * Copy constructor */ Image(const Image& i) {Image::operator = (i);} /** * Assignment operator */ Image& operator = (const Image& i); /** * Sets the magnitude data */ Image& set_magnitude(const farray& magn) {magnitude=magn; return *this;} /** * Scale magnitude to values between 0 and 1 */ Image& normalize_magnitude() {magnitude.normalize(); return *this;} /** * Returns the magnitude data */ const farray& get_magnitude() const {return magnitude;} /** * Interpret data as 3D volume data and return size for given axis */ unsigned int size(axis ax) const; /** * Sets the parameter set which describes the area imaged */ Image& set_geometry(const Geometry& g) {geo=g; return *this;} /** * Returns the parameter set which describes the area imaged */ const Geometry& get_geometry() const {return geo;} /** * Transpose image in-plane, 'reverse_read' and 'reverse_phase' * can be used to reverse read/phase direction before transposing. */ Image& transpose_inplane(bool reverse_read=false, bool reverse_phase=false); // dummy comparison operator for lists bool operator < (const Image& img) const {return STD_string(get_label()) images; Image dummy; }; /** @} */ #endif odin-1.8.5/odindata/fileio_vtk.cpp0000644000175000017500000000714411712547771014043 00000000000000#include "fileio.h" #ifdef VTKSUPPORT #include #include ////////////////////////////////////////////////////////////// struct VtkFormat : public FileFormat { STD_string description() const {return "Visualization Toolkit";} svector suffix() const { svector result; result.resize(1); result[0]="vtk"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("VtkFormat","read"); ODINLOG(odinlog,errorLog) << "Implement me" << STD_endl; return -1; } int write(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) { Log odinlog("VtkFormat","write"); vtkStructuredPointsWriter *out_write=vtkStructuredPointsWriter::New(); vtkStructuredPoints *out=vtkStructuredPoints::New(); out_write->SetInput(out); // setting format STD_string datatype=selectDataType(prot,opts); if(datatype==TypeTraits::type2label((float)0)) out->SetScalarTypeToFloat (); if(datatype==TypeTraits::type2label((double)0)) out->SetScalarTypeToDouble (); if(datatype==TypeTraits::type2label((s32bit)0)) out->SetScalarTypeToInt (); if(datatype==TypeTraits::type2label((u32bit)0)) out->SetScalarTypeToUnsignedInt (); if(datatype==TypeTraits::type2label((s16bit)0)) out->SetScalarTypeToShort (); if(datatype==TypeTraits::type2label((u16bit)0)) out->SetScalarTypeToUnsignedShort (); if(datatype==TypeTraits::type2label((s8bit)0)) out->SetScalarTypeToChar (); if(datatype==TypeTraits::type2label((u8bit)0)) out->SetScalarTypeToUnsignedChar (); // Data data3d; const Geometry& geo=prot.geometry; // const STD_string type(prot.system.get_data_type()); // if(type!="float" && type!="double")data.convert_to(data3d,noupscale); // else data.convert_to(data3d); int nrep=data.extent(timeDim); int nslice=data.extent(sliceDim); int nphase=data.extent(phaseDim); int nread=data.extent(readDim); ODINLOG(odinlog,normalDebug) << "nrep/nslice/nphase/nread "<< nrep << "/" << nslice << "/" << nphase << "/" << nread << STD_endl; out->SetDimensions(nread,nphase,nslice); out->SetSpacing(voxel_extent(geo, readDirection, nread), voxel_extent(geo, phaseDirection, nphase),voxel_extent(geo, sliceDirection, nslice)); out->SetOrigin(0,0,0); out->SetNumberOfScalarComponents(1); JDXfileName fname(filename); for(int irep=0; irepSetScalarComponentFromFloat(i,j,k,0,data(irep,k,j,i)); } } } STD_string onefilename=fname.get_dirname()+SEPARATOR_STR+fname.get_basename_nosuffix(); if(nrep>1) onefilename+="_time"+itos(irep,nrep-1); onefilename+="."+fname.get_suffix(); ODINLOG(odinlog,normalDebug) << "writing file "<< onefilename << STD_endl; out_write->SetFileName(onefilename.c_str()); out_write->SetScalarsName(onefilename.c_str()); // if(ascii) out_write->SetFileTypeToASCII(); // else out_write->SetFileTypeToBinary(); ostream *fp=out_write->OpenVTKFile(); out_write->Write(); out_write->CloseVTKFile(fp); } out->Delete(); out_write->Delete(); return nslice; } }; #endif ////////////////////////////////////////////////////////////// void register_vtk_format() { #ifdef VTKSUPPORT static VtkFormat vf; vf.register_format(); #endif } odin-1.8.5/odindata/converter.h0000644000175000017500000002743311712547771013367 00000000000000/*************************************************************************** converter.h - description ------------------- begin : Tue Dec 4 2001 copyright : (C) 2001 by Michael von Mengershausen email : mengers@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef CONVERTER_H #define CONVERTER_H #include #include #include #include #include #include /** * @addtogroup odindata * @{ */ // helper class used for debugging the odindata component class OdinData { public: static const char* get_compName(); }; //////////////////////////////////////////////////////////////////// /** * Scaling strategy when converting data to integer types: * - noscale: No scaling * - autoscale: scale/offset values so they will fit into the numeric limits of the destination (0 < scaling factor < inv) * - noupscale: dont upscale values to fit them into the destination (0 < scaling factor <=1) * Note: if destination is non integer no scaling is done at all */ enum autoscaleOption {noscale, autoscale,noupscale}; //////////////////////////////////////////////////////////////////// /** * Helper class for conversion between numbers */ class Converter { public: ////////////////////////////////////////////////////////// // get_elements function overloading // specializations for complex type static unsigned int get_elements(const STD_complex&) { return 2; } /** * Returns number of scalar numbers in this number type, e.g. complex has 2 */ template static unsigned int get_elements(const T&) { return 1; } ////////////////////////////////////////////////////////// /** * Converts array 'src' with 'srcsize' elements to array 'dst' with 'dstsize' elements * Will scale "around 0" if 0 is part of the source value range. Elsewise values will be offset towards 0. * If destination is unsigned values will be offset to be positive domain if necessary. * If autoscaleOption is "noscale" or if destination is floating point no scaling is done at all. */ template static void convert_array(const Src* src, Dst* dst, unsigned int srcsize, unsigned int dstsize, autoscaleOption scaleopt=autoscale) { Log odinlog("Converter","convert_array"); unsigned int srcstep=get_elements(*dst); unsigned int dststep=get_elements(*src); bool doScale = (scaleopt!=noscale && std::numeric_limits::is_integer); if(dststep*srcsize != srcstep*dstsize) { ODINLOG(odinlog,warningLog) << "size mismatch: dststep(" << dststep << ") * srcsize(" << srcsize << ") != srcstep(" << srcstep << ") * dstsize(" << dstsize << ")" << STD_endl; } double scale=1.0; double offset=0.0; if(doScale) { const double domain_minus=creal(std::numeric_limits::min());//negative value domain of this dst const double domain_plus =creal(std::numeric_limits::max());//positive value domain of this dst double minval=std::numeric_limits::min(); double maxval=std::numeric_limits::max(); if(srcsize>0) minval=maxval=creal(src[0]); for(unsigned int i=1; imaxval) maxval=creal(src[i]); } ODINLOG(odinlog,normalDebug) << "src Range:" << minval << "=>" << maxval << STD_endl; ODINLOG(odinlog,normalDebug) << "dst Domain:" << domain_minus << "=>" << domain_plus << STD_endl; assert(domain_minus<=0 && domain_plus>=0); //I think we can assume this assert(domain_minus0 || !domain_minus)offset=-minval; else if(maxval<0 || !domain_plus)offset=-maxval; //calculate range of values which will be on postive/negative domain when offset is applied const double range_plus =maxval+offset; //allways >=0 const double range_minus=minval+offset; //allways <=0 //set scaling factor to fit src-range into dst domain //some compilers dont make x/0 = inf, so we use std::numeric_limits::max() instead, in this case const double scale_plus = range_plus ? domain_plus/range_plus : std::numeric_limits::max(); const double scale_minus= range_minus ? domain_minus/ range_minus: std::numeric_limits::max(); ODINLOG(odinlog,normalDebug) << "scale_minus/scale_plus=" << scale_minus << "/" << scale_plus << STD_endl; scale = STD_min(scale_plus,scale_minus);//get the smaller scaling factor so the bigger range will fit into his domain if(scale<1){ ODINLOG(odinlog,normalDebug) << "Downscaling your values by Factor " << scale << " you might lose information."<< STD_endl; } else if(scaleopt==noupscale){ if(scale>1) { ODINLOG(odinlog,normalDebug) << "upscale not given, clamping scale " << scale << " to 1"<< STD_endl; } scale=1; } doScale=(scale!=1. || offset); offset*=scale;//calc offset for dst } if(doScale)ODINLOG(odinlog,normalDebug) << "converting with scale/offset=" << scale << "/" << offset << STD_endl; else ODINLOG(odinlog,normalDebug) << "converting without scaling" << STD_endl; if(srcstep==dststep)//use common convert for data of same complexity { if(doScale) convert_array_impl(src,dst, srcsize < dstsize?srcsize:dstsize,scale,offset); else convert_array_impl(src,dst, srcsize < dstsize?srcsize:dstsize); } else //do generic convert for data of different complexity { unsigned int srcindex=0, dstindex=0; while(srcindex static void convert_array_impl(const Src* src, Dst* dst, unsigned int count,double scale=1,double offset=0) { Log odinlog("Converter","convert_array_impl(generic)"); ODINLOG(odinlog,normalDebug) << "generic convert " << TypeTraits::type2label(*src) << "=>" << TypeTraits::type2label(*dst) << STD_endl; ODINLOG(odinlog,normalDebug) << "scale/offset=" << scale << "/" << offset << STD_endl; while(count--) convert(src++, dst++,scale,offset); } // Implementing our own round functions since lround/lroundf do not work for unsigned numbers, and they are flawed in MinGW template static T round(double x) { return (T)(x < 0 ? x - 0.5 : x + 0.5); } // specialized converter functions // to complex static void convert(const s8bit* src, STD_complex* dst,float scale,float offset) { (*dst)=STD_complex(src[0]*scale+offset,src[1]*scale); } static void convert(const u8bit* src, STD_complex* dst,float scale,float offset) { (*dst)=STD_complex(src[0]*scale+offset,src[1]*scale); } static void convert(const u16bit* src, STD_complex* dst,float scale,float offset) { (*dst)=STD_complex(src[0]*scale+offset,src[1]*scale); } static void convert(const s16bit* src, STD_complex* dst,float scale,float offset) { (*dst)=STD_complex(src[0]*scale+offset,src[1]*scale); } static void convert(const u32bit* src, STD_complex* dst,float scale,float offset) { (*dst)=STD_complex(src[0]*scale+offset,src[1]*scale); } static void convert(const s32bit* src, STD_complex* dst,float scale,float offset) { (*dst)=STD_complex(src[0]*scale+offset,src[1]*scale); } static void convert(const float *src, STD_complex* dst,float scale,float offset) { dst[0]=STD_complex(src[0]*scale+offset,src[1]*scale); } static void convert(const double *src, STD_complex* dst,float scale,float offset) { dst[0]=STD_complex(src[0]*scale+offset,src[1]*scale); } // from complex static void convert(const STD_complex* src, s8bit* dst,float scale,float offset) { dst[0]=round(src->real()*scale+offset); dst[1]=round(src->imag()*scale); } static void convert(const STD_complex* src, u8bit* dst,float scale,float offset) { dst[0]=round(src->real()*scale+offset); dst[1]=round(src->imag()*scale); } static void convert(const STD_complex* src, s16bit* dst,float scale,float offset) { dst[0]=round(src->real()*scale+offset); dst[1]=round(src->imag()*scale); } static void convert(const STD_complex* src, u16bit* dst,float scale,float offset) { dst[0]=round(src->real()*scale+offset); dst[1]=round(src->imag()*scale); } static void convert(const STD_complex* src, s32bit* dst,float scale,float offset) { dst[0]=round(src->real()*scale+offset); dst[1]=round(src->imag()*scale); } static void convert(const STD_complex* src, u32bit* dst,float scale,float offset) { dst[0]=round(src->real()*scale+offset); dst[1]=round(src->imag()*scale); } static void convert(const STD_complex* src, float* dst,float scale,float offset) { dst[0]=src->real()*scale+offset; dst[1]=src->imag()*scale; } static void convert(const STD_complex* src, double* dst,float scale,float offset) { dst[0]=src->real()*scale+offset; dst[1]=src->imag()*scale; } // from float to integer static void convert(const float* src, s8bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const float* src, u8bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const float* src, s16bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const float* src, u16bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const float* src, s32bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const float* src, u32bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } // from double to integer static void convert(const double* src, s8bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const double* src, u8bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const double* src, s16bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const double* src, u16bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const double* src, s32bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } static void convert(const double* src, u32bit* dst,float scale,float offset) { dst[0]=round(src[0]*scale+offset); } //default template static void convert(const Src* src, Dst* dst,float scale,float offset) { dst[0]=(Dst)(src[0]*scale+offset); } ////////////////////////////////////////////////////////// Converter() {} // Do not allow instances }; /** @} */ #endif odin-1.8.5/odindata/gridding.h0000644000175000017500000002476611322062337013140 00000000000000/*************************************************************************** gridding.h - description ------------------- begin : Fri Jun 25 2004 copyright : (C) 2004 by Michael von Mengershausen email : mengers@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef GRIDDING_H #define GRIDDING_H #include #include #include /** * @addtogroup odindata * @{ */ /** * Coordinate with extra weight for gridding */ template struct GriddingPoint { GriddingPoint(const TinyVector& c=0.0, float w=1.0) : coord(c), weight(w) {} TinyVector coord; float weight; }; ///////////////////////////////////////////////////// /** * Functor for gridding, i.e. bringing values with arbitrary * coordinates onto a rectangular grid. */ template class Gridding { public: /** * Creates uninitialized gridding object */ Gridding() : shape(0) {} /** * Initializes a gridding object to perform a gridding operation with the following parameters: * - dst_shape: The dimensions of the gridded array * - dst_extent: The total extent of the gridded array, the gridded array is created symmetrically about the origin * - src_coords: The coordinates of the input array: First is tthe coordinate, second is an extra weight for the coordinate * - kernel: The gridding kernel used * - kernel_diameter: The maximum diameter of the gridding kernel in units of the source coordinates * Returns the density of source points on the gridded array */ Array init(const TinyVector& dst_shape, const TinyVector& dst_extent, const STD_vector >& src_coords, const JDXfilter& kernel, float kernel_diameter); /** * Put input array 'src' on the grid by stepping linearly through the inidices. * Gridding will start at the linear index 'offset' of the 'src_coords' * specified in the init() function. * Returns gridded array. */ template Array operator () (const Array& src, unsigned int offset=0) const; private: TinyVector shape; // numof src-steps x numof indices on dst grid x pair(dst-index, weight) STD_vector< STD_vector< STD_pair, float> > > recipe; }; ///////////////////////////////////////////////////// template Array Gridding::init(const TinyVector& dst_shape, const TinyVector& dst_extent, const STD_vector >& src_coords, const JDXfilter& kernel, float kernel_diameter) { Log odinlog("Gridding","init"); shape=dst_shape; unsigned int nsrc=src_coords.size(); ODINLOG(odinlog,normalDebug) << "nsrc/kernel/kernel_diameter=" << nsrc << "/" << kernel.get_function_name() << "/" << kernel_diameter << STD_endl; recipe.resize(nsrc); // array to collect sum of all weights for later normalization Array weight_sum(dst_shape); weight_sum=0.0; TinyVector dst_step=dst_extent/dst_shape; ODINLOG(odinlog,normalDebug) << "dst_step=" << dst_step << STD_endl; TinyVector kernel_extent; // In units of indices for(int irank=0; irank0.0) kernel_extent(irank)=kernel_diameter/dst_step(irank); else kernel_extent(irank)=0.0; } ODINLOG(odinlog,normalDebug) << "kernel_extent=" << kernel_extent << STD_endl; TinyVector offset=0.5*(dst_shape-1.0); // coordinate is at center of destination voxels // Iterate over src coordinates for(unsigned int isrc=0; isrc& point=src_coords[isrc]; // Find grid points in neighboordhood TinyVector root; // In units of indices on destination grid for(int irank=0; irank0.0) root(irank)=point.coord(irank)/dst_step(irank); else root(irank)=0.0; } root += offset; ODINLOG(odinlog,normalDebug) << "root=" << root << STD_endl; TinyVector lowindex=(root-0.5*kernel_extent)+0.5; // round up to next higher grid point TinyVector uppindex=(root+0.5*kernel_extent); // round down to next lower grid point ODINLOG(odinlog,normalDebug) << "lowindex/uppindex=" << lowindex << "/" << uppindex << STD_endl; // Possible points in neighboorhood TinyVector neighbours=uppindex-lowindex+1; ODINLOG(odinlog,normalDebug) << "neighbours=" << neighbours << STD_endl; // Get actual points in neighbourhood and their weight if they are within the support of the given kernel and whether point lies on destination grid STD_vector, float> >& dstvec=recipe[isrc]; dstvec.clear(); for(int ineighb=0; ineighb neighb_index=index2extent(neighbours, ineighb); // Check whether point is on grid TinyVector index=lowindex+neighb_index; bool ongrid=true; for(int i=0; i=dst_shape(i)) ongrid=false; } // Check whether point is within the support of the kernel if(ongrid) { TinyVector diff=(root-index)*dst_step; float radius=sqrt(sum(diff*diff))/(0.5*kernel_diameter); float weight=point.weight*kernel.calculate(radius); if(weight>=0.0) dstvec.push_back(STD_pair, float>(index,weight)); } } // Sum up weights for each index for(unsigned int idst=0; idst, float> >& dstvec=recipe[isrc]; for(unsigned int idst=0; idst, float>& weightpair=dstvec[idst]; float weightsum=weight_sum(weightpair.first); if(weightsum>0.0) weightpair.second/=weightsum; } } return weight_sum; } ///////////////////////////////////////////////////// template template Array Gridding::operator () (const Array& src, unsigned int offset) const { Log odinlog("Gridding","()"); Array result; unsigned int nsrc=src.size(); if((offset+nsrc)>recipe.size()) { ODINLOG(odinlog,errorLog) << "Max index of src=" << offset+nsrc << " exceeds recipe.size()=" << recipe.size() << STD_endl; return result; } result.resize(shape); result=T(0); for(unsigned int isrc=0; isrc, float> >& dstvec=recipe[offset+isrc]; for(unsigned int idst=0; idst, float>& weightpair=dstvec[idst]; result(weightpair.first) += weightpair.second * src(index2extent(src.shape(),isrc)); } } return result; } ///////////////////////////////////////////////////////////////////////////////// /** * Functor for coordinate transformation using gridding */ template class CoordTransformation { public: /** * Initializes a transformation of an array with shape 'shape' to new coordinates using a gridding algorithm. * New coordinates (...z',y',x') are obtained by multiplying (...z,y,x) * with 'rotation' and adding 'offset'. Origin is the center of the data set. */ CoordTransformation(const TinyVector& shape, const TinyMatrix& rotation, const TinyVector& offset, float kernel_size=2.5); /** * Transforms 'A' to new coordinates and returns the result */ Array operator () (const Array& A) const; private: TinyVector shape_cache; Gridding gridder; }; ///////////////////////////////////////////////////// template CoordTransformation::CoordTransformation(const TinyVector& shape, const TinyMatrix& rotation, const TinyVector& offset, float kernel_size) : shape_cache(shape) { Log odinlog("CoordTransformation","CoordTransformation"); int nsrc=product(shape); STD_vector > src_coords(nsrc); ODINLOG(odinlog,normalDebug) << "N_rank/nsrc=" << N_rank << "/" << nsrc << STD_endl; TinyVector extent_half; if(OnPixelRot) extent_half=shape/2; // suitable for rotating k-space else extent_half=0.5*(shape-1); // center of even size is between voxels TinyVector index; TinyVector findex; for(int isrc=0; isrc Array CoordTransformation::operator () (const Array& A) const { Log odinlog("CoordTransformation","()"); if(A.shape()!=shape_cache) { ODINLOG(odinlog,errorLog) << "Shape mismatch" << STD_endl; return A; } return gridder(A); } /** @} */ #endif odin-1.8.5/odindata/fileio_3db.cpp0000644000175000017500000000374511322062337013675 00000000000000// // C++ Implementation: fileio_3Db // // Description: // // // Author: <>, (C) 2008 // // Copyright: See COPYING file that comes with this distribution // // #include "fileio.h" #include "complexdata.h" ////////////////////////////////////////////////////////////// struct Iris3DFormat : public FileFormat { struct i3Dblock { short nx, ny, nz, veclen; float x0, y0, z0, dx, dy, dz; }; STD_string description() const {return "Iris3D binary data";} svector suffix() const { svector result; result.resize(1); result[0]="3db"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("Iris3DFormat","read"); ODINLOG(odinlog,errorLog) << "Read of Iris3D not yet supported, sorry"<< STD_endl; return -1; } int write(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) { Log odinlog("Iris3DFormat","write"); FILE *out=FOPEN( filename.c_str(), "w"); if(!out){ ODINLOG(odinlog,errorLog) << "could not open "<< filename <<" for writing"<< STD_endl; return -1; } Data data_copy(data); const TinyVector data_shape=data.shape(); const dvector center(prot.geometry.get_center()); const i3Dblock head={ data_shape[3],data_shape[2],data_shape[1], 1, center[0],center[2],center[2], voxel_extent(prot.geometry,readDirection, data.extent(3)), voxel_extent(prot.geometry,phaseDirection, data.extent(2)), prot.geometry.get_sliceDistance() }; fwrite(&head,sizeof(i3Dblock),1,out); size_t cnt=fwrite(data_copy.c_array(),sizeof(float),product(data_shape),out); fclose(out); return int(cnt)==product(data_shape); } }; ////////////////////////////////////////////////////////////// void register_Iris3D_format() { static Iris3DFormat iris; iris.register_format(); } odin-1.8.5/odindata/filter_tile.cpp0000644000175000017500000000250011322062337014164 00000000000000#include "filter_tile.h" void FilterTile::init(){ cols.set_description("columns"); append_arg(cols,"cols"); } bool FilterTile::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); Range all=Range::all(); int nrep=data.extent(0); int nslice=data.extent(1); int nphase=data.extent(2); int nread=data.extent(3); if(cols<=0 || cols>nslice) { ODINLOG(odinlog,errorLog) << "cols=" << int(cols) << " out of range" << STD_endl; return false; } int rows=nslice/cols; if(nslice%cols) rows++; ODINLOG(odinlog,normalDebug) << "nslice/cols/rows=" << nslice << "/" << int(cols) << "/" << rows << STD_endl; int newnphase=rows*nphase; int newnread=cols*nread; Data outdata(nrep,1,newnphase,newnread); outdata=0.0; int icol=0; int irow=0; for(int islice=0; islice=cols) { icol=0; irow++; } } data.reference(outdata); // adjust protocol prot.geometry.set_nSlices(1); prot.seqpars.set_MatrixSize(phaseDirection,newnphase); prot.seqpars.set_MatrixSize(readDirection,newnread); return true; } odin-1.8.5/odindata/fileio_png.cpp0000644000175000017500000001564411725203122014006 00000000000000#include "fileio.h" #ifdef PNGSUPPORT #include /* write a png file */ bool write_png(const char *filename, Data &buff){ FILE *fp; png_structp png_ptr; png_infop info_ptr; Log odinlog("PNGFormat","write"); ODINLOG(odinlog,normalDebug) << "Saving data of shape " << buff.shape() << " to " << filename << STD_endl; /* open the file */ fp = fopen(filename, "wb"); if (fp == NULL){ ODINLOG(odinlog,errorLog) << "Opening " << filename << " failed: " << strerror(errno) << STD_endl; errno=0; return false; } /* Create and initialize the png_struct with the desired error handler * functions. If you want to use the default stderr and longjump method, * you can supply NULL for the last three parameters. We also check that * the library version is compatible with the one used at compile time, * in case we are using dynamically linked libraries. REQUIRED. */ png_ptr = png_create_write_struct(PNG_LIBPNG_VER_STRING, NULL /*user_error_ptr*/, NULL /*user_error_fn*/, NULL /*user_warning_fn*/); if (png_ptr == NULL){ fclose(fp); ODINLOG(odinlog,errorLog) << "png_create_write_struct failed: " << (errno ? strerror(errno):"") << STD_endl; errno=0; return false; } /* Allocate/initialize the image information data. REQUIRED */ info_ptr = png_create_info_struct(png_ptr); if (info_ptr == NULL){ fclose(fp); ODINLOG(odinlog,errorLog) << "png_create_info_struct failed: " << (errno ? strerror(errno):"") << STD_endl; errno=0; return false; } /* Set error handling. REQUIRED if you aren't supplying your own * error handling functions in the png_create_write_struct() call. */ if (setjmp(png_jmpbuf(png_ptr))){ /* If we get here, we had a problem writing the file */ ODINLOG(odinlog,errorLog) << "Could not write to " << filename << " " << (errno ? strerror(errno):"") << STD_endl; errno=0; fclose(fp); png_destroy_write_struct(&png_ptr, &info_ptr); return false; } /* set up the output control if you are using standard C streams */ png_init_io(png_ptr, fp); png_set_IHDR(png_ptr, info_ptr, buff.shape()(readDim), buff.shape()(phaseDim),8, PNG_COLOR_TYPE_GRAY, PNG_INTERLACE_NONE,PNG_COMPRESSION_TYPE_DEFAULT, PNG_FILTER_TYPE_DEFAULT); /* png needs a pointer to each row */ u8bit *rp=buff.c_array(); png_byte** row_pointers= new png_byte*[buff.shape()(thirdDim)]; for (unsigned short r=0; r read_png(const char *filename){ Log odinlog("PNGFormat","read_png"); Data ret; png_byte header[8]; // 8 is the maximum size that can be checked /* open file and test for it being a png */ FILE *fp = fopen(filename, "rb"); if (!fp){ ODINLOG(odinlog,normalDebug) << "File " << filename << " could not be opened." << STD_endl; return -1; } fread(header, 1, 8, fp); if (png_sig_cmp(header, 0, 8)){ ODINLOG(odinlog,normalDebug) << "File " << filename << " is not recognized as a PNG file." << STD_endl; return -1; } png_structp png_ptr; png_infop info_ptr; /* initialize stuff */ png_ptr = png_create_read_struct(PNG_LIBPNG_VER_STRING, NULL, NULL, NULL); assert(png_ptr); info_ptr = png_create_info_struct(png_ptr); assert(info_ptr); if (setjmp(png_jmpbuf(png_ptr))); png_init_io(png_ptr, fp); png_set_sig_bytes(png_ptr, 8); png_read_info(png_ptr, info_ptr); unsigned int height=png_get_image_height(png_ptr, info_ptr); // = info_ptr->height; unsigned int width=png_get_image_width(png_ptr, info_ptr); // = info_ptr->width; unsigned char colortype=png_get_color_type(png_ptr, info_ptr); // = info_ptr->color_type; unsigned char bitdepth=png_get_bit_depth(png_ptr, info_ptr); // = info_ptr->bit_depth; ret.resize(height, width); png_set_interlace_handling(png_ptr); ODINLOG(odinlog,normalDebug) << "color_type/bit_depth=" << int(colortype) << "/" << int(bitdepth) << STD_endl; if(colortype!=PNG_COLOR_TYPE_GRAY) { ODINLOG(odinlog,errorLog) << "Unsupported color mode, only grayscale images are supported" << STD_endl; fclose(fp); return -1; } png_read_update_info(png_ptr, info_ptr); /* png needs a pointer to each row */ png_bytep* row_pointers = (png_bytep*) malloc(sizeof(png_bytep) * height); png_bytep rp=ret.c_array(); for (unsigned short r=0; r& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot){ read_png(filename.c_str()).convert_to(data); return 1; } int write(const Data& data, const STD_string& filename, const FileWriteOpts& opts, const Protocol& prot) { Log odinlog("PNGFormat","write"); Range all=Range::all(); TinyVector shape(data.shape()); unsigned short time=shape(timeDim),slices=shape(sliceDim); ODINLOG(odinlog,normalDebug) << "filename=" << filename << STD_endl; JDXfileName fname(filename); bool ok=true; int s=0,t=0; Data buff; const STD_string type(prot.system.get_data_type()); if(type!="float" && type!="double")data.convert_to(buff,noupscale); else data.convert_to(buff); for(t=0;ok && t1) onefilename+="_time"+itos(t,time-1); if(slices>1) onefilename+="_slice"+itos(s,slices-1); onefilename+="."+fname.get_suffix(); ODINLOG(odinlog,normalDebug) << "Writing " << onefilename << STD_endl; Data slice(buff(Range(t),Range(s),all,all)); ok = write_png(onefilename.c_str(), slice); } if(ok){ODINLOG(odinlog,normalDebug) << "Wrote " << t*s << " images" << STD_endl;return t*s;} else return -1; } }; #endif ////////////////////////////////////////////////////////////// void register_png_format() { #ifdef PNGSUPPORT static PNGFormat format; format.register_format(); #endif } odin-1.8.5/odindata/fileio_jdx.cpp0000644000175000017500000001417211363773554014025 00000000000000#include "fileio.h" #include "image.h" ///////////////////////////////////////////////////////////// void resize4dim(farray& fdata) { if(fdata.dim()==4) return; // leave untouched if it is already 4dim fdata.autosize(); ndim nn=fdata.get_extent(); bool add_first_dim=true; if(nn.dim()==1) add_first_dim=false; while(nn.dim()<4) nn.add_dim(1,add_first_dim); while(nn.dim()>4) --nn; fdata.redim(nn); } ///////////////////////////////////////////////////////////// struct JdxFormat : public FileFormat { STD_string description() const {return "JCAMP-DX data sets";} svector suffix() const { svector result; result.resize(2); result[0]="smp"; result[1]="coi"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("JdxFormat","read"); STD_string arrlabel=opts.jdx; if(arrlabel=="") { if(JDXfileName(filename).get_suffix()=="smp") arrlabel="spinDensity"; else { ODINLOG(odinlog,errorLog) << "No array label provided, use the 'jdx' option to specify one" << STD_endl; return -1; } } JcampDxBlock block; farray fdata; bool valid_type=false; if(!valid_type) { JDXdoubleArr dpar; dpar.set_label(arrlabel); block.clear(); block.append(dpar); if(block.load(filename)>0) { ODINLOG(odinlog,normalDebug) << "JDXdoubleArr detected" << STD_endl; fdata.redim(dpar.get_extent()); for(unsigned int i=0; i0) { ODINLOG(odinlog,normalDebug) << "JDXfloatArr detected" << STD_endl; fdata.redim(fpar.get_extent()); for(unsigned int i=0; i0) { ODINLOG(odinlog,normalDebug) << "JDXcomplexArr detected" << STD_endl; ndim nn=cpar.get_extent(); nn[0]*=2; fvector amp=amplitude(cpar); fvector pha=phase(cpar); ODINLOG(odinlog,normalDebug) << "nn=" << STD_string(nn) << STD_endl; fdata.redim(nn); unsigned int n=cpar.length(); for(unsigned int i=0; i& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) { Log odinlog("JdxFormat","write"); ODINLOG(odinlog,errorLog) << "Not implemented" << STD_endl; return -1; } }; ///////////////////////////////////////////////////////////// struct ImageFormat : public FileFormat { STD_string description() const {return "JCAMP-DX image format";} svector suffix() const { svector result; result.resize(1); result[0]="jdx"; return result; } svector dialects() const {return svector();} int read(FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileReadOpts& opts, const Protocol& protocol_template) { Log odinlog("ImageFormat","read"); int result=0; ImageSet imgset; if(imgset.load(filename)<0) return -1; int nsets=imgset.get_numof_images(); if(nsets<=0) return -1; ODINLOG(odinlog,normalDebug) << "nsets=" << nsets << STD_endl; Protocol prot(protocol_template); for(int i=0; i& data=pdmap[prot]; farray fdata=imgset.get_image(i).get_magnitude(); resize4dim(fdata); data=fdata; result+=data.extent(0)*data.extent(1); } return result; } int write(const FileIO::ProtocolDataMap& pdmap, const STD_string& filename, const FileWriteOpts& opts) { Log odinlog("ImageFormat","write"); int result=0; ImageSet imgset(filename); for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap.begin(); pdit!=pdmap.end(); ++pdit) { STD_string series; int number; pdit->first.study.get_Series(series, number); Image img(series); // use series description as image label img.set_geometry(pdit->first.geometry); img.set_magnitude(pdit->second); imgset.append_image(img); result+=pdit->second.extent(0)*pdit->second.extent(1); } if(imgset.write(filename)<0) return -1; return result; } }; ///////////////////////////////////////////////////////////// struct ProtFormat : public FileFormat { STD_string description() const {return "ODIN measurement protocols";} svector suffix() const { svector result; result.resize(1); result[0]="pro"; return result; } svector dialects() const {return svector();} int read(Data& data, const STD_string& filename, const FileReadOpts& opts, Protocol& prot) { Log odinlog("ProtFormat","read"); if(prot.load(filename)<0) return false; data.resize(1, prot.seqpars.get_MatrixSize(sliceDirection), prot.seqpars.get_MatrixSize(phaseDirection), prot.seqpars.get_MatrixSize(readDirection)); // only one repetition data=0.0; return data.extent(0)*data.extent(1); } int write(const Data& data, const STD_string& filename, const FileWriteOpts&, const Protocol& prot) { Log odinlog("ProtFormat","write"); return prot.write(filename); } }; ////////////////////////////////////////////////////////////// void register_jdx_format() { static JdxFormat jf; static ImageFormat imf; static ProtFormat pf; jf.register_format(); imf.register_format(); pf.register_format(); } odin-1.8.5/odindata/filter_detrend.cpp0000644000175000017500000000344211712547770014676 00000000000000#include "filter_detrend.h" #include "fitting.h" void FilterDeTrend::init(){ nlow=5; nlow.set_description("Number of low frequency components to be removed"); append_arg(nlow,"nlow"); zeromean=false; zeromean.set_description("Zero mean of resulting timecourse"); append_arg(zeromean,"zeromean"); } bool FilterDeTrend::process(Data& data, Protocol& prot) const { Log odinlog(c_label(),"process"); Range all=Range::all(); TinyVector shape=data.shape(); if(nlow<2 || shape(0)<2) { ODINLOG(odinlog,warningLog) << "Too few time points: nlow=" << int(nlow) << ", shape=" << shape << STD_endl; return true; } if(nlow==2) { // Remove linear trend LinearFunction linf; for(int islice=0; islice lowshape=shape; lowshape(0)=nlow; Data lowdata(data.copy()); lowdata.congrid(lowshape); lowdata.congrid(shape); if(!zeromean) { for(int islice=0; islice class FilterScale : public FilterStep { JDXfloat slope; JDXfloat offset; STD_string label() const {return "scale";} STD_string description() const {return "Rescale image values";} bool process(Data& data, Protocol& prot) const; FilterStep* allocate() const {return new FilterScale();} void init(); }; #endif odin-1.8.5/odindata/fileio_opts.cpp0000644000175000017500000000673611665172216014225 00000000000000#include "fileio_opts.h" #include "fileio.h" FileReadOpts::FileReadOpts() { format.add_item(AUTODETECTSTR); svector formats(FileIO::autoformats()); for(unsigned int i=0; i& data, Protocol& prot) const { Log odinlog(c_label(),"process"); Range all=Range::all(); ODINLOG(odinlog,normalDebug) << "angle=" << angle << STD_endl; RotMatrix rotmat; rotmat.set_inplane_rotation(angle*PII/180.0); ODINLOG(odinlog,normalDebug) << "rotmat=" << rotmat.print() << STD_endl; TinyVector offset=0.0; TinyMatrix rotation; for(int irow=0; irow<2; irow++) { for(int icol=0; icol<2; icol++) { rotation(1-irow,1-icol)=rotmat[irow][icol]; } } CoordTransformation transform(TinyVector(data.extent(phaseDim),data.extent(readDim)), rotation, offset, kernel); for(int irep=0; irep /** * @addtogroup odindata * @{ */ /** * Solves the linear system A x = b and returns x. * All singular values less than sv_truncation * max_singular_value * will be set to zero. * The algorithm uses the singular value decomposition from LAPACK (or from GSL if LAPACK is not available). * */ Data solve_linear(const Data& A, const Data& b, float sv_truncation=0.0); /** * Solves the complex linear system A x = b and returns x. * All singular values less than sv_truncation * max_singular_value * will be set to zero. * The algorithm uses the singular value decomposition from LAPACK (or from GSL if LAPACK is not available). * */ ComplexData<1> solve_linear(const ComplexData<2>& A, const ComplexData<1>& b, float sv_truncation=0.0); /** * Computes the eigenvalues of symmetric matrix A using LAPACK (or with GSL if LAPACK is not available). * */ Data eigenvalues(const Data& A); /** @} */ #endif odin-1.8.5/odindata/utils.cpp0000644000175000017500000000610111734622163013031 00000000000000#include "utils.h" #include "fitting.h" // for unit test #include "complexdata.h" // for unit test #include Data unwrap_phase(const Data& phase, int startindex) { Log odinlog("","unwrap_phase"); int n=phase.size(); Data result(n); if(startindex<0 || startindex>=n) { ODINLOG(odinlog,errorLog) << "startindex=" << startindex << " out of range (0," << (n-1) << ")" << STD_endl; return result; } for(int j=0; jPII) { ODINLOG(odinlog,errorLog) << "phase(" << j << ")=" << phase(j) << " out of range (" << -PII << "," << PII << ")" << STD_endl; return result; } } result(startindex)=phase(startindex); // unwrap going to higher indices int i=startindex; int mod=0; while( (i+1) < n ) { float diff=phase(i+1)-phase(i); if(diff>PII) mod--; if(diff<-PII) mod++; result(i+1)=phase(i+1)+mod*2.0*PII; i++; } // unwrap going to lower indices i=startindex; mod=0; while( (i-1) >= 0 ) { float diff=phase(i-1)-phase(i); if(diff>PII) mod--; if(diff<-PII) mod++; result(i-1)=phase(i-1)+mod*2.0*PII; i--; } return result; } ////////////////////////////////////////////////// // Unit Test #ifndef NO_UNIT_TEST class DataUtilsTest : public UnitTest { public: DataUtilsTest() : UnitTest("DataUtils") {} private: bool check() const { Log odinlog(this,"check"); PolynomialFunction<3> poly; poly.a[0].val=-20.0; poly.a[1].val=-10.0; poly.a[2].val=2.0; poly.a[3].val=0.5; int nx=1000; float xrange=10.0; Data xvals(nx); for(int i=0; i yvals(poly.get_function(xvals)); // yvals.autowrite("yvals.asc"); ComplexData<1> cplxdata(expc(float2imag(yvals))); Data pha(phase(cplxdata)); // pha.autowrite("pha.asc"); int nstart=5; int startindex[nstart]; startindex[0]=0; startindex[1]=nx/3; startindex[2]=nx/2; startindex[3]=3*nx/4; startindex[4]=nx-1; for(int istart=0; istart pha_unwrap(unwrap_phase(pha,startindex[istart])); pha_unwrap-=pha_unwrap(startindex[istart])-yvals(startindex[istart]); // pha_unwrap.autowrite("pha_unwrap.asc"); float diff=sum(fabs(pha_unwrap-yvals))/nx; if(diff>1.0e-5) { ODINLOG(odinlog,errorLog) << "unwrap_phase(...," << startindex[istart] << "), diff=" << diff << STD_endl; return false; } } return true; } }; void alloc_DataUtilsTest() {new DataUtilsTest();} // create test instance #endif ////////////////////////////////////////////////// // Test Instantiations #ifdef ODIN_DEBUG template Array matrix_product(const Array&, const Array&); template Array vector_product(const Array&, const Array&); template bool same_shape(const Array&, const Array&,const TinyVector&); template bool check_range(float&, float, float); #endif odin-1.8.5/odinpara/0000755000175000017500000000000011735135550011261 500000000000000odin-1.8.5/odinpara/seqpars.h0000644000175000017500000001335611455553536013047 00000000000000/*************************************************************************** seqpars.h - description ------------------- begin : Mon Mar 3 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SEQPARS_H #define SEQPARS_H #include #include #include #include #include /** * @ingroup odinpara * * \brief Sequence Parameter proxy * * This class is used to hold all common sequence parameters */ class SeqPars : public JcampDxBlock { public: /** * Constructs a SeqPars with the given label */ SeqPars(const STD_string& label="unnamedSeqPars"); /** * Constructs a copy of 'sp' */ SeqPars(const SeqPars& sp) {SeqPars::operator = (sp);} /** * Specifies the size of the image in the given direction 'dir' to 'size' */ SeqPars& set_MatrixSize(direction dir,unsigned int size, parameterMode parmode=edit); /** * Returns the size of the image in the given direction */ unsigned int get_MatrixSize(direction dir) const; /** * Specifies the repetition time of the sequence */ SeqPars& set_RepetitionTime(double time, parameterMode parmode=edit); /** * Returns the repetition time of the sequence */ double get_RepetitionTime() const {return RepetitionTime;} /** * Specifies the number of times the sequence will be repeated */ SeqPars& set_NumOfRepetitions(unsigned int times, parameterMode parmode=edit); /** * Returns the number of times the sequence will be repeated */ unsigned int get_NumOfRepetitions() const {return NumOfRepetitions;} /** * Specifies the echo time of the sequence */ SeqPars& set_EchoTime(double time, parameterMode parmode=edit); /** * Returns the echo time of the sequence */ double get_EchoTime() const {return EchoTime;} /** * Specifies the sweep width of the acquisition window */ SeqPars& set_AcqSweepWidth(double sw, parameterMode parmode=edit); /** * Returns the sweep width of the acquisition window */ double get_AcqSweepWidth() const {return AcqSweepWidth;} /** * Specifies the flip angle of the excitation pulse */ SeqPars& set_FlipAngle(double fa, parameterMode parmode=edit); /** * Returns the flip angle of the excitation pulse */ double get_FlipAngle() const {return FlipAngle;} /** * Specifies the reduction factor for parallel imaging */ SeqPars& set_ReductionFactor(unsigned int factor, parameterMode parmode=edit); /** * Returns the reduction factor for parallel imaging */ unsigned int get_ReductionFactor() const {return ReductionFactor;} /** * Specifies the partial Fourier factor (0.0 = full k-space, 1.0 = half k-space) */ SeqPars& set_PartialFourier(float factor, parameterMode parmode=edit); /** * Returns the partial Fourier factor (0.0 = full k-space, 1.0 = half k-space) */ float get_PartialFourier() const {return PartialFourier;} /** * Specifies whether RF spoiling is used */ SeqPars& set_RFSpoiling(bool flag, parameterMode parmode=edit); /** * Returns whether RF spoiling is used */ bool get_RFSpoiling() const {return RFSpoiling;} /** * Specifies whether gradient intro will be played out prior to sequence */ SeqPars& set_GradientIntro(bool flag, parameterMode parmode=edit); /** * Returns whether gradient intro will be played out prior to sequence */ bool get_GradientIntro() const {return GradientIntro;} /** * Specifies whether a physiological trigger is used */ SeqPars& set_PhysioTrigger(bool flag, parameterMode parmode=edit); /** * Returns whether a physiological trigger is used */ bool get_PhysioTrigger() const {return PhysioTrigger;} /** * Sets the label of the sequence used */ SeqPars& set_Sequence(const STD_string& seqid) {Sequence=seqid; return *this;} /** * Returns the label of the sequence used */ const STD_string& get_Sequence() const {return Sequence;} /** * Sets the total duration of the sequence in minutes */ SeqPars& set_ExpDuration(double dur) {ExpDuration=dur; return *this;} /** * Returns the total duration of the sequence in minutes */ double get_ExpDuration() const {return ExpDuration;} /** * Sets the starting time point of the sequence */ SeqPars& set_AcquisitionStart(double time) {AcquisitionStart=time; return *this;} /** * Returns the starting time point of the sequence */ double get_AcquisitionStart() const {return AcquisitionStart;} /** * Assignment operator */ SeqPars& operator = (const SeqPars& pars2); private: void append_all_members(); JDXdouble ExpDuration; JDXstring Sequence; JDXdouble AcquisitionStart; JDXint MatrixSizeRead; JDXint MatrixSizePhase; JDXint MatrixSizeSlice; JDXdouble RepetitionTime; JDXint NumOfRepetitions; JDXdouble EchoTime; JDXdouble AcqSweepWidth; JDXdouble FlipAngle; JDXint ReductionFactor; JDXfloat PartialFourier; JDXbool RFSpoiling; JDXbool GradientIntro; JDXbool PhysioTrigger; }; #endif odin-1.8.5/odinpara/jdxarrays.cpp0000644000175000017500000004654211322062341013714 00000000000000#include "jdxarrays.h" #include "jdxblock.h" // for UnitTest #include #include #define ENCODING_ID_STR "Encoding:" #define BASE64_LINELEN 72 class Base64 { public: Base64() { int i; for (i = 0; i < 9; i++) { dtable_encode[i] = 'A' + i; dtable_encode[i + 9] = 'J' + i; dtable_encode[26 + i] = 'a' + i; dtable_encode[26 + i + 9] = 'j' + i; } for (i = 0; i < 8; i++) { dtable_encode[i + 18] = 'S' + i; dtable_encode[26 + i + 18] = 's' + i; } for (i = 0; i < 10; i++) { dtable_encode[52 + i] = '0' + i; } dtable_encode[62] = '+'; dtable_encode[63] = '/'; for (i = 0; i < 255; i++) dtable_decode[i] = 0x80; for (i = 'A'; i <= 'I'; i++) dtable_decode[i] = 0 + (i - 'A'); for (i = 'J'; i <= 'R'; i++) dtable_decode[i] = 9 + (i - 'J'); for (i = 'S'; i <= 'Z'; i++) dtable_decode[i] = 18 + (i - 'S'); for (i = 'a'; i <= 'i'; i++) dtable_decode[i] = 26 + (i - 'a'); for (i = 'j'; i <= 'r'; i++) dtable_decode[i] = 35 + (i - 'j'); for (i = 's'; i <= 'z'; i++) dtable_decode[i] = 44 + (i - 's'); for (i = '0'; i <= '9'; i++) dtable_decode[i] = 52 + (i - '0'); dtable_decode[(int)'+'] = 62; dtable_decode[(int)'/'] = 63; dtable_decode[(int)'='] = 0; } static const char* get_encoding_id() {return "base64";} bool encode(STD_string* ostring, STD_ostream* ostream, unsigned char* data, unsigned int nbytes) const { int i; bool hiteof=false; unsigned int counter=0; unsigned int linelength=0; while (!hiteof) { unsigned char igroup[3], ogroup[4]; int n; unsigned char c; igroup[0] = igroup[1] = igroup[2] = 0; for (n = 0; n < 3; n++) { if(counter 0) { ogroup[0] = dtable_encode[igroup[0] >> 2]; ogroup[1] = dtable_encode[((igroup[0] & 3) << 4) | (igroup[1] >> 4)]; ogroup[2] = dtable_encode[((igroup[1] & 0xF) << 2) | (igroup[2] >> 6)]; ogroup[3] = dtable_encode[igroup[2] & 0x3F]; if (n < 3) { ogroup[3] = '='; if (n < 2) { ogroup[2] = '='; } } for (i = 0; i < 4; i++) { if (linelength >= BASE64_LINELEN) { if(ostream) (*ostream) << STD_endl; if(ostring) (*ostring)+="\n"; linelength = 0; } if(ostream) (*ostream) << ogroup[i]; if(ostring) (*ostring)+=STD_string(1,ogroup[i]); linelength++; } } } return true; } bool decode(const STD_string& istring, unsigned char* data, unsigned int reserved_nbytes) const { Log odinlog("Base64","decode"); int string_counter=0; int output_counter=0; int stringsize=istring.length(); if(!stringsize) { if(reserved_nbytes) { ODINLOG(odinlog,errorLog) << "empty string" << STD_endl; return false; } return true; } unsigned char c; unsigned char a[4], b[4], o[3]; int i; string_counter=textbegin(istring,string_counter); while (string_counter>=0 && string_counter=stringsize ) { ODINLOG(odinlog,errorLog) << "string has illegal size: string_counter/stringsize=" << string_counter << "/" << stringsize << STD_endl; return false; } c = istring[string_counter]; string_counter++; string_counter=textbegin(istring,string_counter); if (dtable_decode[c] & 0x80) { ODINLOG(odinlog,errorLog) << "Illegal character >" << c << "< in input string" << STD_endl; return false; } a[i] = c; b[i] = (unsigned char) dtable_decode[c]; } o[0] = (b[0] << 2) | (b[1] >> 4); o[1] = (b[1] << 4) | (b[2] >> 2); o[2] = (b[2] << 6) | b[3]; int nbytes2copy = a[2] == '=' ? 1 : (a[3] == '=' ? 2 : 3); for (i = 0; i < nbytes2copy; i++) { if(output_counter void JDXarray::common_init() { Log odinlog(this,"common_init"); JcampDxClass::set_parmode(noedit); // Do NOT call virtual function in constructor! guiprops.scale[xPlotScale].label="Data Point"; } template JDXarray::JDXarray (const A& a,const STD_string& name, bool userParameter, compatMode mode, parameterMode parameter_mode, const STD_string& parx_equivalent, float parx_assign_factor,float parx_assign_offset) : A(a) { Log odinlog(name.c_str(),"JDXarray(const A&)"); common_init(); set_label(name); JcampDxClass::set_compatmode(mode); // Do NOT call virtual function in constructor! set_userDefParameter(userParameter); parx_equiv.name=parx_equivalent; parx_equiv.factor=parx_assign_factor; parx_equiv.offset=parx_assign_offset; JcampDxClass::set_parmode(parameter_mode); // Do NOT call virtual function in constructor! } template JDXarray& JDXarray::operator = (const A& a) { Log odinlog(this,"operator = (const A&)"); A::operator = (a); return *this; } template JDXarray& JDXarray::operator = (const JDXarray& ja) { JcampDxClass::operator = (ja); A::operator = (ja); parx_equiv=ja.parx_equiv; return *this; } template STD_string JDXarray::get_dim_str() const { ndim nn(A::get_extent()); J basetype; if( get_compatmode()==bruker && basetype.get_typeInfo()==STD_string("string") ) { if(nn.dim()==1 && nn[0]==1) --nn; unsigned int l=0; // val.length()*_BRUKER_MODE_STRING_CAP_FACTOR_; if(l<_BRUKER_MODE_STRING_CAP_START_) l=_BRUKER_MODE_STRING_CAP_START_; nn.add_dim(l,false); } return STD_string(nn); } template bool JDXarray::encode(STD_string* ostring, STD_ostream* ostream) const { Base64 b64; unsigned char* data=(unsigned char*)A::c_array(); if(!data) return false; JDXendianess endianess; J jdxdummy; STD_string header=STD_string(ENCODING_ID_STR) +b64.get_encoding_id()+"," +endianess.JDXenum::operator STD_string ()+"," +jdxdummy.get_typeInfo()+"\n"; if(ostring) (*ostring) += header; if(ostream) (*ostream) << header; return b64.encode(ostring,ostream,data,A::length()*A::elementsize()); } template STD_ostream& JDXarray::print2stream(STD_ostream& os) const { os << get_dim_str() << "\n"; if( !(use_compression() && encode(0,&os)) ) { A::printbody2stream(os); } return os; } template STD_string JDXarray::printvalstring() const { STD_string result; if(get_filemode()==exclude) return result; result+=get_dim_str()+"\n"; if( !(use_compression() && encode(&result,0)) ) { result+=A::printbody(); } return result; } template bool JDXarray::parsevalstring(const STD_string& parstring) { Log odinlog(this,"parsevalstring"); J basetype; STD_string ps=parstring+"\n##"; STD_string sizestring="("+extract(ps,"(",")")+")"; ndim nn(sizestring); if( get_compatmode()==bruker && basetype.get_typeInfo()==STD_string("string") ) nn--; ODINLOG(odinlog,normalDebug) << "sizestring=>" << sizestring << "<" << STD_endl; STD_string valstring=extract(ps,"\n","##"); unsigned long lnn=nn.total(); if(valstring.find(ENCODING_ID_STR)==0) { // array is encoded ODINLOG(odinlog,normalDebug) << "array data is encoded, lnn=" << lnn << STD_endl; Base64 b64; STD_string header=extract(valstring,STD_string(ENCODING_ID_STR),"\n"); svector headertokens(tokens(header,',')); if(headertokens.size()!=3) { ODINLOG(odinlog,errorLog) << "Invalid encoding header" << STD_endl; return false; } STD_string encodingtype=shrink(headertokens[0]); if(encodingtype!=b64.get_encoding_id()) { ODINLOG(odinlog,errorLog) << "Unknown encoding type " << encodingtype << STD_endl; return false; } JDXendianess endianess; STD_string endianess_string=shrink(headertokens[1]); endianess.JDXenum::operator = (endianess_string); ODINLOG(odinlog,normalDebug) << "header/encodingtype/endianess_string=" << header << "/" << encodingtype << "/" << endianess_string << STD_endl; STD_string typestring=shrink(headertokens[2]); J ldrdummy; if(typestring!=ldrdummy.get_typeInfo()) { // avoid confusing error message in miview // ODINLOG(odinlog,errorLog) << "Type mismatch of encoded data: " << typestring << "!=" << ldrdummy.get_typeInfo() << STD_endl; return false; } STD_string encoded_string=extract(valstring,header,""); unsigned int elsize=A::elementsize(); unsigned int nbytes=lnn*elsize; ODINLOG(odinlog,normalDebug) << "elsize/lnn/nbytes=" << elsize << "/" << lnn << "/" << nbytes << STD_endl; // allocate correctly aligned memory unsigned char* data=(unsigned char*)A::allocate_memory(lnn); if(data) { bool encresult; if(encresult=b64.decode(encoded_string,data,nbytes)) { if(int(endianess)!=int(little_endian_byte_order())) { ODINLOG(odinlog,normalDebug) << "swapping data" << STD_endl; swabdata(data,elsize,lnn); } A::redim(nn); ODINLOG(odinlog,normalDebug) << "nn=" << STD_string(nn) << STD_endl; A::set_c_array(data,lnn); } delete[] data; return encresult; } else return false; } // array is plain ASCII svector tokenvector(tokens(valstring)); unsigned long lstr=tokenvector.size(); if(lstr<1) { A::resize(0); return true; } if(lstr!=lnn) { ODINLOG(odinlog,errorLog) << "size mismatch ("<< lstr << "!=" << lnn << ")" << STD_endl; return false; } ODINLOG(odinlog,normalDebug) << "anlayzed " << lnn << " tokens" << STD_endl; A::redim(nn); J jdxdummy; for(unsigned long i=0;i STD_string JDXarray::get_parx_code(parxCodeType type, const ParxEquiv& equiv) const { #ifdef PARAVISION_PLUGIN Log odinlog(this,"get_parx_code"); STD_string result=JcampDxClass::get_parx_code(type,equiv); int d; if(type==parx_def) { J jdxdummy; d=A::dim(); if( get_compatmode()==bruker && jdxdummy.get_typeInfo()==STD_string("string") ) d++; if(d<=0) d=1; STD_string parx_type(jdxdummy.get_parx_equiv().type); if(parx_type=="float") parx_type="double"; return get_parx_def_string(parx_type,d); } if(type==parx_passval) { if(!A::dim()) return ""; STD_string src,dst,transformation; result=""; dst=equiv.name; src=get_label(); STD_string dstpostfix,srcelement,dstelement; STD_string dstprefix(dst); if(dstprefix.find("[]")!=STD_string::npos) { dstprefix=replaceStr(dstprefix,"[]",""); result+="PARX_change_dims(\""+dstprefix+dstpostfix+"\","; for(d=0;d const char* JDXarray::get_typeInfo() const { J jdxdummy; typeInfo_cache=STD_string(jdxdummy.get_typeInfo())+"Arr"; return typeInfo_cache.c_str(); } //////////////////////////////////////////////////////////// template class JDXarray; template class JDXarray; template class JDXarray; template class JDXarray; template class JDXarray; //////////////////////////////////////////////////////////// JDXtriple::JDXtriple (float xpos,float ypos, float zpos, const STD_string& name,bool userParameter, compatMode, parameterMode parameter_mode) : JDXfloatArr(farray(3),name,userParameter,bruker,parameter_mode) { (*this)[0]=xpos; (*this)[1]=ypos; (*this)[2]=zpos; } /////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class JDXstringArrTest : public UnitTest { public: JDXstringArrTest() : UnitTest("JDXstringArr") {} private: bool check() const { Log odinlog(this,"check"); sarray sarr(3); sarr(0)="item1"; sarr(1)="item2"; sarr(2)="item3"; JDXstringArr teststrarr1(sarr,"teststrarr1",true,notBroken); JDXstringArr teststrarr2(sarr,"teststrarr2",true,bruker); // testing JDXstringArr::print STD_string expected="##$teststrarr1=( 3 )\n \n"; STD_string printed=teststrarr1.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXstringArr::print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } expected="##$teststrarr2=( 3, "+itos(_BRUKER_MODE_STRING_CAP_START_)+" )\n \n"; printed=teststrarr2.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXstringArr::print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } // testing JDXstringArr::parse JcampDxBlock arrblock; arrblock.append(teststrarr1); arrblock.append(teststrarr2); int parseresult_arr=arrblock.parseblock("##TITLE=arrblock\n##$teststrarr1=(2)\n \n##$teststrarr2=(2,123)\n \n##END="); if(parseresult_arr!=2) { ODINLOG(odinlog,errorLog) << "JcampDxBlock::parseblock() failed: parseresult_arr=" << parseresult_arr << "!=" << 2 << STD_endl; return false; } if(STD_string(arrblock.get_label())!="arrblock") { ODINLOG(odinlog,errorLog) << "JcampDxBlock::get_label() failed: " << arrblock.get_label() << "!=arrblock" << STD_endl; return false; } if(STD_string(teststrarr2[1])!="str2") { ODINLOG(odinlog,errorLog) << "element 1 of JDXstringArr: " << STD_string(teststrarr1[1]) << "!=" << "str2" << STD_endl; ODINLOG(odinlog,errorLog) << "teststrarr2=" << teststrarr2.printbody() << STD_endl; return false; } teststrarr2.set_compatmode(notBroken); if(STD_vector(teststrarr1)!=STD_vector(teststrarr2)) { // cast required for vxworks ODINLOG(odinlog,errorLog) << "after arrblock.parseblock(): " << teststrarr1 << "!=" << teststrarr2 << STD_endl; return false; } return true; } }; void alloc_JDXstringArrTest() {new JDXstringArrTest();} // create test instance /////////////////////////////////////////////////////////////////// class JDXintArrTest : public UnitTest { public: JDXintArrTest() : UnitTest("JDXintArr") {} private: bool check() const { Log odinlog(this,"check"); // testing JDXintArr JDXintArr testintarr(iarray(2,2),"testintarr"); testintarr(0,0)=1; testintarr(0,1)=2; testintarr(1,0)=3; testintarr(1,1)=4; STD_string expected="##$testintarr=( 2, 2 )\n1 2 3 4\n"; STD_string printed=testintarr.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXintArr::print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } JcampDxBlock intarrblock; intarrblock.append(testintarr); intarrblock.parseblock("##TITLE=intarrblock\n##$testintarr=(2,2)\n3 4 5 6\n##END="); if(testintarr.sum()!=18) { ODINLOG(odinlog,errorLog) << "after intarrblock.parseblock(): " << testintarr.sum() << "!=" << 18 << STD_endl; return false; } testintarr=testintarr*2; if(testintarr.sum()!=36) { ODINLOG(odinlog,errorLog) << "JDXintArr *= " << testintarr.sum() << "!=" << 36 << STD_endl; return false; } return true; } }; void alloc_JDXintArrTest() {new JDXintArrTest();} // create test instance /////////////////////////////////////////////////////////////////// class JDXcomplexArrTest : public UnitTest { public: JDXcomplexArrTest() : UnitTest("JDXcomplexArr") {} private: bool check() const { Log odinlog(this,"check"); // testing compression of JDXcomplexArr JDXcomplexArr testcarr(carray(100,20),"testcarr"); testcarr.set_filemode(compressed); for(unsigned int i=0; i" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } return true; } }; void alloc_JDXcomplexArrTest() {new JDXcomplexArrTest();} // create test instance #endif odin-1.8.5/odinpara/jdxbase.h0000644000175000017500000003467711363773555013025 00000000000000/*************************************************************************** jdxbase.h - description ------------------- begin : Sun Jun 6 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXBASE_H #define JDXBASE_H #include #include #include #include // some defines for Bruker-type strings #define _BRUKER_MODE_STRING_CAP_START_ 1000 #define _BRUKER_MODE_STRING_MIN_SIZE_ 256 #define _BRUKER_MODE_STRING_CAP_FACTOR_ 3 /** * @addtogroup jcampdx * @{ */ /** * * This enum performs some fine tuning with the JcampDx classes according * its value: * - bruker: Strings are treated as arrays of characters (size after '=' and contents on next line). * Used to be compatible with Brukers JCAMP-DX implementation. * - notBroken: Strings are written directly into the file (after '='). */ enum compatMode {bruker,notBroken}; /** * This enum determines whether the parameter can be seen/edited in the graphical user interface * - edit: Parameter is visible and can be edited * - noedit: Parameter is visible but cannot be edited * - hidden: Parameter is invisible */ enum parameterMode {edit,noedit,hidden}; /** * This enum determines whether the parameter will be included/compressed/excluded when reading/writing a file * - include: Parameter is included in the file * - compressed: Parameter is included in the file in compressed ASCII-format (e.g. Base64 encoding) * if its representation exceeds a certain size * - exclude: Parameter is excluded from the file */ enum fileMode {include,compressed,exclude}; /////////////////////////////////////////////////////////////////////// class JcampDxBlock; // Forward Declaration class JDXfunction; // Forward Declaration class JDXtriple; // Forward Declaration class JDXaction; // Forward Declaration class JDXenum; // Forward Declaration class JDXfileName; // Forward Declaration class JDXformula; // Forward Declaration class JDXrecoIndices; // Forward Declaration /////////////////////////////////////////////////////////////////////// /** * * Helper class for debugging the JcampDx component */ class JcampDx { public: static const char* get_compName(); }; /////////////////////////////////////////////////////////////////////// /** * Enum for plot/display scales/axes in the GUI * - displayScale: Scale for 2D/3D display * - xPlotScale: x-axis (bottom) * - yPlotScaleLeft: First y-axis (left) * - yPlotScaleRight: Second y-axis (left) */ enum scaleType {displayScale=0,xPlotScale,yPlotScaleLeft,yPlotScaleRight,n_ScaleTypes}; /** * Data structure to store info about scales of JDXarrays in GUI */ struct ArrayScale { ArrayScale() : minval(0), maxval(0) {} ArrayScale(const STD_string& scalelabel, const STD_string& scaleunit, float scalemin=0.0, float scalemax=0.0); STD_string get_label_with_unit() const; /** * Axis label */ STD_string label; /** * Axis physical unit */ STD_string unit; /** * Lower and upper bound of scale */ float minval,maxval; }; /////////////////////////////////////////////////////////////////////// /** * Data structure to store info about 2D/3D plots of JDXarrays */ struct PixmapProps { PixmapProps() : minsize(128), maxsize(1024), autoscale(true), color(false), overlay_minval(0), overlay_maxval(0), overlay_firescale(false), overlay_rectsize(0.8f) {} void get_overlay_range(float& min, float& max) const; /** * The min and max width/height in the GUI */ unsigned int minsize, maxsize; /** * Do auto-windowing/scaling of values */ bool autoscale; /** * Display values color encoded */ bool color; /** * Extra map to be overlaid on plot in color code */ farray overlay_map; /** * Range of displayed values of overlay map. If both are zero, autoscaling is applied. */ float overlay_minval, overlay_maxval; /** * Use only yellow to red from color wheel */ bool overlay_firescale; /** * The relative size (between 0 and 1) of rectangles representing overlayed voxels */ float overlay_rectsize; }; /////////////////////////////////////////////////////////////////////// /** * Data structure to store info about GUI display of JDXarrays */ struct GuiProps { GuiProps() : fixedsize(true) {} /** * The scales in 1D or 2D display */ ArrayScale scale[n_ScaleTypes]; /** * Whether the size is fixed in 1D mode. If so, it is possible to detach the widget * to display it in larger size. */ bool fixedsize; /** * Properties of the map in 2D mode */ PixmapProps pixmap; }; /////////////////////////////////////////////////////////////////////// /** * * Enum for PARX code generation: * - parx_def: Parameter definitions * - parx_passval: Parameter assignment * - parx_passval_head: Function head for parameter assignment * - parx_parclass_def: Definition of parameter class * - parx_parclass_init: Initialization of parameter class * - parx_parclass_passval: Assignment of parameter class */ enum parxCodeType {parx_def, parx_passval, parx_passval_head, parx_parclass_def, parx_parclass_init, parx_parclass_passval}; /** * Data structure to store info about the equivalent PARX(Bruker) parameter * to which this parameter will be mapped */ struct ParxEquiv { ParxEquiv() : factor(1.0), offset(0.0) {} /** * Parx name */ STD_string name; /** * Parx type */ STD_string type; /** * Scaling factor in assignment */ double factor; /** * Offset in assignment */ double offset; }; /////////////////////////////////////////////////////////////////////// /** * * This is the (virtual) base class * that carries the JcampDx specific interface, i.e. all common * functions that are specific to JcampDx. Most of the elements * show a simple default behaviour that will be overwritten by * a reasonable behaviour in the derived classes. */ class JcampDxClass : public ListItem, public virtual Labeled { public: virtual ~JcampDxClass(); /** * * This function returns the parameter in JcampDx-ASCII-format */ virtual STD_string print() const; /** * Passes the parameter in ASCII format to the ostream 'os' */ virtual STD_ostream& print2stream(STD_ostream& os) const {return os << printvalstring();} /** * Stream operator */ friend STD_ostream& operator << (STD_ostream& s,const JcampDxClass& value) { return value.print2stream(s);} /** * Parses the JCAMP-DX parameter. Except for blocks, this is done by * stripping the label (e.g. "##$MyParameter=" ) from the string and passing the * result to the function 'parsevalstring' of the underlying data type. * For blocks, a re-implemented 'parse' function is called. * Returns 'true' if the parameter was parsed successfully. */ virtual bool parse(STD_string& parstring); /** * * Loads the parameter(s) from a JCAMP-DX file. In case of calling this function * of a single paramter, the file is searched for this parameter and the value * is assigned. In case of a parameter block, all parameter values are taken * from the file. * The return value is the number of parameters which are successfully parsed. * If an error occurs, -1 is returned. */ virtual int load(const STD_string &filename); /** * * Writes the parameter(s) to a JCAMP-DX file. In case of calling this function * of a single paramter, the file will consist of only this parameter. In case * of a parameter block, all parameter values are written to the file. * If an error occurs, -1 is returned. */ virtual int write(const STD_string &filename) const; /** * * Parses and assigns the value in the given string */ virtual bool parsevalstring (const STD_string&) = 0; /** * * Returns the value of the parameter as a string */ virtual STD_string printvalstring() const = 0; /** * * Sets the compatability mode. See the documentation to 'compatMode' */ virtual JcampDxClass& set_compatmode(compatMode compat_mode) {compatmode=compat_mode; return *this;} /** * * Returns the compatability mode. See the documentation to 'compatMode' */ virtual compatMode get_compatmode() const {return compatmode;} /** * Returns a string describing the type of the parameter */ virtual const char* get_typeInfo() const = 0; /** * Returns the minimum allowed value of the parameter. * Only used when editing the parameter in a GUI */ virtual double get_minval() const {return 0.0;} /** * Returns the maximum allowed value of the parameter * Only used when editing the parameter in a GUI */ virtual double get_maxval() const {return 0.0;} /** * Returns whether the paramerer has a valid interval of allowed values. * Only used when editing the parameter in a GUI */ bool has_minmax() const {return get_maxval()>get_minval();} /** * Returns a deep copy of the parameter */ virtual JcampDxClass* create_copy() const = 0; /** * * Determines whether the parameter is user defined, see [1,2] for details. */ JcampDxClass& set_userDefParameter(bool userDef) {userDefParameter=userDef; return *this;} /** * * Returns whether the parameter is user defined, see [1,2] for details. */ bool isUserDefParameter() const {return userDefParameter;} /** * * Returns the description of the parameter, used in the text of tooltips in a GUI */ const STD_string& get_description() const {return description;} /** * * Sets the description of the parameter, used in the text of tooltips in a GUI */ JcampDxClass& set_description(const STD_string& descr) {description=descr; return *this;} /** * Returns possible alternative values of the parameter, i.e. the item strings of an enum */ virtual svector get_alternatives() const {return svector();} /** * * Returns the physical unit of the parameter */ const STD_string& get_unit() const {return unit;} /** * * Sets the physical unit of the parameter */ JcampDxClass& set_unit(const STD_string& un) {unit=un; return *this;} /** * * Returns the parameterMode */ virtual parameterMode get_parmode() const {return parmode;} /** * * Sets the parameterMode */ virtual JcampDxClass& set_parmode(parameterMode parameter_mode) {parmode=parameter_mode; return *this;} /** * * Returns the fileMode */ virtual fileMode get_filemode() const {return filemode;} /** * * Sets the fileMode */ virtual JcampDxClass& set_filemode(fileMode file_mode) {filemode=file_mode; return *this;} /** * * Returns the properties of axis display in the GUI, only useful for JDXarrays */ virtual GuiProps get_gui_props() const {return GuiProps();} /** * * Sets the properties of axis display in the GUI, only useful for JDXarrays */ virtual JcampDxClass& set_gui_props(const GuiProps&) {return *this;} /** * * Returns C code that can be used together with the PARX(Bruker) compiler. */ virtual STD_string get_parx_code(parxCodeType type, const ParxEquiv& equiv=ParxEquiv()) const; /** * * Returns the name and scaling of an equivalent parameter in PARX. Code for automatic * mapping to the PARX parameter space can be generated using the function * get_parx_code(). */ virtual ParxEquiv get_parx_equiv() const {ParxEquiv pe; pe.type=get_typeInfo(); return pe;} // virtual functions to emulate a dynamic cast virtual JcampDxBlock* cast(JcampDxBlock*) {return 0;} virtual int* cast(int*) {return 0;} virtual long* cast(long*) {return 0;} virtual float* cast(float*) {return 0;} virtual double* cast(double*) {return 0;} virtual bool* cast(bool*) {return 0;} virtual STD_complex* cast(STD_complex*) {return 0;} virtual JDXenum* cast(JDXenum*) {return 0;} virtual STD_string* cast(STD_string*) {return 0;} virtual JDXfileName* cast(JDXfileName*) {return 0;} virtual JDXformula* cast(JDXformula*) {return 0;} virtual JDXaction* cast(JDXaction*) {return 0;} virtual iarray* cast(iarray*) {return 0;} virtual darray* cast(darray*) {return 0;} virtual farray* cast(farray*) {return 0;} virtual carray* cast(carray*) {return 0;} virtual sarray* cast(sarray*) {return 0;} virtual JDXtriple* cast(JDXtriple*) {return 0;} virtual JDXfunction* cast(JDXfunction*) {return 0;} // with these functions it is possible to assign a unique id to each paramerer int set_parameter_id(int newid) {id=newid; return 0;} int get_parameter_id() const {return id;} JcampDxClass& set_cmdline_option(const STD_string& opt) {cmdline_option=opt; return *this;} STD_string get_cmdline_option() const {return cmdline_option;} protected: JcampDxClass(); JcampDxClass(const JcampDxClass& jdc); JcampDxClass& operator = (const JcampDxClass& jdc); STD_string get_parx_def_string(const STD_string type, unsigned int dim) const; private: friend class JDXwidget; friend class JcampDxBlock; virtual STD_string get_jdx_prefix() const; virtual STD_string get_jdx_postfix() const {return "\n";} compatMode compatmode; bool userDefParameter; parameterMode parmode; fileMode filemode; STD_string description; STD_string unit; int id; STD_string cmdline_option; }; /////////////////////////////////////////////////////////////// // // Some interface classes which help editing parameters in a GUI class JDXeditWidget { public: virtual void updateWidget() = 0; virtual ~JDXeditWidget() {} // to avoid compiler warnings }; class JDXeditCaller { public: virtual void parameter_relations(JDXeditWidget* editwidget) = 0; virtual ~JDXeditCaller() {} // to avoid compiler warnings }; /** @} */ #endif odin-1.8.5/odinpara/geometry.cpp0000644000175000017500000006032211725203122013531 00000000000000#include "geometry.h" #include RotMatrix::RotMatrix(const STD_string& label) { int i,j; set_label(label); for( i = 0; i < 3; i++) for( j = 0; j < 3; j++) if ( i == j) matrix[i][j] = 1; else matrix[i][j] = 0; }; RotMatrix::RotMatrix(const RotMatrix& sct) { RotMatrix::operator =(sct); }; RotMatrix& RotMatrix::operator =(const RotMatrix& sct){ set_label(sct.get_label()); int i,j; for( i = 0; i < 3; i++) for( j = 0; j < 3; j++) matrix[i][j] = sct[i][j]; // check_and_correct(); return *this; }; bool RotMatrix::operator == (const RotMatrix& srm) const{ for(int i=0; i < 3; i++) for(int j=0; j < 3; j++) if(fabs(srm[i][j]-matrix[i][j])>ODIN_GEO_CHECK_LIMIT) return false; return true; }; bool RotMatrix::operator < (const RotMatrix& srm) const{ for(int i=0; i < 3; i++) for(int j=0; j < 3; j++) if(!(srm[i][j] < matrix[i][j])) return false; return true; }; dvector RotMatrix::operator * (const dvector& vec) const { dvector result(3); result=0; for(int i=0; i < 3; i++) for(int j=0; j < 3; j++) result[i]+=matrix[i][j]*vec[j]; return result; } RotMatrix RotMatrix::operator * (const RotMatrix& matrix) const { RotMatrix result; int i,j,k; double scalprod; for(j=0; j<3; j++) { for(i=0; i<3; i++) { scalprod=0.0; for(k=0; k<3; k++) { scalprod+= matrix [k][i]*(*this)[j][k]; } result[j][i]=scalprod; } } return result; } RotMatrix::operator farray () const { farray result(3,3); for(int i=0; i < 3; i++) { for(int j=0; j < 3; j++) { result(i,j)=matrix[i][j]; } } return result; } STD_string RotMatrix::print() const { // make C-style 9-array so that it can be reused in code generator STD_string result("{"); for(int i=0; i < 3; i++) { for(int j=0; j < 3; j++) { if(fabs(matrix[i][j])>10e-5) result+=ftos(matrix[i][j]); else result+="0"; if(i!=2 || j!=2) { result+=","; if(j==2) result+=" "; } } } result+="}"; return result; } RotMatrix& RotMatrix::set_inplane_rotation(float phi) { Log odinlog(this,"set_inplane_rotation"); ODINLOG(odinlog,normalDebug) << "phi=" << phi << STD_endl; float si=sin(phi); float co=cos(phi); (*this)[0][0]=co; (*this)[0][1]=-si; (*this)[0][2]=0.0; (*this)[1][0]=si; (*this)[1][1]=co; (*this)[1][2]=0.0; (*this)[2][0]=0.0; (*this)[2][1]=0.0; (*this)[2][2]=1.0; return *this; } //////////////////////////////////////////////////////////////////////////// Geometry& Geometry::reset() { FOVread=ODIN_DEFAULT_FOV; offsetRead=0.0; FOVphase=ODIN_DEFAULT_FOV; offsetPhase=0.0; FOVslice=ODIN_DEFAULT_FOV; offsetSlice=0.0; nSlices=1; sliceThickness=5.0; sliceDistance=10.0; heightAngle=0.0; azimutAngle=0.0; inplaneAngle=0.0; reverseSlice=false; return *this; } Geometry::Geometry(const STD_string& label) : JcampDxBlock(label) { Log odinlog(this,"Geometry(const STD_string&)"); Mode.add_item("SlicePack",slicepack); Mode.add_item("Voxel/3D",voxel_3d); Mode.set_actual(slicepack); Mode.set_description("Acquisition mode, i.e. whether sequence is multi-slice- or voxel/3D-selective"); FOVread.set_unit(ODIN_SPAT_UNIT).set_description("FOV in read direction").set_cmdline_option("fr"); offsetRead.set_unit(ODIN_SPAT_UNIT).set_description("Spatial offset in read direction relative to isocenter"); FOVphase.set_unit(ODIN_SPAT_UNIT).set_description("FOV in phase direction").set_cmdline_option("fp"); offsetPhase.set_unit(ODIN_SPAT_UNIT).set_description("Spatial offset in phase direction relative to isocenter"); FOVslice.set_unit(ODIN_SPAT_UNIT).set_description("FOV in slice direction").set_cmdline_option("fs"); offsetSlice.set_unit(ODIN_SPAT_UNIT).set_description("Spatial offset in slice direction relative to isocenter"); nSlices.set_description("Number of sices"); sliceThickness.set_unit(ODIN_SPAT_UNIT).set_cmdline_option("st").set_description("Slice thickness"); sliceDistance.set_unit(ODIN_SPAT_UNIT).set_cmdline_option("sd").set_description("Inter-slice distance (from center to center)"); heightAngle.set_description("1st orientation angle"); azimutAngle.set_description("2nd orientation angle"); inplaneAngle.set_description("3rd orientation angle"); reverseSlice.set_description("Reverse direction of slice vector"); Reset.set_description("Reset to default values"); Transpose.set_description("Transpose in-plane"); reset(); // set default values FOVread.set_minmaxval(0.0,2.0*ODIN_DEFAULT_FOV); offsetRead.set_minmaxval(0.5*-ODIN_DEFAULT_FOV,0.5*ODIN_DEFAULT_FOV); FOVphase.set_minmaxval(0.0,2.0*ODIN_DEFAULT_FOV); offsetPhase.set_minmaxval(0.5*-ODIN_DEFAULT_FOV,0.5*ODIN_DEFAULT_FOV); FOVslice.set_minmaxval(0.0,2.0*ODIN_DEFAULT_FOV); offsetSlice.set_minmaxval(0.5*-ODIN_DEFAULT_FOV,0.5*ODIN_DEFAULT_FOV); nSlices.set_minmaxval(1,ODIN_MAX_NUMOF_SLICES); sliceThickness.set_minmaxval(0.0,50.0); sliceDistance.set_minmaxval(0.0,0.5*ODIN_DEFAULT_FOV); heightAngle.set_minmaxval(-180.0,180.0); azimutAngle.set_minmaxval(-180.0,180.0); inplaneAngle.set_minmaxval(-180.0,180.0); Reset.set_filemode(exclude); Transpose.set_filemode(exclude); append_all_members(); update(); } Geometry::Geometry(const Geometry& ia) { Log odinlog(this,"Geometry(const Geometry&)"); Geometry::operator = (ia); } Geometry& Geometry::operator = (const Geometry& ia) { Log odinlog(this,"Geometry::operator ="); JcampDxBlock::operator = (ia); append_all_members(); // copy only visible members of JcampDxBlock copy_ldr_vals(ia); update(); return *this; } Geometry& Geometry::set_Mode(geometryMode mode) { Log odinlog(this,"set_Mode"); Mode.set_actual(mode); ODINLOG(odinlog,normalDebug) << "Mode/mode=" << Mode.JDXenum::operator STD_string() << "/" << mode << STD_endl; update(); return *this; } Geometry& Geometry::update() { Log odinlog(this,"update"); if(Reset) reset(); if(Transpose) transpose_inplane(); FOVslice.set_parmode(edit); nSlices.set_parmode(edit); sliceThickness.set_parmode(edit); sliceDistance.set_parmode(edit); if(int(Mode)==slicepack) { FOVslice=sliceThickness+(double)(nSlices-1)*sliceDistance; FOVslice.set_parmode(hidden); } if(int(Mode)==voxel_3d) { nSlices=1; nSlices.set_parmode(hidden); sliceThickness=double(FOVslice); sliceThickness.set_parmode(hidden); sliceDistance=0.0; sliceDistance.set_parmode(hidden); } cache_up2date=false; return *this; } /* int Geometry::load(const STD_string &filename) { int stat=JcampDxBlock::load(filename); // read once to set correct mode if(stat<=0) return -1; update(); // set new mode return JcampDxBlock::load(filename); } */ Geometry& Geometry::set_FOV(direction dir,double fov) { if(dir==readDirection) FOVread=fov; if(dir==phaseDirection) FOVphase=fov; if(dir==sliceDirection) FOVslice=fov; update(); return *this; } double Geometry::get_FOV(direction dir) const { if(dir==readDirection) return FOVread; if(dir==phaseDirection) return FOVphase; if(dir==sliceDirection) return FOVslice; return 0.0; } Geometry& Geometry::set_offset(direction dir,double offset) { if(dir==readDirection) offsetRead=offset; if(dir==phaseDirection) offsetPhase=offset; if(dir==sliceDirection) offsetSlice=offset; update(); return *this; } double Geometry::get_offset(direction dir) const { if(dir==readDirection) return offsetRead; if(dir==phaseDirection) return offsetPhase; if(dir==sliceDirection) return offsetSlice; return 0.0; } Geometry& Geometry::set_nSlices(unsigned int nslices) {nSlices=nslices; update(); return *this;} Geometry& Geometry::set_sliceThickness(double thick) {sliceThickness=thick; update(); return *this;} Geometry& Geometry::set_sliceDistance(double dist) {sliceDistance=dist; update(); return *this;} dvector Geometry::get_readVector_inplane() const { Log odinlog(this,"get_readVector_inplane"); double phiplus=deg2rad(azimutAngle)+0.5*PII; ODINLOG(odinlog,normalDebug) << "azimutAngle=" << double(azimutAngle) << STD_endl; ODINLOG(odinlog,normalDebug) << "phiplus=" << phiplus << STD_endl; dvector result(3); result[xAxis]=sin(phiplus); result[yAxis]=0.0; result[zAxis]=cos(phiplus); ODINLOG(odinlog,normalDebug) << "=" << result.printbody() << STD_endl; return result; } dvector Geometry::get_phaseVector_inplane() const { Log odinlog(this,"get_phaseVector_inplane"); double tetaplus=deg2rad(heightAngle)+0.5*PII; double phi=deg2rad(azimutAngle); dvector result(3); result[xAxis]=cos(tetaplus)*sin(phi); result[yAxis]=sin(tetaplus); result[zAxis]=cos(tetaplus)*cos(phi); ODINLOG(odinlog,normalDebug) << "=" << result.printbody() << STD_endl; return result; } dvector Geometry::get_readVector() const { double cos_inplane=cos(deg2rad(inplaneAngle)); double sin_inplane=sin(deg2rad(inplaneAngle)); return cos_inplane*get_readVector_inplane()-sin_inplane*get_phaseVector_inplane(); } dvector Geometry::get_phaseVector() const { return sin(deg2rad(inplaneAngle))*get_readVector_inplane()+cos(deg2rad(inplaneAngle))*get_phaseVector_inplane(); } dvector Geometry::get_sliceVector() const { double teta=deg2rad(heightAngle); double phi=deg2rad(azimutAngle); dvector result(3); result[xAxis]=cos(teta)*sin(phi); result[yAxis]=sin(teta); result[zAxis]=cos(teta)*cos(phi); return pow(-1.0,reverseSlice)*result; } dvector Geometry::get_sliceOffsetVector() const { dvector result(nSlices); double range=(double)(nSlices-1)*sliceDistance; result.fill_linear(offsetSlice-0.5*range,offsetSlice+0.5*range); return result; } darray Geometry::get_cornerPoints(const Geometry& background, unsigned int backgrslice) const { Log odinlog(this,"get_cornerPoints"); unsigned int n_boundaries_slice=n_boundaries; if(Mode==slicepack) n_boundaries_slice=1; darray result(nSlices,n_boundaries,n_boundaries,n_boundaries_slice,n_axes); dvector sliceoffset=get_sliceOffsetVector(); ODINLOG(odinlog,normalDebug) << "sliceoffset=" << sliceoffset.printbody() << STD_endl; dvector slicevector(3); dvector readvector(3); dvector phasevector(3); dvector totalvector(3); double signread,signphase,signslice; double backgrslicedelta=background.get_sliceOffsetVector()[backgrslice]-background.get_offset(sliceDirection); ODINLOG(odinlog,normalDebug) << "backgrslicedelta[" << backgrslice << "]=" << backgrslicedelta << STD_endl; ODINLOG(odinlog,normalDebug) << background.get_label() << "=" << background.get_gradrotmatrix().print() << STD_endl; for(unsigned int j=0;j=xabs) && (yabs>=zabs)) result=coronal; if((xabs>=yabs) && (xabs>=zabs)) result=sagittal; ODINLOG(odinlog,normalDebug) << "result("<< svec.printbody() << ")=" << result << STD_endl; return result; } void Geometry::get_orientation(double& heightAng, double& azimutAng, double& inplaneAng, bool& revSlice) const { heightAng=heightAngle; azimutAng=azimutAngle; inplaneAng=inplaneAngle; revSlice=reverseSlice; } Geometry& Geometry::set_orientation(double heightAng, double azimutAng, double inplaneAng, bool revSlice) { heightAngle=heightAng; azimutAngle=azimutAng; inplaneAngle=inplaneAng; reverseSlice=revSlice; update(); return *this; } Geometry& Geometry::set_orientation_and_offset(const dvector& readvec, const dvector& phasevec, const dvector& slicevec, const dvector& centervec) { Log odinlog(this,"set_orientation_and_offset"); dvector rvec(3); dvector pvec(3); dvector svec(3); // calculate length 1 vectors double inv_length; inv_length=secureInv(norm3(readvec[0], readvec[1], readvec[2])); rvec=inv_length*readvec; inv_length=secureInv(norm3(phasevec[0],phasevec[1],phasevec[2])); pvec=inv_length*phasevec; inv_length=secureInv(norm3(slicevec[0],slicevec[1],slicevec[2])); svec=inv_length*slicevec; // check orthogonality double deviation=0.0; deviation=STD_max(deviation, fabs((rvec*pvec).sum())); deviation=STD_max(deviation, fabs((pvec*svec).sum())); deviation=STD_max(deviation, fabs((svec*rvec).sum())); if(deviation>ODIN_GEO_CHECK_LIMIT) { ODINLOG(odinlog,errorLog) << "Non-orthogonal read/phase/slice-system provided, deviation=" << deviation << STD_endl; return *this; } // calculate handness dvector rp_crossproduct(3); rp_crossproduct[0] = rvec[1]*pvec[2] - rvec[2]*pvec[1]; rp_crossproduct[1] = rvec[2]*pvec[0] - rvec[0]*pvec[2]; rp_crossproduct[2] = rvec[0]*pvec[1] - rvec[1]*pvec[0]; // check handness of coordinate system double handness_product=(svec*rp_crossproduct).sum(); ODINLOG(odinlog,normalDebug) << "handness_product=" << handness_product << STD_endl; reverseSlice=(handness_product<0.0); // calculate polar orientation angles, use rp_crossproduct which has positive handness azimutAngle=180.0/PII*atan2(rp_crossproduct[0],rp_crossproduct[2]); heightAngle=180.0/PII*asin(rp_crossproduct[1]); ODINLOG(odinlog,normalDebug) << "azimutAngle/heightAngle=" << azimutAngle << "/" << heightAngle << STD_endl; // calculate inplane rotation dvector rvec_inplane(get_readVector_inplane()); dvector pvec_inplane(get_phaseVector_inplane()); double rr_scalarproduct=(rvec*rvec_inplane).sum(); double rp_scalarproduct=(rvec*pvec_inplane).sum(); if(rr_scalarproduct>1.0) rr_scalarproduct=1.0; if(rr_scalarproduct<-1.0) rr_scalarproduct=-1.0; if(rp_scalarproduct>1.0) rp_scalarproduct=1.0; if(rp_scalarproduct<-1.0) rp_scalarproduct=-1.0; ODINLOG(odinlog,normalDebug) << "rr/rp_scalarproduct=" << rr_scalarproduct << "/" << rp_scalarproduct << STD_endl; inplaneAngle=180.0/PII*atan2(-rp_scalarproduct,rr_scalarproduct); // clock-wise angle ODINLOG(odinlog,normalDebug) << "inplaneAngle=" << inplaneAngle << STD_endl; // calculate spatial offsets offsetRead =(centervec*rvec).sum(); //scalar product offsetPhase=(centervec*pvec).sum(); //scalar product offsetSlice=(centervec*svec).sum(); //scalar product ODINLOG(odinlog,normalDebug) << "offset=" << offsetRead << "/" << offsetPhase << "/" << offsetSlice << STD_endl; update(); return *this; } dvector Geometry::get_center() const { return get_offset(readDirection) *get_readVector() + get_offset(phaseDirection)*get_phaseVector() + get_offset(sliceDirection)*get_sliceVector(); } RotMatrix Geometry::get_gradrotmatrix(bool transpose) const { Log odinlog(this,"get_gradrotmatrix"); RotMatrix result; dvector perpvector(3); // double s1,s2,s3,s4,s5,s6; unsigned int i; perpvector=get_readVector(); ODINLOG(odinlog,normalDebug) << "perpRead=" << perpvector.printbody() << STD_endl; for(i=0;i<3;i++) { if(transpose) result[0][i]=perpvector[i]; else result[i][0]=perpvector[i]; } /* s1=perpvector[0]; s2=perpvector[2]; s3=perpvector[1]; s4=perpvector[2]; s5=perpvector[1]; s6=perpvector[0]; */ perpvector=get_phaseVector(); ODINLOG(odinlog,normalDebug) << "perpPhase=" << perpvector.printbody() << STD_endl; for(i=0;i<3;i++) { if(transpose) result[1][i]=perpvector[i]; else result[i][1]=perpvector[i]; } /* s1*=perpvector[1]; s2*=perpvector[0]; s3*=perpvector[2]; s4*=perpvector[1]; s5*=perpvector[0]; s6*=perpvector[2]; */ perpvector=get_sliceVector(); ODINLOG(odinlog,normalDebug) << "perpSlice=" << perpvector.printbody() << STD_endl; for(i=0;i<3;i++) { if(transpose) result[2][i]=perpvector[i]; else result[i][2]=perpvector[i]; } /* s1*=perpvector[2]; s2*=perpvector[1]; s3*=perpvector[0]; s4*=perpvector[0]; s5*=perpvector[2]; s6*=perpvector[1]; ODINLOG(odinlog,normalDebug) << "determinante=" << s1+s2+s3-s4-s5-s6 << STD_endl; ODINLOG(odinlog,normalDebug) << "0=" << result(0,0) << " " << result(0,1) << " " << result(0,2) << STD_endl; ODINLOG(odinlog,normalDebug) << "1=" << result(1,0) << " " << result(1,1) << " " << result(1,2) << STD_endl; ODINLOG(odinlog,normalDebug) << "2=" << result(2,0) << " " << result(2,1) << " " << result(2,2) << STD_endl; */ return result; } dvector Geometry::transform(const dvector& rpsvec, bool inverse) const { Log odinlog(this,"transform"); int ichan; dvector result(3); if(rpsvec.size()!=3) { ODINLOG(odinlog,errorLog) << "Size of input vector != 3" << STD_endl; return result; } if(!cache_up2date || (inverse!=inv_trans_cache)) { for(ichan=0; ichan odinlog(this,"append_all_members"); JcampDxBlock::clear(); append_member(Mode,"Mode"); append_member(Reset,"Reset"); append_member(FOVread,"FOVread"); append_member(offsetRead,"offsetRead"); append_member(FOVphase,"FOVphase"); append_member(offsetPhase,"offsetPhase"); append_member(FOVslice,"FOVslice"); append_member(offsetSlice,"offsetSlice"); append_member(nSlices,"nSlices"); append_member(sliceThickness,"sliceThickness"); append_member(sliceDistance,"sliceDistance"); append_member(heightAngle,"heightAngle"); append_member(azimutAngle,"azimutAngle"); append_member(inplaneAngle,"inplaneAngle"); append_member(reverseSlice,"reverseSlice"); append_member(Transpose,"Transpose"); } //////////////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class GeometryTest : public UnitTest { public: GeometryTest() : UnitTest("Geometry") {} private: bool check() const { Log odinlog(this,"check"); int i; Geometry ia; // testing self-consistency of orientation with some arbitrary angles and offsets ia.set_orientation(-66.7, 78.2, -124.7, true); ia.set_offset(readDirection,22.7); ia.set_offset(phaseDirection,-5.9); ia.set_offset(sliceDirection,99.9); RotMatrix matrix_ang(ia.get_gradrotmatrix()); dvector offset(3); for(i=0; i<3; i++) offset[i]=ia.get_offset(direction(i)); ////////////////////////////////////////////////////// // Self-consistency check of set_orientation_and_offset Geometry ia2; ia2.set_orientation_and_offset(ia.get_readVector(),ia.get_phaseVector(),ia.get_sliceVector(),ia.get_center()); RotMatrix matrix_vec(ia2.get_gradrotmatrix()); if(!(matrix_ang==matrix_vec)) { ODINLOG(odinlog,errorLog) << " matrix_ang=" << matrix_ang.print() << STD_endl << " matrix_vec=" << matrix_vec.print() << STD_endl; return false; } dvector offset2(3); for(i=0; i<3; i++) offset2[i]=ia2.get_offset(direction(i)); if((offset-offset2).sum()>ODIN_GEO_CHECK_LIMIT) { ODINLOG(odinlog,errorLog) << " offset =" << offset << STD_endl << " offset2=" << offset2 << STD_endl; return false; } ////////////////////////////////////////////////////// // Check othogonality of rotation matrix RotMatrix matprod=ia.get_gradrotmatrix()*ia.get_gradrotmatrix(true); RotMatrix unitmat; if(!(matprod==unitmat)) { ODINLOG(odinlog,errorLog) << " matprod=" << matprod.print() << STD_endl << " unitmat=" << unitmat.print() << STD_endl; return false; } ////////////////////////////////////////////////////// // Check whether 'transform' preserves length and perpendicularity double norm1_expected,norm2_expected; dvector origin(3); origin=0.0; dvector testvec1(3); testvec1[0]=norm1_expected=5.0; testvec1[1]=0.0; testvec1[2]=0.0; dvector testvec2(3); testvec2[0]=0.0; testvec2[1]=norm2_expected=6.0; testvec2[2]=0.0; dvector origin_tr=ia.transform(origin); dvector testvec1_tr=ia.transform(testvec1)-origin_tr; dvector testvec2_tr=ia.transform(testvec2)-origin_tr; double norm1=norm3(testvec1_tr[0],testvec1_tr[1],testvec1_tr[2]); // check length after 'transform' if(fabs(norm1-norm1_expected)>ODIN_GEO_CHECK_LIMIT) { ODINLOG(odinlog,errorLog) << " testvec1/testvec1_tr =" << testvec1.printbody() << "/" << testvec1_tr.printbody() << STD_endl << " norm_expected1/norm1=" << norm1_expected << "/" << norm1 << STD_endl; return false; } // check scalar product after 'transform' double scalprod=(testvec1_tr*testvec2_tr).sum(); if(fabs(scalprod)>ODIN_GEO_CHECK_LIMIT) { ODINLOG(odinlog,errorLog) << " scalprod =" << scalprod << STD_endl; return false; } ////////////////////////////////////////////////////// // Testing == operator Geometry geo1; Geometry geo2; if(!(geo1==geo2)) { ODINLOG(odinlog,errorLog) << "Geometry::operator == (equal) failed: geo1=" << geo1 << "geo2=" << geo2 << STD_endl; return false; } geo1.set_nSlices(3); if(geo1==geo2) { ODINLOG(odinlog,errorLog) << "Geometry::operator == (unequal) failed: geo1=" << geo1 << "geo2=" << geo2 << STD_endl; return false; } ////////////////////////////////////////////////////// // Testing copy constructor Geometry geo3(geo1); if(!(geo1==geo3)) { ODINLOG(odinlog,errorLog) << "Geometry(const Geometry&) failed: geo1=" << geo1 << "geo3=" << geo3 << STD_endl; return false; } return true; } }; void alloc_GeometryTest() {new GeometryTest();} // create test instance #endif odin-1.8.5/odinpara/sample.h0000644000175000017500000001537511363773555012660 00000000000000/*************************************************************************** sample.h - description ------------------- begin : Mon Jul 11 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SAMPLE_H #define SAMPLE_H #include #include #include #include /** * @addtogroup odinpara * @{ */ /** * Dimension inidices of the 5-dim sample grid * - frameDim: time dimension * - freqDim: frequency direction * - zDim: axial direction of the scanner coordinate system * - yDim: 2nd transversal direction of the scanner coordinate system * - xDim: 1st transversal direction of the scanner coordinate system */ enum sampleDim { frameDim=0, freqDim, zDim, yDim, xDim, n_sampleDim }; //////////////////////////////////////////////////////////////////////////////////////////////////// /** * \brief Virtual Sample for Simulation * * Class to store properties of a virtual sample which is used as input to * simulation. The arrays are 4-dimensional: one frequency dimension * and 3 spatial dimensions. Coordinates are in the laboratory frame of * reference. */ class Sample : public JcampDxBlock { public: /** * Constructs a sample consisting of single voxel with the given label and the parameters: * - uniformFOV: A uniform FOV is used in each spatial dimension * - uniformT1T2: Uniform relaxation constants T1 and T2 are used, set_T1/2map has no effect */ Sample(const STD_string& label="unnamedSample", bool uniformFOV=true, bool uniformT1T2=false); /** * Constructs a copy of 'ss' */ Sample(const Sample& ss); /** * Assignment operator that makes this Sample become a copy of 'ss' */ Sample& operator = (const Sample& ss); /** * Sets the uniform FOV of the sample */ Sample& set_FOV(float fov); /** * Sets the FOV of the sample in the given direction */ Sample& set_FOV(axis direction, float fov); /** * Returns the FOV of the sample in the given direction */ float get_FOV(axis direction) const; /** * Sets the spatial offset in the given direction */ Sample& set_spatial_offset(axis direction, float offs) {offset[direction]=offs; return *this;} /** * Returns the spatial offset in the given direction */ float get_spatial_offset(axis direction) const {return offset[direction];} /** * Sets the frequency range */ Sample& set_freqrange(float range) {freqrange=range; return *this;} /** * Returns the frequency range */ float get_freqrange() const {return freqrange;} /** * Sets the frequency offset */ Sample& set_freqoffset(float offs) {freqoffset=offs; return *this;} /** * Returns the frequency offset */ float get_freqoffset() const {return freqoffset;} /** * Sets a vector of time intervals to cycle through frames periodically. * For maps with a time dimension, the index of the current interval * will also be used to index the time dimension of the map. */ Sample& set_frame_durations(const dvector& intervals) {frameDurations=intervals; return *this;} /** * Returns the vector of time intervals of the frames. */ const dvector& get_frame_durations() const {return frameDurations;} /** * Resize the sample in the four dimensions according to the given sizes: * - framesize: Number of frames (time intervals) * - freqsize: Number of frequency intervals * - zsize: Spatial extent in the axial direction of the scanner coordinate system * - ysize: Spatial extent in the 2nd transversal direction of the scanner coordinate system * - xsize: Spatial extent in the 1st transversal direction of the scanner coordinate system */ Sample& resize(unsigned int framesize, unsigned int freqsize, unsigned int zsize, unsigned int ysize, unsigned int xsize); /** * Returns the extent vector */ const ndim& get_extent() const {return spinDensity.get_extent();} /** * Sets a uniform longitudinal relaxation time */ Sample& set_T1(float relaxation_time) {T1=relaxation_time; haveT1map=false; return *this;} /** * Sets a uniform transverse relaxation time */ Sample& set_T2(float relaxation_time) {T2=relaxation_time; haveT2map=false; return *this;} /** * Sets an array for the longitudinal relaxation time */ Sample& set_T1map(const farray& t1map); /** * Returns the array for the longitudinal relaxation time */ const farray& get_T1map() const; /** * Sets an array for the transverse relaxation time */ Sample& set_T2map(const farray& t2map); /** * Returns the array for the transverse relaxation time */ const farray& get_T2map() const; /** * Sets an array for the relative frequency offset (in ppm) */ Sample& set_ppmMap(const farray& ppmmap); /** * Returns an array for the relative frequency offset (in ppm) */ const farray& get_ppmMap() const; /** * Sets an array for the spin density of each voxel */ Sample& set_spinDensity(const farray& sd); /** * Returns an array for the spin density of each voxel */ const farray& get_spinDensity() const; /** * Sets the diffusion coefficient map */ Sample& set_DcoeffMap(const farray& dmap); /** * Returns the diffusion coefficient map */ const farray& get_DcoeffMap() const; /** * Updates all parameter relations */ Sample& update(); // overwriting virtual functions from JcampDxClass int load(const STD_string& filename); private: friend class SeqSimMagsi; int append_all_members(); bool check_and_correct(const char* mapname, const farray& srcmap, farray& dstmap); JDXfloat FOVall; JDXtriple FOV; bool uniFOV; JDXtriple offset; JDXfloat freqrange; JDXfloat freqoffset; JDXdoubleArr frameDurations; mutable JDXfloatArr spinDensity; bool uniT1T2; JDXfloat T1; JDXfloat T2; mutable JDXfloatArr T1map; mutable JDXfloatArr T2map; mutable bool haveT1map; mutable bool haveT2map; mutable JDXfloatArr ppmMap; mutable bool have_ppmMap; mutable JDXfloatArr DcoeffMap; mutable bool have_DcoeffMap; }; /** @} */ #endif odin-1.8.5/odinpara/odinpara.cpp0000644000175000017500000000020111322062341013460 00000000000000#include "odinpara.h" #include const char* Para::get_compName() {return "Para";} LOGGROUNDWORK(Para) odin-1.8.5/odinpara/jdxtypes.h0000644000175000017500000004053211322062341013215 00000000000000/*************************************************************************** jdxtypes.h - description ------------------- begin : Sun Jun 6 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXTYPES_H #define JDXTYPES_H #include /** * @addtogroup jcampdx * @{ */ ////////////////////////////////////////////////////////////////// /** * * JCAMP-DX class for representing strings */ class JDXstring : public STD_string, public virtual JcampDxClass { public: /** * Default constructor */ JDXstring () : STD_string() {} /** * Constructor with the following arguments: * - ss: Initial value for the string * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter * - parx_equivalent: Equivalent parameter in PARX to which this parameter will be assigned */ JDXstring (const STD_string& ss,const STD_string& name="",bool userParameter=true, compatMode mode=notBroken,parameterMode parameter_mode=edit, const STD_string& parx_equivalent=""); /** * Constructs a string of length i with c as their initial content */ JDXstring (int i,const char c=' ') : STD_string(i,c) {} /** * Copy constructor from a C-string */ JDXstring (const char *charptr) : STD_string(charptr) {} /** * Copy constructor */ JDXstring (const JDXstring& str) {JDXstring::operator = (str);} /** * Assigns the string ss to the parameter */ JDXstring& operator = (const STD_string& ss) {STD_string::operator = (ss); return *this;} /** * Assigns the C-string charptr to the parameter */ JDXstring& operator = (const char *charptr) {STD_string::operator = (charptr); return *this;} /** * Copy assignment */ JDXstring& operator = (const JDXstring& ss); /** * Final overrider for stream output */ friend STD_ostream& operator << (STD_ostream& s,const JDXstring& t) {return s << STD_string(t);} // overwriting virtual functions from JcampDxClass bool parsevalstring (const STD_string& parstring); STD_string printvalstring() const; STD_string get_parx_code(parxCodeType type, const ParxEquiv& equiv) const; ParxEquiv get_parx_equiv() const {parx_equiv.type="char"; return parx_equiv;} const char* get_typeInfo() const {return "string";} JcampDxClass* create_copy() const {return new JDXstring(*this);} STD_string* cast(STD_string*) {return this;} private: mutable ParxEquiv parx_equiv; }; ////////////////////////////////////////////////////////////////// /** * * JCAMP-DX class for representing Boolean values */ class JDXbool : public virtual JcampDxClass { public: /** * Default constructor */ JDXbool () : val(false) {} /** * Constructor with the following arguments: * - flag: Initial value for the Boolean value * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter * - parx_equivalent: Equivalent parameter in PARX to which this parameter will be assigned */ JDXbool(bool flag, const STD_string& name="", bool userParameter=true, compatMode mode=notBroken, parameterMode parameter_mode=edit, const STD_string& parx_equivalent=""); /** * Copy constructor */ JDXbool(const JDXbool& jb) {JDXbool::operator = (jb);} /** * Assigns the value of flag to the parameter */ JDXbool& operator = (bool flag) {val=flag; return *this;} /** * Assigns the value of s to the parameter, s may contain "yes" or "true" * (upper- or lowercase) to indicate a value of true, otherwise false */ JDXbool& operator = (const STD_string& s) {parsevalstring(s); return *this;} /** * Copy assignment */ JDXbool& operator = (const JDXbool& jb); /** * type conversion operator of the current value of the parameter */ operator bool () const {return val;} // overwriting virtual functions from JcampDxClass bool parsevalstring (const STD_string& parstring); STD_string printvalstring() const; STD_string get_parx_code(parxCodeType type, const ParxEquiv& equiv) const; ParxEquiv get_parx_equiv() const {parx_equiv.type="YesNo"; return parx_equiv;} const char* get_typeInfo() const {return "bool";} JcampDxClass* create_copy() const {return new JDXbool(*this);} bool* cast(bool*) {return &val;} private: bool val; mutable ParxEquiv parx_equiv; }; ////////////////////////////////////////////////////////////////// /** * * JCAMP-DX class to represent enumerations */ class JDXenum : public virtual JcampDxClass { public: /** * Default constructor */ JDXenum() {actual=entries.end();} /** * Constructor with the following arguments: * - first_entry: Initial value for the first entry of the enumeration * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter * - parx_equivalent: Equivalent parameter in PARX to which this parameter will be assigned */ JDXenum(const STD_string& first_entry, const STD_string& name="", bool userParameter=true, compatMode mode=notBroken, parameterMode parameter_mode=edit, const STD_string& parx_equivalent=""); /** * Copy constructor */ JDXenum(const JDXenum& je) {JDXenum::operator = (je);} /** * Sets the current value of the enumeration to the given item */ JDXenum& operator = (const char* item) {set_actual(STD_string(item)); return *this;} /** * Sets the current value of the enumeration to the given item */ JDXenum& operator = (const STD_string& item) {set_actual(item); return *this;} /** * Sets the current value of the enumeration to the given item */ JDXenum& operator = (int item) {set_actual(item); return *this;} /** * Assignment operator */ JDXenum& operator = (const JDXenum& je); /** * Appends an item to the the list of items in the enumeration. * If index is non-negative, the item will be inserted at the * position indicated by index. */ JDXenum& add_item(const STD_string& item, int index=-1); /** * Sets the current value of the enumeration to the given item */ JDXenum& set_actual(const STD_string& item); /** * Sets the current value of the enumeration to the given item */ JDXenum& set_actual(int index); /** * Clears the list of items in the enumeration */ JDXenum& clear(); /** * type conversion operator of the current value of the enumeration */ operator int () const; /** * type conversion operator of the current value of the enumeration */ operator STD_string () const; /** * Compares the current value with s for equality */ bool operator == (const STD_string& s) const {return (operator STD_string ())==s;} /** * Compares the current value with s for equality */ bool operator == (const char* s) const {return (operator STD_string ())==STD_string(s);} /** * Compares the current index with i for equality */ bool operator == (int i) const {return (operator int ())==i;} /** * Compares the current value with s for inequality */ bool operator != (const STD_string& s) const {return (operator STD_string ())!=s;} /** * Compares the current value with s for inequality */ bool operator != (const char* s) const {return (operator STD_string ())!=STD_string(s);} /** * Compares the current index with i for inequality */ bool operator != (int i) const {return (operator int ())!=i;} /** * Returns the number of items in the enumeration */ unsigned int n_items() const {return entries.size();} /** * Returns the item at the position 'index' in the label-index map */ const STD_string& get_item(unsigned int index) const; /** * Returns the current position in the label-index map */ unsigned int get_item_index() const; /** * Sets the current position 'index' in the label-index map */ JDXenum& set_item_index(unsigned int index); // overwriting virtual functions from JcampDxClass bool parsevalstring (const STD_string& parstring); STD_string printvalstring() const; svector get_alternatives() const; STD_string get_parx_code(parxCodeType type, const ParxEquiv& equiv) const; ParxEquiv get_parx_equiv() const; const char* get_typeInfo() const {return "enum";} JcampDxClass* create_copy() const {return new JDXenum(*this);} JDXenum* cast(JDXenum*) {return this;} private: STD_map entries; STD_map::const_iterator actual; mutable ParxEquiv parx_equiv; STD_string parxtype_cache; }; ////////////////////////////////////////////////////////////////// /** * * JCAMP-DX class to trigger actions from the GUI */ class JDXaction : public virtual JcampDxClass { public: /** * Default constructor */ JDXaction() : state(false) {set_filemode(exclude);} /** * Constructor with the following arguments: * - init_state: Initial value for the action * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter */ JDXaction(bool init_state, const STD_string& name="", bool userParameter=true, compatMode mode=notBroken, parameterMode parameter_mode=edit); /** * Copy constructor */ JDXaction(const JDXaction& ja) {JDXaction::operator = (ja);} /** * Copy assignment */ JDXaction& operator = (const JDXaction& ja); /** * Returns whether an action should be triggered and resets the action flag */ operator bool () const; /** * After calling this function, the next type conversion to bool will return true */ JDXaction& trigger_action() {state=true; return *this;} // overwriting virtual functions from JcampDxClass bool parsevalstring (const STD_string& parstring); STD_string printvalstring() const; const char* get_typeInfo() const {return "action";} JcampDxClass* create_copy() const {return new JDXaction(*this);} JDXaction* cast(JDXaction*) {return this;} private: mutable bool state; }; ////////////////////////////////////////////////////////////////// /** * * JCAMP-DX class for representing file names. Besides using JDXfileName * as a convenient way within the UI to display/retrieve/browse file names, * it can be used to analyze file paths, for example in the following way: * \verbatim STD_string myfile="/somedir/anotherdir/file.txt"; STD_string myfile_base=JDXfileName(myfile).get_basename(); STD_cout << "myfile_base=" << myfile_base << STD_endl; STD_string myfile_base_nosuffix=JDXfileName(myfile).get_basename_nosuffix(); STD_cout << "myfile_base_nosuffix=" << myfile_base_nosuffix << STD_endl; STD_string myfile_dir= JDXfileName(myfile).get_dirname(); STD_cout << "myfile_dir=" << myfile_dir << STD_endl; \endverbatim * */ class JDXfileName : public JDXstring { public: /** * Default constructor */ JDXfileName () {common_init();} /** * Constructor with the following arguments: * - filename: Initial value for the file name * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter */ JDXfileName (const STD_string& filename, const STD_string& name="", bool userParameter=true, compatMode mode=notBroken, parameterMode parameter_mode=edit); /** * Copy constructor */ JDXfileName(const JDXfileName& jf); /** * Assignment from a string */ JDXfileName& operator = (const STD_string& filename); /** * Assignment operator */ JDXfileName& operator = (const JDXfileName& jf); /** * Returns 'true' only if the file/directory exists */ bool exists() const; /** * Returns the filename without preceeding directories */ STD_string get_basename() const {return basename_cache;} /** * Returns the filename without preceeding directories and without * a previously specified suffix (file extension) */ STD_string get_basename_nosuffix() const; /** * Returns the directory of the filename */ STD_string get_dirname() const {return dirname_cache;} /** * Returns the suffix (file extension) of the filename */ STD_string get_suffix() const {return suffix_cache;} /** * Sets/overwrites the suffix (file extension) of the filename */ JDXfileName& set_suffix(const STD_string& suff) {suffix_cache=suff; return *this;} /** * Returns the default location of the filename */ STD_string get_defaultdir() const {return defaultdir;} /** * Sets the default location of the filename */ JDXfileName& set_defaultdir(const STD_string& defdir); /** * Returns whether used exclusively for directory names */ bool is_dir() const {return dir;} /** * Specifies whether used exclusively for directory names */ JDXfileName& set_dir(bool flag) {dir=flag; return *this;} // overwriting virtual functions from JcampDxClass bool parsevalstring (const STD_string& parstring); const char* get_typeInfo() const {return "fileName";} JcampDxClass* create_copy() const {return new JDXfileName(*this);} JDXfileName* cast(JDXfileName*) {return this;} private: static void normalize(const STD_string& fname, bool dir, STD_string& result, STD_string& result_dirname, STD_string& result_basename, STD_string& result_suffix); void common_init() {dir=false;} STD_string defaultdir; STD_string dirname_cache; STD_string basename_cache; STD_string suffix_cache; bool dir; }; ////////////////////////////////////////////////////////////////// /** * * JCAMP-DX class for representing mathematic formulas */ class JDXformula : public JDXstring { public: /** * Default constructor */ JDXformula () : JDXstring() {} /** * Constructor with the following arguments: * - formula: Initial value for the formula * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter */ JDXformula (const STD_string& formula, const STD_string& name="", bool userParameter=true, compatMode mode=notBroken, parameterMode parameter_mode=edit); /** * Copy constructor */ JDXformula (const JDXformula& jf) {JDXformula::operator = (jf);} /** * Assignment from a formula string */ JDXformula& operator = (const STD_string& formula) {JDXstring::operator = (formula); return *this;} /** * Copy assignment */ JDXformula& operator = (const JDXformula& jf); /** * Sets a string describing the formulas syntax */ JDXformula& set_syntax(const STD_string& syn) {syntax=syn; return *this;} /** * Returns a string describing the formulas syntax */ STD_string get_syntax() const {return syntax;} // overwriting virtual functions from JcampDxClass const char* get_typeInfo() const {return "formula";} JcampDxClass* create_copy() const {return new JDXformula(*this);} JDXformula* cast(JDXformula*) {return this;} private: STD_string syntax; }; /** @} */ #endif odin-1.8.5/odinpara/protocol.h0000644000175000017500000000510311322062341013177 00000000000000/*************************************************************************** protocol.h - description ------------------- begin : Tue Jul 5 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef PROTOCOL_H #define PROTOCOL_H #include #include #include #include /** * @ingroup odinpara * * \brief Protcol proxy * * Class to hold the whole MR Protocol, that is system, geometry and seqpars */ class Protocol : public JcampDxBlock { public: /** * Create a default protocol with the given label for the sequence with label 'seqid' */ Protocol(const STD_string& label="unnamedProtocol"); /** * Copy constructor */ Protocol(const Protocol& p) {Protocol::operator = (p);} /** * Assignment operator */ Protocol& operator = (const Protocol& p); /** * Special comparison operator for Protocol which does not consider * 'AcquisitionStart' and 'offsetSlice' so that tempo-spatial data has the * 'same' protocol. This behaviour is required in FileIO::autoread. */ bool operator < (const Protocol& rhs) const; /** * Special comparison operator for Protocol which does not consider * 'AcquisitionStart' and 'offsetSlice' so that tempo-spatial data has the * 'same' protocol. This behaviour is required in FileIO::autoread. */ bool operator == (const Protocol& rhs) const {return !( ((*this) #include #include #include /** * @addtogroup odinpara * @{ */ /** * Enum to specify which boundary of a slice to take for a given direction */ enum sliceBoundary {lowerBound=0,upperBound,n_boundaries}; /** * The principal slice direction in the anatomical system of reference * - sagittal: Slice is perpendicular to left-right direction * - coronal: Slice is perpendicular to anterior-posterior direction * - axial: Slice is perpendicular to head-foot direction */ enum sliceOrientation {sagittal=0,coronal,axial,n_orientations}; /** * The geometry mode * - slicepack: A stack of equidistant parallel slices * - voxel_3d: A single 3D volume */ enum geometryMode {slicepack=0,voxel_3d,n_geometry_modes}; //////////////////////////////////////////////////////////////////////////// /** * \brief Rotation Matrix * * This class represents 3 by 3 rotation matrix */ class RotMatrix : public virtual Labeled { public: /** * default constructor for a 3 by 3 rotation matrix */ RotMatrix(const STD_string& object_label = "unnamedRotMatrix" ); /** * constructs a rotation matrix from an existing rotation matrix */ RotMatrix(const RotMatrix& sct); /** * returns a row of rotation matrix */ dvector& operator [] (unsigned int index) {return matrix[index%3];} // make sure index is lower than 3 /** * returns a row of rotation matrix */ const dvector& operator [] (unsigned int index) const {return matrix[index%3];} // make sure index is lower than 3 /** * assignment operator */ RotMatrix& operator = (const RotMatrix& sct); /** * returns true if srm is element-wise equal to this. Two elements are * considered equal if their difference does not exceed GEO_CHECK_LIMIT. * */ bool operator == (const RotMatrix& srm) const; // dummy comparison operator for lists bool operator < (const RotMatrix& srm) const; /** * returns the product this * vec */ dvector operator * (const dvector& vec) const; /** * returns the product this * matrix */ RotMatrix operator * (const RotMatrix& matrix) const; /** * Returns the matrix as a 2-dim farray */ operator farray () const; /** * Create anti-clockwise in-plane rotation matrix with angle 'phi' (in rad). */ RotMatrix& set_inplane_rotation(float phi); /** * returns a string describing the rotation matrix */ STD_string print() const; private: friend class RotMatrixVector; class rowVec : public dvector { public: rowVec() : dvector(3) {}; ~rowVec() {}; }; // bool check_and_correct(); rowVec matrix[3]; // static dvector returndummy; }; //////////////////////////////////////////////////////////////////////////// /** * \brief Geometry Settings * * Depending on the selected geometryMode, this class describes a pack * of parallel and congruent slices, or a 3D volume, .i.e. a voxel. * * The patients x,y,z coordinate system used for the gradients is as follows: * If standing in front of the magnet with the feet of the patient * pointing towards you, the axes are oriented * * - x: from right to left (in the final image left/right will then have the correct polarity) * - y: from bottom to top (floor to ceiling) * - z: pointing away from you to the patients head * * * The three orientation angles 'heightAngle', 'azimutAngle', and 'inplaneAngle' * (in degree) describe the orientation of the slicepack/voxel relative to * the x/y/z-coordinate system of the gradients. * If all these angles are zero, the read/phase/slice-system * of the slicepack/voxel is the same as the x/y/z-system of * the gradients. Otherwise, the system is rotated by the following * angles (in the given order): * * - azimutAngle: Anti-clockwise rotation around y-axis. * - heightAngle: Angle between slice vector (which is perp. to the slice) and x-z-plane * - inplaneAngle: Clockwise rotation around slice vector. * */ class Geometry : public JcampDxBlock { public: /** * Constructs a Geometry with the given label */ Geometry(const STD_string& label="unnamedGeometry"); /** * Copy constructor */ Geometry(const Geometry& ia); /** * Assignment operator */ Geometry& operator = (const Geometry& ia); /** * Sets the geometry selection mode */ Geometry& set_Mode(geometryMode mode); /** * Returns the geometry selection mode */ geometryMode get_Mode() const {return geometryMode(int(Mode));} /** * Sets the Field Of View in the specified direction */ Geometry& set_FOV(direction dir,double fov); /** * Returns the Field Of View in the specified direction */ double get_FOV(direction dir) const; /** * Sets the spatial offset in the specified direction */ Geometry& set_offset(direction dir,double offset); /** * Returns the spatial offset in the specified direction */ double get_offset(direction dir) const; /** * Sets the number of slices of the current slice pack */ Geometry& set_nSlices(unsigned int nslices); /** * Returns the number of slices of the current slice pack */ unsigned int get_nSlices() const {return nSlices;}; /** * Sets the slice thickness of the current slice pack */ Geometry& set_sliceThickness(double thick); /** * Sets the slice interslice distance */ Geometry& set_sliceDistance(double dist); /** * Returns the slice interslice distance */ double get_sliceDistance() const {return sliceDistance;} /** * Returns the normalised vector for the read direction in the laboratory system of reference */ dvector get_readVector() const; /** * Returns the normalised vector for the phase direction in the laboratory system of reference */ dvector get_phaseVector() const; /** * Returns the normalised vector for the slice direction in the laboratory system of reference */ dvector get_sliceVector() const; /** * Returns the vector of spatial offsets in slice direction for the different slices of the slicepack. */ dvector get_sliceOffsetVector() const; /** * Returns the slice thickness for the slices */ double get_sliceThickness() const {return sliceThickness;} /** * Returns a 5-dimensional array that contains the corner points of the slices/voxels where indexing is as follows: * (unsigned int slice,sliceBoundary boundary1,sliceBoundary boundary2,sliceBoundary boundary3, axis direction) with * - slice: The slice for the point * - boundary1: The boundary in the read direction * - boundary2: The boundary in the phase direction * - boundary3: The boundary in the slice direction, the size is 1 in slicepack mode * - direction: The x,y,z index * * The points are transformed to slice 'backgrslice' the coordinate system of 'background'. * */ darray get_cornerPoints(const Geometry& background, unsigned int backgrslice) const; /** * Set the angle parameters to match the specified anatomical slice orientation */ Geometry& set_orientation(sliceOrientation orientation); /** * Returns the principal anatomical slice orientation of slice normal 'svec'. */ static sliceOrientation get_slice_orientation(const dvector& svec); /** * Returns the principal anatomical slice orientation */ sliceOrientation get_orientation() const {return get_slice_orientation(get_sliceVector());} /** * Returns the orientation of the slice, i.e. the three orientation angles * 'heightAng', 'azimutAng' and 'inplaneAng'. * 'revSlice' returns whether the slice direction (handness) is reversed. */ void get_orientation(double& heightAng, double& azimutAng, double& inplaneAng, bool& revSlice) const; /** * Specifies the orientation of the slice pack by giving the three orientation angles * 'heightAng', 'azimutAng' and 'inplaneAng'. * Optionally, the slice direction can be reversed by setting 'revSlice' to true. */ Geometry& set_orientation(double heightAng, double azimutAng, double inplaneAng, bool revSlice=false); /** * Specifies the orientation of the slicepack/voxel by giving the three * vectors 'readvec', 'phasevec', and 'slicevec' which point in read, * phase, and slice direction. The vector 'offset' must contain the spatial * offset of the center of the slicepack/voxel. */ Geometry& set_orientation_and_offset(const dvector& readvec, const dvector& phasevec, const dvector& slicevec, const dvector& centervec); /** * Returns a vector pointing to the center of the slicepack/voxel. */ dvector get_center() const; /** * Returns the rotation matrix to convert the gradient strengths in the * sequence coordinate system (read,phase,slice) to the laboratory system (x,y,z). * If 'transpose' is set to true, the transposed matrix is returned. */ RotMatrix get_gradrotmatrix(bool transpose=false) const; /** * Coordinate transformation from sequence coordinate system (read,phase,slice) * of slice 'slice' to laboratory system (x,y,z), or vice versa if * 'inverse' is set to 'true'. */ dvector transform(const dvector& rpsvec, bool inverse=false) const; /** * Transpose geometry in-plane, 'reverse_read' and 'reverse_phase' * can be used to reverse read/phase direction before transposing. */ Geometry& transpose_inplane(bool reverse_read=false, bool reverse_phase=false); /** * Resets the slicepacks geometry to its inintial state */ Geometry& reset(); /** * Updates internal relations of the geometry parameters */ Geometry& update(); private: dvector get_readVector_inplane() const; dvector get_phaseVector_inplane() const; void append_all_members(); double deg2rad(double degree) const {return degree/180.0*PII;} JDXenum Mode; JDXdouble FOVread; JDXdouble offsetRead; JDXdouble FOVphase; JDXdouble offsetPhase; JDXdouble FOVslice; JDXdouble offsetSlice; JDXdouble heightAngle; JDXdouble azimutAngle; JDXdouble inplaneAngle; JDXbool reverseSlice; JDXint nSlices; JDXdouble sliceDistance; JDXdouble sliceThickness; JDXaction Reset; JDXaction Transpose; // cache to speed up repetitive calls to transform() mutable bool cache_up2date; mutable bool inv_trans_cache; mutable double rotmat_cache[3][3]; mutable double offset_cache[3]; }; /** @} */ #endif odin-1.8.5/odinpara/jdxarrays.h0000644000175000017500000001457011322062341013355 00000000000000/*************************************************************************** jdxarrays.h - description ------------------- begin : Mon Jul 5 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXARRAYS_H #define JDXARRAYS_H #include #include #include #include #define COMPRESSION_THRESHOLD_SIZE 256 /** * @addtogroup jcampdx * @{ */ /** * * JCAMP-DX template class for representing multi-dimensional arrays */ template class JDXarray : public A, public virtual JcampDxClass { public: /** * Default constructor */ JDXarray () : A() {common_init();} /** * Constructor with the following arguments: * - a: Initial value for the array base class * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter * - parx_equivalent: Equivalent parameter in PARX to which this parameter will be assigned * - parx_assign_factor: Scaling factor when assigning to the equivalent parameter in PARX * - parx_assign_offset: Offset when assigning to the equivalent parameter in PARX */ JDXarray (const A& a,const STD_string& name="",bool userParameter=true, compatMode mode=notBroken,parameterMode parameter_mode=edit, const STD_string& parx_equivalent="", float parx_assign_factor=1.0,float parx_assign_offset=0.0); /** * Assignment from scalar, i.e. fill all elements with this value */ // JDXarray (const J& jv) {common_init(); A::operator = (jv);} /** * Copy constructor */ JDXarray (const JDXarray& ja) {common_init(); JDXarray::operator = (ja);} /** * Assignment operator from an array */ JDXarray& operator = (const A& a); /** * Assignment operator from scalar, i.e. fill all elements with this value */ JDXarray& operator = (const J& jv) {A::operator = (jv); return *this;} /** * Copy assignment */ JDXarray& operator = (const JDXarray& ja); // overwriting virtual functions from JcampDxClass STD_ostream& print2stream(STD_ostream& os) const; STD_string printvalstring() const; bool parsevalstring (const STD_string& parstring); STD_string get_parx_code(parxCodeType type, const ParxEquiv& equiv) const; ParxEquiv get_parx_equiv() const {return parx_equiv;} GuiProps get_gui_props() const {return guiprops;} JcampDxClass& set_gui_props(const GuiProps& gp) {guiprops=gp; return *this;} const char* get_typeInfo() const; JcampDxClass* create_copy() const {return new JDXarray(*this);} A* cast(A*) {return this;} // final overrider friend STD_ostream& operator << (STD_ostream& s,const JDXarray& ja) { return ja.print2stream(s);} int write(const STD_string& filename) const {return JcampDxClass::write(filename);} int load(const STD_string &filename) {return JcampDxClass::load(filename);} private: void common_init(); STD_string get_dim_str() const; bool encode(STD_string* ostring, STD_ostream* ostream) const; bool use_compression() const {return (get_filemode()==compressed)&&(A::total()>COMPRESSION_THRESHOLD_SIZE);} ParxEquiv parx_equiv; GuiProps guiprops; mutable STD_string typeInfo_cache; }; ////////////////////////////////////////////////////////////////////////////////// // // Aliases: // /** * A JCAMP-DX array of strings */ typedef JDXarray JDXstringArr; /** * A JCAMP-DX array of integer numbers */ typedef JDXarray JDXintArr; /** * A JCAMP-DX array of single-precision floating point numbers */ typedef JDXarray JDXfloatArr; /** * A JCAMP-DX array of double-precision floating point numbers */ typedef JDXarray JDXdoubleArr; /** * A JCAMP-DX array of single-precision complex numbers */ typedef JDXarray JDXcomplexArr; ///////////////////////////////////////////////////////////////////////////// // Specialised array classes: /** * A JCAMP-DX vector of 3 float values which is used to store spatial positions, FOVs, etc. */ class JDXtriple : public JDXfloatArr { public: /** * Default constructor */ JDXtriple () : JDXfloatArr(farray(3)) {} /** * Constructor with the following arguments: * - xpos: Spatial position in the first dimension * - ypos: Spatial position in the second dimension * - zpos: Spatial position in the third dimension * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter */ JDXtriple (float xpos,float ypos, float zpos, const STD_string& name="",bool userParameter=true, compatMode mode=notBroken,parameterMode parameter_mode=edit); /** * Copy constructor */ JDXtriple (const JDXtriple& pos) {JDXtriple::operator = (pos);} /** * Copy assignment */ JDXtriple& operator = (const JDXtriple& pos) { JDXfloatArr::operator = (pos); return *this; } // overwriting virtual functions from JcampDxClass const char* get_typeInfo() const {return "triple";} JcampDxClass* create_copy() const {return new JDXtriple(*this);} JDXtriple* cast(JDXtriple*) {return this;} farray* cast(farray*) {return 0;} // disable casting to base class }; /** @} */ #endif odin-1.8.5/odinpara/system.cpp0000644000175000017500000003676711363773555013266 00000000000000#include "system.h" #include Nuclei::Nuclei() { // nuclist.push_back(Nucleus("1n", 183.247215)); // nuclist.push_back(Nucleus("1H", 267.522322)); nuclist.push_back(Nucleus("1H", 267.50998)); nuclist.push_back(Nucleus("1Hb",267.50998)); nuclist.push_back(Nucleus("2H", 41.066271)); nuclist.push_back(Nucleus("3H", 285.349604)); nuclist.push_back(Nucleus("3He", 203.801399)); nuclist.push_back(Nucleus("6Li", 39.371067)); nuclist.push_back(Nucleus("7Li", 103.976035)); nuclist.push_back(Nucleus("9Be", 37.599838)); nuclist.push_back(Nucleus("10B", 28.746829)); nuclist.push_back(Nucleus("11B", 85.847161)); nuclist.push_back(Nucleus("13C", 67.282862)); nuclist.push_back(Nucleus("14N", 19.337759)); nuclist.push_back(Nucleus("15N", 27.126396)); // nuclist.push_back(Nucleus("17O", 36.280369)); nuclist.push_back(Nucleus("17O",36.265437)); nuclist.push_back(Nucleus("19F", 251.814987)); nuclist.push_back(Nucleus("21Ne", 21.130981)); nuclist.push_back(Nucleus("23Na", 70.803959)); nuclist.push_back(Nucleus("25Mg", 16.388432)); nuclist.push_back(Nucleus("27Al", 69.762835)); nuclist.push_back(Nucleus("29Si", 53.190305)); // nuclist.push_back(Nucleus("31P", 108.394371)); nuclist.push_back(Nucleus("31P",108.28945)); nuclist.push_back(Nucleus("33S", 20.556697)); nuclist.push_back(Nucleus("35Cl", 26.241723)); nuclist.push_back(Nucleus("37Cl", 21.843494)); nuclist.push_back(Nucleus("37Ar", 36.561855)); nuclist.push_back(Nucleus("39Ar", 21.739821)); nuclist.push_back(Nucleus("39K", 12.499141)); nuclist.push_back(Nucleus("40K", 15.542715)); nuclist.push_back(Nucleus("41K", 6.860610)); nuclist.push_back(Nucleus("43Ca", 18.025202)); nuclist.push_back(Nucleus("45Sc", 65.088145)); nuclist.push_back(Nucleus("47Ti", 15.105406)); nuclist.push_back(Nucleus("49Ti", 15.109804)); nuclist.push_back(Nucleus("50V", 26.706679)); nuclist.push_back(Nucleus("51V", 70.455242)); nuclist.push_back(Nucleus("53Cr", 15.151901)); nuclist.push_back(Nucleus("55Mn", 66.452853)); nuclist.push_back(Nucleus("57Fe", 8.680849)); nuclist.push_back(Nucleus("59Co", 63.315658)); nuclist.push_back(Nucleus("61Ni", 23.947732)); nuclist.push_back(Nucleus("63Cu", 70.988684)); nuclist.push_back(Nucleus("65Cu", 76.045392)); nuclist.push_back(Nucleus("67Zn", 16.772335)); nuclist.push_back(Nucleus("69Ga", 64.388826)); nuclist.push_back(Nucleus("71Ga", 81.812099)); nuclist.push_back(Nucleus("73Ge", 9.360061)); nuclist.push_back(Nucleus("75As", 45.961501)); nuclist.push_back(Nucleus("77Se", 51.252571)); nuclist.push_back(Nucleus("79Br", 67.256472)); nuclist.push_back(Nucleus("81Br", 72.497905)); nuclist.push_back(Nucleus("83Kr", 10.330813)); nuclist.push_back(Nucleus("85Rb", 25.920653)); nuclist.push_back(Nucleus("87Rb", 87.845842)); nuclist.push_back(Nucleus("87Sr", 11.639601)); nuclist.push_back(Nucleus("89Y", 13.162645)); nuclist.push_back(Nucleus("91Zr", 24.974405)); nuclist.push_back(Nucleus("93Nb", 65.673738)); nuclist.push_back(Nucleus("95Mo", 17.513751)); nuclist.push_back(Nucleus("97Mo", 17.883830)); nuclist.push_back(Nucleus("99Tc", 60.503305)); nuclist.push_back(Nucleus("99Ru", 12.285512)); nuclist.push_back(Nucleus("101Ru", 13.770229)); nuclist.push_back(Nucleus("103Rh", 8.467849)); nuclist.push_back(Nucleus("105Pd", 12.296194)); nuclist.push_back(Nucleus("107Ag", 10.889388)); nuclist.push_back(Nucleus("109Ag", 12.518618)); nuclist.push_back(Nucleus("111Cd", 56.983464)); nuclist.push_back(Nucleus("113Cd", 59.609207)); nuclist.push_back(Nucleus("113In", 58.845172)); nuclist.push_back(Nucleus("115In", 58.971464)); nuclist.push_back(Nucleus("115Sn", 88.012975)); nuclist.push_back(Nucleus("117Sn", 95.887691)); nuclist.push_back(Nucleus("119Sn", 100.317337)); nuclist.push_back(Nucleus("121Sb", 64.434694)); nuclist.push_back(Nucleus("123Sb", 34.891785)); nuclist.push_back(Nucleus("123Te", 70.590959)); nuclist.push_back(Nucleus("125Te", 85.108258)); nuclist.push_back(Nucleus("127I", 53.895907)); nuclist.push_back(Nucleus("129Xe", 74.521091)); nuclist.push_back(Nucleus("131Xe", 22.091051)); nuclist.push_back(Nucleus("133Cs", 35.332864)); nuclist.push_back(Nucleus("135Ba", 26.755060)); nuclist.push_back(Nucleus("137Ba", 29.929325)); nuclist.push_back(Nucleus("138La", 35.572254)); nuclist.push_back(Nucleus("139La", 38.083643)); nuclist.push_back(Nucleus("137Ce", 30.661944)); nuclist.push_back(Nucleus("139Ce", 33.866369)); nuclist.push_back(Nucleus("141Ce", 14.891149)); nuclist.push_back(Nucleus("141Pr", 81.906975)); nuclist.push_back(Nucleus("143Nd", 14.570707)); nuclist.push_back(Nucleus("145Nd", 8.978672)); nuclist.push_back(Nucleus("143Pm", 72.822118)); nuclist.push_back(Nucleus("147Pm", 35.311501)); nuclist.push_back(Nucleus("147Sm", 11.151397)); nuclist.push_back(Nucleus("149Sm", 9.192928)); nuclist.push_back(Nucleus("151Eu", 66.511286)); nuclist.push_back(Nucleus("153Eu", 29.370750)); nuclist.push_back(Nucleus("155Gd", 8.243539)); nuclist.push_back(Nucleus("157Gd", 10.807079)); nuclist.push_back(Nucleus("159Tb", 64.276986)); nuclist.push_back(Nucleus("161Dy", 9.207380)); nuclist.push_back(Nucleus("163Dy", 12.885556)); nuclist.push_back(Nucleus("165Ho", 57.103473)); nuclist.push_back(Nucleus("167Er", 7.716380)); nuclist.push_back(Nucleus("169Tm", 22.185927)); nuclist.push_back(Nucleus("171Yb", 47.287881)); nuclist.push_back(Nucleus("173Yb", 13.025043)); nuclist.push_back(Nucleus("175Lu", 30.552617)); nuclist.push_back(Nucleus("176Lu", 21.683272)); nuclist.push_back(Nucleus("177Hf", 10.858601)); nuclist.push_back(Nucleus("179Hf", 6.821026)); nuclist.push_back(Nucleus("180Ta", 25.679378)); nuclist.push_back(Nucleus("181Ta", 32.438201)); nuclist.push_back(Nucleus("183W", 11.282716)); nuclist.push_back(Nucleus("185Re", 61.057482)); nuclist.push_back(Nucleus("187Re", 61.682030)); nuclist.push_back(Nucleus("187Os", 6.192707)); nuclist.push_back(Nucleus("189Os", 21.071290)); nuclist.push_back(Nucleus("191Ir", 4.811663)); nuclist.push_back(Nucleus("191Ir", 5.226982)); nuclist.push_back(Nucleus("195Pt", 58.384615)); nuclist.push_back(Nucleus("197Au", 4.653327)); nuclist.push_back(Nucleus("199Hg", 48.457810)); nuclist.push_back(Nucleus("201Hg", 17.887600)); nuclist.push_back(Nucleus("203Tl", 155.393226)); nuclist.push_back(Nucleus("205Tl", 156.921925)); nuclist.push_back(Nucleus("207Pb", 56.762296)); nuclist.push_back(Nucleus("209Bi", 43.749819)); nuclist.push_back(Nucleus("209Po", 73.513268)); nuclist.push_back(Nucleus("211Rn", 57.553977)); nuclist.push_back(Nucleus("223Fr", 37.384953)); nuclist.push_back(Nucleus("223Ra", 8.636867)); nuclist.push_back(Nucleus("225Ra", 70.289994)); nuclist.push_back(Nucleus("227Ac", 35.185838)); nuclist.push_back(Nucleus("229Th", 8.796459)); nuclist.push_back(Nucleus("231Pa", 64.088490)); nuclist.push_back(Nucleus("235U", 5.215044)); nuclist.push_back(Nucleus("237Np", 60.130083)); nuclist.push_back(Nucleus("239Pu", 19.415043)); nuclist.push_back(Nucleus("243Am", 28.902652)); } double Nuclei::get_gamma(const STD_string& nucName) const { NucList::const_iterator resultit=nuclist.begin(); for(NucList::const_iterator it=nuclist.begin();it!=nuclist.end();++it) { if(it->first == nucName) resultit=it; } return resultit->second; } double Nuclei::get_nuc_freq(const STD_string& nucName,float B0) const { float freq; float b0=B0; if (b0==0.0) b0=-1.0; freq= ( get_gamma(nucName) *b0) / (2.0*PII); if(freq==0.0) freq=-1.0; return freq; } JDXenum Nuclei::get_nuc_enum() const { JDXenum result; for(STD_list::const_iterator it=nuclist.begin();it!=nuclist.end();++it) { result.add_item(it->first); } return result; } ///////////////////////////////////////////////////////////////////////////// System::System(const STD_string& object_label) : JcampDxBlock(object_label) { Log odinlog(this, "System(...)"); platformstr.set_parmode(hidden).set_description("The current platform"); main_nucleus=get_nuc_enum(); main_nucleus.set_actual(0); main_nucleus.set_description("The main nucleus for transmit/receive"); delay_rastertime=0.0; delay_rastertime.set_unit(ODIN_TIME_UNIT).set_description("Delay duration must be multiple of this interval"); grad_rastertime=0.0; grad_rastertime.set_unit(ODIN_TIME_UNIT).set_description("Gradient duration must be multiple of this interval"); min_grad_rastertime=0.005; min_grad_rastertime.set_unit(ODIN_TIME_UNIT).set_description("Minimum gradient raster time possible"); rf_rastertime=0.0; rf_rastertime.set_unit(ODIN_TIME_UNIT).set_description("RF pulse duration must be multiple of this interval"); acq_rastertime=0.0; acq_rastertime.set_unit(ODIN_TIME_UNIT).set_description("Acquisition duration must be multiple of this interval"); max_rf_samples=3000; max_rf_samples.set_description("Maximum number of points in RF waveform"); max_grad_samples=-1; max_grad_samples.set_description("Maximum number of points in gradient waveform"); reference_gain=20.0; reference_gain.set_unit("dB").set_description("RF reference gain"); transmit_coil_name="Unknown"; transmit_coil_name.set_cmdline_option("tcname").set_description("Name of transmit coil"); inter_grad_delay=0.0; inter_grad_delay.set_unit(ODIN_TIME_UNIT).set_description("Minimum delay between gradient objects"); max_grad=_DEFAULT_MAX_SYSTEM_GRADIENT_; max_grad.set_unit(ODIN_GRAD_UNIT).set_description("Maximum gradient strength"); max_slew_rate=_DEFAULT_MAX_SYSTEM_SLEWRATE_; max_slew_rate.set_unit(STD_string(ODIN_GRAD_UNIT)+"/"+ODIN_TIME_UNIT).set_description("Maximum gradient slew rate"); grad_shift=0.0; grad_shift.set_unit(ODIN_TIME_UNIT).set_description("Latency difference between RF/acquistion and gradient channels"); B0=_DEFAULT_B0_; B0.set_unit(ODIN_FIELD_UNIT).set_description("Main field strength"); datatype=TypeTraits::type2label(float(0)); datatype.set_description("Digital representation of raw data"); grad_reson_center.set_filemode(exclude).set_unit(ODIN_FREQ_UNIT).set_description("Center of gradient resonance frequencies"); grad_reson_width.set_filemode(exclude).set_unit(ODIN_FREQ_UNIT).set_description("Width of gradient resonance frequencies"); min_duration.resize(endObj); min_duration=0.0; System::append_all_members(); } System& System::operator = (const System& s) { JcampDxBlock::operator = (s); System::append_all_members(); // copy only visible members of JcampDxBlock copy_ldr_vals(s); return *this; } odinPlatform System::get_platform() const { return SystemInterface::get_current_pf(); } System& System::set_main_nucleus(const STD_string& nucname) { main_nucleus.set_actual(nucname); return *this; } System& System::set_transmit_coil_name(const STD_string& tcname) { transmit_coil_name=tcname; return *this; } float System::get_grad_switch_time(float graddiff) const { return ( secureDivision(fabs(graddiff),max_slew_rate) + get_inter_grad_delay() ); } System& System::set_reference_gain(float refgain) { reference_gain=refgain; return *this; } System& System::set_B0_from_freq(double freq, const STD_string& nucName) { B0=2.0*PII*secureDivision(freq,get_gamma(nucName)); return *this; } double System::get_gamma(const STD_string& nucName) const { return nuc.get_gamma(nucName); } System& System::set_scandir(const STD_string& dir) { Log odinlog(this,"set_scandir"); #ifndef NO_FILEHANDLING if(!checkdir(dir.c_str())) ODINLOG(odinlog,errorLog) << "scan directory " << dir << " does not exist" << STD_endl; #endif scandir=dir; return *this; } STD_string System::get_scandir() const {return scandir+"/";} double System::get_nuc_freq(const STD_string& nucName) const { return nuc.get_nuc_freq(nucName,B0); } JDXenum System::get_nuc_enum() const {return nuc.get_nuc_enum();} double System::get_rastertime(objCategory cat) const { if(cat==pulsObj) return rf_rastertime; if(cat==gradObj) return grad_rastertime; if(cat==delayObj) return delay_rastertime; if(cat==acqObj) return acq_rastertime; if(cat==freqObj) return rf_rastertime; if(cat==syncObj) return grad_rastertime; return 0.0; } double System::get_rasteredtime(objCategory cat, double time) const { double rastime=get_rastertime(cat); if(rastime) { int eventtime_round=int(time/rastime+0.5); return double(eventtime_round)*rastime; } else return time; } bool System::allowed_grad_freq(double freq, double& low, double& upp) const { low=upp=freq; for(unsigned int i=0; i odinlog(this,"load"); ODINLOG(odinlog,errorLog) << "called" << STD_endl; return -1; } int System::append_all_members() { append_member(platformstr,"Platform"); append_member(main_nucleus,"MainNucleus"); append_member(max_grad,"MaximumGradientStrength"); append_member(max_slew_rate,"MaximumGradientSlewRate"); append_member(grad_shift,"GradientChannelShiftDelay"); append_member(B0,"MagneticFieldStrength"); append_member(reference_gain,"ReferenceGain"); append_member(transmit_coil_name,"TransmitCoilName"); append_member(inter_grad_delay,"InterGradientSwitchingDelay"); append_member(delay_rastertime,"DelayRasterTime"); append_member(grad_rastertime,"GradientRasterTime"); append_member(min_grad_rastertime,"MinGradientRasterTime"); append_member(rf_rastertime,"RFRasterTime"); append_member(acq_rastertime,"AcquisitionRasterTime"); append_member(max_rf_samples,"MaxNumOfSamplesPerRF"); append_member(max_grad_samples,"MaxNumOfSamplesPerGradWave"); append_member(grad_reson_center,"GradResonCenter"); append_member(grad_reson_width,"GradResonWidth"); append_member(datatype,"Datatype"); return 0; } ///////////////////////////////////////////////////////////////////////////// System* SystemInterface::get_sysinfo_ptr() { int pfint=current_pf->operator int (); return systemInfo_platform[pfint].unlocked_ptr(); } const System* SystemInterface::get_const_sysinfo_ptr() { int pfint=current_pf->operator int (); const SingletonHandler& shs=systemInfo_platform[pfint]; return shs.operator -> (); // return &(const System&)(*shs); } void SystemInterface::init_static() { current_pf.init("current_pf"); systemInfo_platform= new SingletonHandler[numof_platforms]; for(unsigned int i=0; iset_label("systemInfo"); } } void SystemInterface::destroy_static() { for(unsigned int i=0; i odinlog("SystemInterface","set_current_pf"); ODINLOG(odinlog,normalDebug) << "pf=" << pf << STD_endl; if(current_pf) current_pf->operator = (pf); else ODINLOG(odinlog,errorLog) << "current_pf not yet initialized" << STD_endl; } template class SingletonHandler; SingletonHandler SystemInterface::current_pf; template class SingletonHandler; SingletonHandler* SystemInterface::systemInfo_platform=0; EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/odinpara/jdxnumbers.cpp0000644000175000017500000001105711322062341014057 00000000000000#include "jdxnumbers.h" #include "jdxblock.h" // for UnitTest #include /////////////////////////////////////////////////////////////// template void JDXnumber::set_defaults() { val=T(0); minval=0.0; maxval=0.0; parx_equiv.type=TypeTraits::type2label(val); } template JDXnumber::JDXnumber(T v,const STD_string& name,bool userParameter, compatMode mode,parameterMode parameter_mode, const STD_string& parx_equivalent, float parx_assign_factor,float parx_assign_offset) { set_defaults(); val=v; set_label(name); JcampDxClass::set_compatmode(mode); // Do NOT call virtual function in constructor! set_userDefParameter(userParameter); parx_equiv.name=parx_equivalent; parx_equiv.factor=parx_assign_factor; parx_equiv.offset=parx_assign_offset; JcampDxClass::set_parmode(parameter_mode); // Do NOT call virtual function in constructor! } template JDXnumber& JDXnumber::operator = (const JDXnumber& bi) { JcampDxClass::operator = (bi); val=bi.val; parx_equiv=bi.parx_equiv; minval=bi.minval; maxval=bi.maxval; return *this; } template STD_string JDXnumber::printvalstring() const { return TypeTraits::type2string(val); } template bool JDXnumber::parsevalstring(const STD_string& parstring) { TypeTraits::string2type(parstring,val); return true; } template STD_string JDXnumber::get_parx_code(parxCodeType type, const ParxEquiv& equiv) const { #ifdef PARAVISION_PLUGIN Log odinlog(this,"get_parx_code"); STD_string result=JcampDxClass::get_parx_code(type,equiv); if(type==parx_def) result=get_parx_def_string(get_typeInfo(),0); if(type==parx_passval) { STD_string transformation; if (equiv.offset) transformation+=ftos(equiv.offset)+"+"; if (equiv.factor!=1.0) transformation+=ftos(equiv.factor)+"*"; result=equiv.name+"="+transformation+get_label()+";\n"; } return result; #else return ""; #endif } /////////////////////////////////////////////////////////////////// // Instantiations template class JDXnumber; template class JDXnumber; template class JDXnumber; template class JDXnumber; /////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class JDXintTest : public UnitTest { public: JDXintTest() : UnitTest("JDXint") {} private: bool check() const { Log odinlog(this,"check"); // testing JDXint JDXint testint(23,"testint"); STD_string expected="##$testint=23\n"; STD_string printed=testint.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXint::print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } JcampDxBlock builtinblock; builtinblock.append(testint); builtinblock.parseblock("##TITLE=builtinblock\n##$testint=46\n##END="); if(int(testint)!=46) { ODINLOG(odinlog,errorLog) << "after builtinblock.parseblock(): for int " << int(testint) << "!=" << 46 << STD_endl; return false; } testint*=2; if(int(testint)!=92) { ODINLOG(odinlog,errorLog) << "JDXint *= " << int(testint) << "!=" << 92 << STD_endl; return false; } return true; } }; void alloc_JDXintTest() {new JDXintTest();} // create test instance class JDXcomplexTest : public UnitTest { public: JDXcomplexTest() : UnitTest("JDXcomplex") {} private: bool check() const { Log odinlog(this,"check"); // testing JDXcomplex JDXcomplex testcplx(STD_complex(1.2,3.4),"testcplx"); STD_string expected="##$testcplx=1.20+3.40i\n"; STD_string printed=testcplx.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXcomplex::print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } JcampDxBlock cplxblock; cplxblock.append(testcplx); cplxblock.parseblock("##TITLE=cplxblock\n##testcplx=5.6+7.8i\n##END="); if(STD_complex(testcplx)!=STD_complex(5.6,7.8)) { ODINLOG(odinlog,errorLog) << "after cplxblock.parseblock(): for complex " << STD_complex(testcplx) << "!=" << STD_complex(5.6,7.8) << STD_endl; return false; } testcplx/=STD_complex(2.0); if(STD_complex(testcplx)!=STD_complex(2.8,3.9)) { ODINLOG(odinlog,errorLog) << "JDXcomplex /= " << STD_complex(testcplx) << "!=" << STD_complex(2.8,3.9) << STD_endl; return false; } return true; } }; void alloc_JDXcomplexTest() {new JDXcomplexTest();} // create test instance #endif odin-1.8.5/odinpara/jdxtypes.cpp0000644000175000017500000005022411322062341013547 00000000000000#include "jdxtypes.h" #include "jdxblock.h" // for UnitTest #include JDXstring::JDXstring(const STD_string& ss,const STD_string& name,bool userParameter, compatMode mode,parameterMode parameter_mode, const STD_string& parx_equivalent) : STD_string(ss) { set_label(name); JcampDxClass::set_compatmode(mode); // Do NOT call virtual function in constructor! set_userDefParameter(userParameter); JcampDxClass::set_parmode(parameter_mode); // Do NOT call virtual function in constructor! parx_equiv.name=parx_equivalent; } JDXstring& JDXstring::operator = (const JDXstring& ss) { JcampDxClass::operator = (ss); STD_string::operator = (ss); parx_equiv=ss.parx_equiv; return *this; } STD_string JDXstring::printvalstring() const { Log odinlog(this,"printvalstring"); if(get_filemode()==exclude) return ""; STD_string result; if(get_compatmode()==bruker) { ndim nn(1); int l=length()*_BRUKER_MODE_STRING_CAP_FACTOR_; if(!l) l=_BRUKER_MODE_STRING_CAP_START_; if(l<_BRUKER_MODE_STRING_MIN_SIZE_) l=_BRUKER_MODE_STRING_MIN_SIZE_; nn[0]=l; result+=STD_string(nn)+"\n"; } if(get_compatmode()==bruker) result+="<"; result+=STD_string(*this); if(get_compatmode()==bruker) result+=">"; ODINLOG(odinlog,normalDebug) << "returning >" << result << "<" << STD_endl; return result; } bool JDXstring::parsevalstring(const STD_string& str) { Log odinlog(this,"parsevalstring"); ODINLOG(odinlog,normalDebug) << "str=>" << str << "<" << STD_endl; STD_string without_size_field; if(get_compatmode()==bruker) without_size_field=extract(str,"\n",""); else without_size_field=str; ODINLOG(odinlog,normalDebug) << "without_size_field=>" << without_size_field << "<" << STD_endl; STD_string shrinked=shrink(without_size_field); ODINLOG(odinlog,normalDebug) << "shrinked=>" << shrinked << "<" << STD_endl; if (shrinked.length()>=2 && shrinked[(unsigned int)0]=='<' && shrinked[shrinked.length()-1]=='>') (*this)=extract(without_size_field,"<",">",true); else (*this)=without_size_field; return true; } STD_string JDXstring::get_parx_code(parxCodeType type, const ParxEquiv& equiv) const { #ifdef PARAVISION_PLUGIN STD_string result=JcampDxClass::get_parx_code(type,equiv); if(type==parx_def) result=get_parx_def_string(get_parx_equiv().type,1); if(type==parx_passval) result="sprintf("+equiv.name+",\"%s\","+get_label()+");\n"; return result; #else return ""; #endif } #ifndef NO_UNIT_TEST class JDXstringTest : public UnitTest { public: JDXstringTest() : UnitTest("JDXstring") {} private: bool check() const { Log odinlog(this,"check"); JDXstring teststr1("value","teststr1",true,notBroken); JDXstring teststr2("value","teststr2",true,bruker); // testing JDXstring::print STD_string expected="##$teststr1=value\n"; STD_string printed=teststr1.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } expected="##$teststr2=( "+itos(_BRUKER_MODE_STRING_MIN_SIZE_)+" )\n\n"; printed=teststr2.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } // testing JDXstring::parse JcampDxBlock block; block.append(teststr1); block.append(teststr2); int parseresult=block.parseblock("##TITLE=block\n##$teststr1=parseval\n##$teststr2=( 64 )\n\n$$ Comment\n##$dummy=dummyval\n##END="); if(parseresult!=2) { ODINLOG(odinlog,errorLog) << "JcampDxBlock::parseblock() failed: parseresult=" << parseresult << "!=" << 2 << STD_endl; return false; } if(STD_string(block.get_label())!="block") { ODINLOG(odinlog,errorLog) << "JcampDxBlock::get_label() failed: >" << block.get_label() << "< != >block<" << STD_endl; return false; } if(STD_string(teststr1)!=STD_string(teststr2)) { ODINLOG(odinlog,errorLog) << "after block.parseblock(): >" << STD_string(teststr1) << "< != >" << STD_string(teststr2) << "<" << STD_endl; return false; } return true; } }; void alloc_JDXstringTest() {new JDXstringTest();} // create test instance #endif ////////////////////////////////////////////////////////////////// JDXbool::JDXbool(bool flag, const STD_string& name,bool userParameter, compatMode mode,parameterMode parameter_mode, const STD_string& parx_equivalent) : val(flag) { set_label(name); JcampDxClass::set_compatmode(mode); // Do NOT call virtual function in constructor! set_userDefParameter(userParameter); JcampDxClass::set_parmode(parameter_mode); // Do NOT call virtual function in constructor! parx_equiv.name=parx_equivalent; } JDXbool& JDXbool::operator = (const JDXbool& jb) { JcampDxClass::operator = (jb); val=jb.val; parx_equiv=jb.parx_equiv; return *this; } bool JDXbool::parsevalstring (const STD_string& parstring) { Log odinlog(this,"parsevalstring"); STD_string yesnostr(shrink(tolowerstr(parstring))); ODINLOG(odinlog,normalDebug) << "yesnostr=" << yesnostr << STD_endl; if(yesnostr=="yes" || yesnostr=="true") val=true; else val=false; ODINLOG(odinlog,normalDebug) << "this=" << bool(*this) << STD_endl; return true; } STD_string JDXbool::printvalstring() const { if(val) return "Yes"; else return "No"; } STD_string JDXbool::get_parx_code(parxCodeType type, const ParxEquiv& equiv) const { #ifdef PARAVISION_PLUGIN STD_string result=JcampDxClass::get_parx_code(type,equiv); if(type==parx_def) result=get_parx_def_string(equiv.type,0); return result; #else return ""; #endif } #ifndef NO_UNIT_TEST class JDXboolTest : public UnitTest { public: JDXboolTest() : UnitTest("JDXbool") {} private: bool check() const { Log odinlog(this,"check"); JDXbool testbool(false,"testbool"); testbool=true; STD_string expected="##$testbool=Yes\n"; STD_string printed=testbool.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } JcampDxBlock boolblock; boolblock.append(testbool); boolblock.parseblock("##TITLE=boolblock\n##$testbool=No\n##END="); if(bool(testbool)!=false) { ODINLOG(odinlog,errorLog) << "after boolblock.parseblock(): for bool " << bool(testbool) << "!=" << false << STD_endl; return false; } return true; } }; void alloc_JDXboolTest() {new JDXboolTest();} // create test instance #endif /////////////////////////////////////////////////////////////// JDXenum::JDXenum(const STD_string& first_entry, const STD_string& name,bool userParameter, compatMode mode,parameterMode parameter_mode, const STD_string& parx_equivalent) { add_item(first_entry); set_label(name); JcampDxClass::set_compatmode(mode); // Do NOT call virtual function in constructor! set_userDefParameter(userParameter); JcampDxClass::set_parmode(parameter_mode); // Do NOT call virtual function in constructor! parx_equiv.name=parx_equivalent; } JDXenum& JDXenum::operator = (const JDXenum& je) { JcampDxClass::operator = (je); entries=je.entries; for(STD_map::const_iterator it=entries.begin();it!=entries.end();++it) { if ( (it->first) == (je.actual->first) ) actual=it; } parx_equiv=je.parx_equiv; return *this; } JDXenum& JDXenum::add_item(const STD_string& item, int index) { if(item=="") return *this; int n=0; if(index<0) { for(STD_map::const_iterator it=entries.begin();it!=entries.end();++it) { if ( it->first > n ) n=it->first; } if(entries.size()) n++; } else n=index; entries[n]=item; actual=entries.find(n); return *this; } JDXenum& JDXenum::set_actual(const STD_string& item) { STD_map::const_iterator it; for(it=entries.begin();it!=entries.end();++it) { if ( (it->second) == item ) actual=it; } return *this; } JDXenum& JDXenum::set_actual(int index) { STD_map::const_iterator it; for(it=entries.begin();it!=entries.end();++it) { if ( (it->first) == index ) actual=it; } return *this; } JDXenum& JDXenum::clear() { entries.clear(); actual=entries.end(); return *this; } JDXenum::operator int () const { if(actual!=entries.end()) return actual->first; else return 0; } JDXenum::operator STD_string () const { if(actual!=entries.end()) return actual->second; else return ""; } static STD_string notext("none"); const STD_string& JDXenum::get_item(unsigned int index) const { STD_map::const_iterator it=entries.begin(); for(unsigned int i=0; isecond; } unsigned int JDXenum::get_item_index() const { unsigned int result=0; for(STD_map::const_iterator it=entries.begin();it!=entries.end();++it) { if ( it==actual ) return result; result++; } return 0; } JDXenum& JDXenum::set_item_index(unsigned int index) { STD_map::const_iterator it=entries.begin(); for(unsigned int i=0; i::const_iterator it; for(it=entries.begin();it!=entries.end();++it) { if ( (it->second) == newpar ) { already_there=true; actual=it; } } if(!already_there && (entries.size()==0) ) add_item(newpar); return true; } STD_string JDXenum::get_parx_code(parxCodeType type, const ParxEquiv& equiv) const { #ifdef PARAVISION_PLUGIN STD_string result=JcampDxClass::get_parx_code(type,equiv); if(type==parx_def) result=get_parx_def_string(equiv.type,0); return result; #else return ""; #endif } ParxEquiv JDXenum::get_parx_equiv() const { parx_equiv.type=toupperstr(STD_string(get_label())); return parx_equiv; } svector JDXenum::get_alternatives() const { unsigned int n=n_items(); svector result; result.resize(n); for(unsigned int i=0; isecond); else return "emptyEnum"; } #ifndef NO_UNIT_TEST class JDXenumTest : public UnitTest { public: JDXenumTest() : UnitTest("JDXenum") {} private: bool check() const { Log odinlog(this,"check"); // testing JDXenum JDXenum testenum("","testenum"); testenum.add_item("item7",7); testenum.add_item("item0",0); testenum.add_item("item5",5); testenum.add_item("item1",1); testenum="item5"; STD_string expected="##$testenum=item5\n"; STD_string printed=testenum.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "testenum::print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } testenum=7; expected="##$testenum=item7\n"; printed=testenum.print(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "testenum::print() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } JcampDxBlock enumblock; enumblock.append(testenum); enumblock.parseblock("##TITLE=enumblock\n##testenum=item1\n##END="); if((int)testenum!=1) { ODINLOG(odinlog,errorLog) << "after enumblock.parseblock(): for JDXenum " << (int)testenum << "!=" << 1 << STD_endl; return false; } return true; } }; void alloc_JDXenumTest() {new JDXenumTest();} // create test instance #endif /////////////////////////////////////////////////////////////// JDXaction::JDXaction(bool init_state, const STD_string& name,bool userParameter, compatMode mode,parameterMode parameter_mode) : state(init_state) { JcampDxClass::set_filemode(exclude); // Do NOT call virtual function in constructor! set_label(name); JcampDxClass::set_compatmode(mode); // Do NOT call virtual function in constructor! set_userDefParameter(userParameter); JcampDxClass::set_parmode(parameter_mode); // Do NOT call virtual function in constructor! } JDXaction& JDXaction::operator = (const JDXaction& ja) { JcampDxClass::operator = (ja); return *this; } JDXaction::operator bool () const { bool result=state; state=false; return result; } bool JDXaction::parsevalstring (const STD_string& parstring) { STD_string actionstr(shrink(tolowerstr(parstring))); if(actionstr=="busy") state=true; else state=false; return true; } STD_string JDXaction::printvalstring() const { if(state) return "CLICK_HERE"; else return "NOW"; } /////////////////////////////////////////////////////////////// JDXfileName::JDXfileName(const STD_string& filename, const STD_string& name, bool userParameter, compatMode mode, parameterMode parameter_mode) : JDXstring(filename, name, userParameter, mode, parameter_mode) { common_init(); normalize(filename, dir, *this, dirname_cache, basename_cache, suffix_cache); } JDXfileName::JDXfileName (const JDXfileName& jf) { common_init(); JDXfileName::operator = (jf); } JDXfileName& JDXfileName::operator = (const STD_string& filename) { normalize(filename, dir, *this, dirname_cache, basename_cache, suffix_cache); return *this; } JDXfileName& JDXfileName::operator = (const JDXfileName& jf) { JDXstring::operator = (jf); dir=jf.dir; normalize(jf, dir, *this, dirname_cache, basename_cache, suffix_cache); defaultdir=jf.defaultdir; return *this; } bool JDXfileName::exists() const { bool result=false; #ifndef NO_FILEHANDLING if(is_dir()) result=checkdir(c_str()); else result=(filesize(c_str())>=0); #endif return result; } STD_string JDXfileName::get_basename_nosuffix() const { STD_string result(get_basename()); if(get_suffix()!="") return replaceStr(result,"."+get_suffix(),""); return result; } JDXfileName& JDXfileName::set_defaultdir(const STD_string& defdir) { STD_string dummystr; normalize(defdir, true, defaultdir, dummystr, dummystr, dummystr); return *this; } bool JDXfileName::parsevalstring (const STD_string& parstring) { normalize(parstring, dir, *this, dirname_cache, basename_cache, suffix_cache); return true; } void JDXfileName::normalize(const STD_string& fname, bool dir, STD_string& result, STD_string& result_dirname, STD_string& result_basename, STD_string& result_suffix) { Log odinlog("JDXfileName","normalize"); STD_string tmpstr(fname); // mutable copy // remove quotes tmpstr=replaceStr(tmpstr, "\"",""); tmpstr=replaceStr(tmpstr, "\'",""); // remove preceeding blanks int beginpos=textbegin(tmpstr,0); if(beginpos<0) beginpos=0; tmpstr=tmpstr.substr(beginpos,tmpstr.length()-beginpos); // check whether we have absolute or relative path bool abspath=false; STD_string drive; #ifdef USING_WIN32 // replace slashes that are left on Windows tmpstr=replaceStr(tmpstr,"/",SEPARATOR_STR); if(tmpstr.length()>=2 && (tmpstr[1]==':') ) { drive=STD_string(1,tmpstr[0])+":"; // store tmpstr=tmpstr.substr(2,tmpstr.length()-2); // and strip off drive letter abspath=true; // accept drive-letter notation } #endif if(tmpstr.length()>=1 && (tmpstr[0]==SEPARATOR_CHAR) ) abspath=true; ODINLOG(odinlog,normalDebug) << "tmpstr/abspath=>" << tmpstr << "1) result_suffix=tolowerstr(sufftoks[sufftoks.size()-1]); } if(dir) result_suffix=""; // No suffix for dirs // set defaults result=drive; result_dirname=drive; result_basename=""; if(!abspath && (ntoks==1)) result_dirname="."; // File is in PWD // Recompose path and store dirname/basename if(ntoks) { if(abspath) { result+=SEPARATOR_STR; result_dirname+=SEPARATOR_STR; } ODINLOG(odinlog,normalDebug) << "result/result_dirname(pre loop)=>" << result << "<>" << result_dirname << "<" << STD_endl; for(int i=0; i" << result << "<>" << result_dirname << "<" << STD_endl; } } #ifndef NO_UNIT_TEST class JDXfileNameTest : public UnitTest { public: JDXfileNameTest() : UnitTest("JDXfileName") {} private: bool check() const { Log odinlog(this,"check"); JDXfileName teststr1=STD_string("image.bmp"); STD_string expected="image.bmp"; STD_string printed=teststr1; if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::STD_string failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } expected="bmp"; printed=teststr1.get_suffix(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::get_suffix()[from filename] failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } expected="cpp"; teststr1.set_suffix(expected); printed=teststr1.get_suffix(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::get_suffix()[when set] failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } teststr1=STD_string(".bmp"); expected="bmp"; printed=teststr1.get_suffix(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::get_suffix()[empty basename] failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } teststr1=STD_string("//tmp///test"); expected=STD_string(SEPARATOR_STR)+"tmp"; printed=teststr1.get_dirname(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::get_dirname() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } teststr1=STD_string("subdir///file"); expected="subdir"+STD_string(SEPARATOR_STR)+"file"; printed=teststr1; if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::STD_string failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } expected="file"; printed=teststr1.get_basename(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::get_basename() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } expected="subdir"; printed=teststr1.get_dirname(); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName::get_dirname() failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } #ifdef USING_WIN32 teststr1=STD_string("C:"); expected="C:"; printed=STD_string(teststr1); if(printed!=expected) { ODINLOG(odinlog,errorLog) << "JDXfileName(WIN32): failed: got >" << printed << "<, but expected >" << expected << "<" << STD_endl; return false; } #endif return true; } }; void alloc_JDXfileNameTest() {new JDXfileNameTest();} // create test instance #endif /////////////////////////////////////////////////////////////// JDXformula::JDXformula(const STD_string& formula, const STD_string& name, bool userParameter, compatMode mode, parameterMode parameter_mode) : JDXstring(formula,name,userParameter,mode,parameter_mode) { } JDXformula& JDXformula::operator = (const JDXformula& jf) { JDXstring::operator = (jf); syntax = jf.syntax; return *this; } odin-1.8.5/odinpara/odinpara.h0000644000175000017500000000443111322062340013135 00000000000000/*************************************************************************** odinpara.h - description ------------------- begin : Tue Jun 28 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINPARA_H #define ODINPARA_H /** * @addtogroup odinpara * @{ */ /** * @ingroup odinpara * This enum is used to specify directions in the coordinate system * of the sequence gradients, i.e. gradient channel: * - readDirection: The first gradient channel * - phaseDirection: The second gradient channel * - sliceDirection: The third gradient channel */ enum direction { readDirection=0, phaseDirection, sliceDirection, n_directions}; static const char* directionLabel[]={"readDirection", "phaseDirection","sliceDirection"}; /** * Enum for the direction of spatial axes in the laboratory system of reference: * - xAxis: The first spatial direction * - yAxis: The second spatial direction * - zAxis: The third spatial direction */ enum axis {xAxis=0,yAxis,zAxis,n_axes}; // Units within ODIN #define ODIN_TIME_UNIT "ms" #define ODIN_FREQ_UNIT "kHz" #define ODIN_SPAT_UNIT "mm" #define ODIN_FIELD_UNIT "mT" #define ODIN_GRAD_UNIT "mT/mm" #define ODIN_ANGLE_UNIT "deg" // some common stuff for geometry and sample #define ODIN_DEFAULT_FOV 220.0 #define ODIN_MAX_NUMOF_SLICES 50 #define ODIN_GEO_CHECK_LIMIT 1e-6 // for debugging odinpara component class Para { public: static const char* get_compName(); }; /** @} */ #endif odin-1.8.5/odinpara/sample.cpp0000644000175000017500000002112411455553536013175 00000000000000#include "sample.h" Sample::Sample(const STD_string& label, bool uniformFOV, bool uniformT1T2) : JcampDxBlock(label) { uniFOV=uniformFOV; uniT1T2=uniformT1T2; resize(1,1,1,1,1); FOVall=20.0; FOVall.set_minmaxval(0.0,ODIN_DEFAULT_FOV).set_unit(ODIN_SPAT_UNIT).set_description("Uniform Field-Of-View (spatial extent) in all spatial dimensions"); FOV[xAxis]=20.0; FOV[yAxis]=20.0; FOV[zAxis]=20.0; FOV.set_unit(ODIN_SPAT_UNIT).set_description("Spatial extent"); offset.set_unit(ODIN_SPAT_UNIT).set_description("Spatial offset"); freqrange=10.0; freqrange.set_minmaxval(0.0,50.0).set_unit(ODIN_FREQ_UNIT).set_description("Extent in frequency dimension"); freqoffset=0.0; freqoffset.set_minmaxval(-100.0,100.0).set_unit(ODIN_FREQ_UNIT).set_description("Frequency offset"); frameDurations.set_parmode(hidden).set_unit(ODIN_TIME_UNIT).set_description("Time intervals to cycle through frames periodically"); T1=0.0; T1.set_minmaxval(0.0,2000.0).set_unit(ODIN_TIME_UNIT).set_description("Uniform longitudinal relaxation constant"); T2=0.0; T2.set_minmaxval(0.0,500.0).set_unit(ODIN_TIME_UNIT).set_description("Uniform transverse relaxation constant"); T1map.set_filemode(compressed).set_parmode(hidden).set_description("Longitudinal relaxation constant as a function of position, frequency and time frame"); T2map.set_filemode(compressed).set_parmode(hidden).set_description("Transverse relaxation constant as a function of position, frequency and time frame"); ppmMap.set_filemode(compressed).set_parmode(hidden).set_description("Frequency offset as a function of position, frequency and time frame"); spinDensity.set_filemode(compressed).set_parmode(hidden).set_description("Spin density as a function of position, frequency and time frame"); DcoeffMap.set_filemode(compressed).set_parmode(hidden).set_description("Diffusion coefficient as a function of position, frequency and time frame"); Sample::append_all_members(); } Sample::Sample(const Sample& ss) { Sample::operator = (ss); } Sample& Sample::operator = (const Sample& ss) { JcampDxBlock::operator = (ss); FOVall=ss.FOVall; FOV=ss.FOV; uniFOV=ss.uniFOV; offset=ss.offset; freqrange=ss.freqrange; freqoffset=ss.freqoffset; frameDurations=ss.frameDurations; uniT1T2=ss.uniT1T2; T1=ss.T1; T2=ss.T2; T1map=ss.T1map; T2map=ss.T2map; haveT1map=ss.haveT1map; haveT2map=ss.haveT2map; ppmMap=ss.ppmMap; have_ppmMap=ss.have_ppmMap; spinDensity=ss.spinDensity; DcoeffMap=ss.DcoeffMap; have_DcoeffMap=ss.have_DcoeffMap; Sample::append_all_members(); return *this; } Sample& Sample::set_FOV(float fov) { FOVall=fov; FOV.farray::operator = (fov); uniFOV=true; return *this; } Sample& Sample::set_FOV(axis direction, float fov) { FOV[direction]=fov; uniFOV=false; return *this; } float Sample::get_FOV(axis direction) const { if(uniFOV) return FOVall; return FOV[direction]; } Sample& Sample::resize(unsigned int framesize, unsigned int freqsize, unsigned int zsize, unsigned int ysize, unsigned int xsize) { Log odinlog(this,"resize"); haveT1map=false; haveT2map=false; have_ppmMap=false; have_DcoeffMap=false; ndim newsize(n_sampleDim); newsize[frameDim]=framesize; newsize[freqDim]=freqsize; newsize[zDim]=zsize; newsize[yDim]=ysize; newsize[xDim]=xsize; ODINLOG(odinlog,normalDebug) << "newsize=" << newsize << STD_endl; ODINLOG(odinlog,normalDebug) << "spinDensity.get_extent()=" << spinDensity.get_extent() << STD_endl; // leave spinDensity untouched if it has already the right size (required for load) if(newsize!=spinDensity.get_extent()) { ODINLOG(odinlog,normalDebug) << "resizing" << STD_endl; spinDensity.redim (newsize); spinDensity.farray::operator = (1.0); } ODINLOG(odinlog,normalDebug) << "extent=" << get_extent() << STD_endl; return *this; } bool Sample::check_and_correct(const char* mapname, const farray& srcmap, farray& dstmap) { Log odinlog(this,"check_and_correct"); ndim nn_map=srcmap.get_extent(); unsigned int n_sampleDim_old=n_sampleDim-1; // for backwards compatability if(nn_map.dim()!=n_sampleDim && nn_map.dim()!=n_sampleDim_old) { ODINLOG(odinlog,normalDebug) << "Map " << mapname << " has incorrect shape size=" << nn_map.dim() << STD_endl; return false; } bool reshape=false; if(nn_map.dim()==n_sampleDim_old) { ODINLOG(odinlog,warningLog) << "Reshaping map " << mapname << " for backwards compatability" << STD_endl; nn_map.add_dim(1,true); reshape=true; } ndim nn=get_extent(); nn[frameDim]=nn_map[frameDim]=1; // ignore size of frame dim if(nn!=nn_map) { ODINLOG(odinlog,errorLog) << "Map " << mapname << " has incorrect shape " << nn_map << STD_endl; return false; } dstmap=srcmap; if(reshape) dstmap.redim(nn_map); return true; } Sample& Sample::set_T1map(const farray& t1map) { if(uniT1T2) return *this; if(!check_and_correct("T1",t1map,T1map)) return *this; haveT1map=true; return *this; } const farray& Sample::get_T1map() const { if(!haveT1map) { T1map.redim(get_extent()); T1map.farray::operator = (T1); haveT1map=true; } return T1map; } Sample& Sample::set_T2map(const farray& t2map) { if(uniT1T2) return *this; if(!check_and_correct("T2",t2map,T2map)) return *this; haveT2map=true; return *this; } const farray& Sample::get_T2map() const { if(!haveT2map) { T2map.redim(get_extent()); T2map.farray::operator = (T2); haveT2map=true; } return T2map; } Sample& Sample::set_ppmMap(const farray& ppmmap) { if(!check_and_correct("ppmMap",ppmmap,ppmMap)) return *this; have_ppmMap=true; return *this; } const farray& Sample::get_ppmMap() const { Log odinlog(this,"get_ppmMap"); ODINLOG(odinlog,normalDebug) << "get_extent()=" << get_extent() << STD_endl; if(!have_ppmMap) { ODINLOG(odinlog,normalDebug) << "Creating zero ppmMap" << STD_endl; ppmMap.redim(get_extent()); ppmMap.farray::operator = (0.0); have_ppmMap=true; } ODINLOG(odinlog,normalDebug) << "ppmMap.get_extent()=" << ppmMap.get_extent() << STD_endl; return ppmMap; } Sample& Sample::set_spinDensity(const farray& sd) { if(!check_and_correct("spinDensity",sd,spinDensity)) return *this; return *this; } const farray& Sample::get_spinDensity() const { return spinDensity; } Sample& Sample::set_DcoeffMap(const farray& dmap) { if(!check_and_correct("Dcoeff",dmap,DcoeffMap)) return *this; have_DcoeffMap=true; return *this; } const farray& Sample::get_DcoeffMap() const { if(!have_DcoeffMap) { DcoeffMap.redim(get_extent()); DcoeffMap.farray::operator = (0.0); have_DcoeffMap=true; } return DcoeffMap; } Sample& Sample::update() { // outdate cache in interactive mode if(uniT1T2) { haveT1map=false; haveT2map=false; } if(T1!=0.0 || T2!=0.0) { if(T1>0.0 && T2>T1) T2=double(T1); } return *this; } int Sample::load(const STD_string& filename) { Log odinlog(this,"load"); int errval=JcampDxBlock::load(filename); ndim nn=spinDensity.get_extent(); if(nn.dim()==(n_sampleDim-1)) { ODINLOG(odinlog,normalDebug) << "Reshaping map for backwards compatability" << STD_endl; nn.add_dim(1,true); spinDensity.redim(nn); } ODINLOG(odinlog,normalDebug) << "nn=" << nn << STD_endl; ODINLOG(odinlog,normalDebug) << "spinDensity.sum()=" << spinDensity.sum() << STD_endl; if(nn.dim()!=n_sampleDim || nn.total()==0) { ODINLOG(odinlog,errorLog) << "spinDensity has invalid extent=" << STD_string(nn) << STD_endl; return -1; } uniFOV=false; uniT1T2=false; ODINLOG(odinlog,normalDebug) << "resizing to " << STD_string(nn) << STD_endl; resize(nn[frameDim],nn[freqDim],nn[zDim],nn[yDim],nn[xDim]); ODINLOG(odinlog,normalDebug) << "ppmMap.get_extent()=" << STD_string(ppmMap.get_extent()) << STD_endl; haveT1map=check_and_correct("T1",T1map,T1map); haveT2map=check_and_correct("T2",T2map,T2map); have_ppmMap=check_and_correct("ppmMap",ppmMap,ppmMap); have_DcoeffMap=check_and_correct("Dcoeff",DcoeffMap,DcoeffMap); ODINLOG(odinlog,normalDebug) << "have_ppmMap=" << have_ppmMap << STD_endl; return errval; } int Sample::append_all_members() { if(uniFOV) { append_member(FOVall,"FOVall"); } else { append_member(FOV,"FOV"); } append_member(freqrange,"FrequencyRange"); append_member(freqoffset,"FrequencyOffset"); append_member(frameDurations,"FrameDurations"); append_member(T1,"RelaxationT1"); append_member(T2,"RelaxationT2"); append_member(T1map,"T1map"); append_member(T2map,"T2map"); append_member(ppmMap,"ppmMap"); append_member(spinDensity,"spinDensity"); append_member(DcoeffMap,"DcoeffMap"); return 0; } odin-1.8.5/odinpara/study.h0000644000175000017500000000766011322062341012520 00000000000000/*************************************************************************** study.h - description ------------------- begin : Mon Mar 3 2003 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef STUDY_H #define STUDY_H #include #include #include #define ODIN_DATE_LENGTH 8 #define ODIN_DATE_FORMAT "%Y%m%d" #define ODIN_TIME_LENGTH 6 #define ODIN_TIME_FORMAT "%H%M%S" /** * @ingroup odinpara * * \brief Study information * * This class is used to hold study information */ class Study : public JcampDxBlock { public: /** * Constructs a Study object with the given label */ Study(const STD_string& label="unnamedStudy"); /** * Constructs a copy of 'sp' */ Study(const Study& s); /** * Specifies the date/time of the scan: * -date: date in DICOM format, i.e yyyymmdd * -time: date in DICOM format, i.e hhmmss */ Study& set_DateTime(const STD_string& date, const STD_string& time); /** * Returns the date/time of the scan in the reference parameters, see set_DateTime() for their description */ void get_DateTime(STD_string& date, STD_string& time) const; /** * Set date/time of the scan to the current date/time */ void set_timestamp(); /** * Specifies the patient information: * -id: The unique ID of the patient * -full_name: Patients full name * -birth_date: Patients date of birth in DICOM format, i.e yyyymmdd * -sex: Patients sex (M,F,O) * -weight: Patients weight [kg] */ Study& set_Patient(const STD_string& id, const STD_string& full_name, const STD_string& birth_date, char sex, float weight); /** * Returns the patient information in the reference parameters, see set_Patient() for their description */ void get_Patient(STD_string& id, STD_string& full_name, STD_string& birth_date, char& sex, float& weight) const; /** * Specifies the study context: * -description: Study description * -scientist: Scientists name */ Study& set_Context(const STD_string& description, const STD_string& scientist); /** * Returns the study context in the reference parameters, see set_Context() for their description */ void get_Context(STD_string& description, STD_string& scientist) const; /** * Specifies the series context: * -description: Series description * -number: Series number */ Study& set_Series(const STD_string& description, int number); /** * Returns the series context in the reference parameters, see set_Series() for their description */ void get_Series(STD_string& description, int& number) const; /** * Assignment operator */ Study& operator = (const Study& s); private: void append_all_members(); static void format_date(STD_string& result, const STD_string& date); static void format_time(STD_string& result, const STD_string& time); JDXstring ScanDate; JDXstring ScanTime; JDXstring PatientId; JDXstring PatientName; JDXstring PatientBirthDate; JDXenum PatientSex; JDXfloat PatientWeight; JDXstring Description; JDXstring ScientistName; JDXstring SeriesDescription; JDXint SeriesNumber; }; #endif odin-1.8.5/odinpara/jdxbase.cpp0000644000175000017500000000736011322062341013320 00000000000000#include "jdxbase.h" #include "jdxtypes.h" #include "jdxblock.h" #include const char* JcampDx::get_compName() {return "JDX";} LOGGROUNDWORK(JcampDx) ///////////////////////////////////////////////// ArrayScale::ArrayScale(const STD_string& scalelabel, const STD_string& scaleunit, float scalemin, float scalemax) : label(scalelabel), unit(scaleunit), minval(scalemin), maxval(scalemax) { } STD_string ArrayScale::get_label_with_unit() const { STD_string result(label); if(unit!="") result+=" ["+unit+"]"; return result; } ///////////////////////////////////////////////// void PixmapProps::get_overlay_range(float& min, float& max) const { min=overlay_minval; max=overlay_maxval; if(overlay_minval==0.0 && overlay_maxval==0.0) { min=overlay_map.minvalue(); max=overlay_map.maxvalue(); } } ///////////////////////////////////////////////// JcampDxClass::JcampDxClass () : compatmode(notBroken), userDefParameter(true), parmode(edit), filemode(include), id(-1) { } JcampDxClass::JcampDxClass(const JcampDxClass& jdc) : id(-1) { JcampDxClass::operator = (jdc); } JcampDxClass::~JcampDxClass() { // for some reason, making this virtual destructor inline on GCC4, causes a crash ... Log odinlog(this,"~JcampDxClass"); ODINLOG(odinlog,normalDebug) << "called" << STD_endl; } JcampDxClass& JcampDxClass::operator = (const JcampDxClass& jdc) { Log odinlog(this,"JcampDxClass::operator = "); ListItem::operator = (jdc); Labeled::operator = (jdc); compatmode=jdc.compatmode; userDefParameter=jdc.userDefParameter; parmode=jdc.parmode; filemode=jdc.filemode; description=jdc.description; unit=jdc.unit; cmdline_option=jdc.cmdline_option; return *this; } STD_string JcampDxClass::print() const { if(get_filemode()==exclude) return ""; return get_jdx_prefix()+printvalstring()+get_jdx_postfix(); } STD_string JcampDxClass::get_parx_code(parxCodeType type, const ParxEquiv& equiv) const { #ifdef PARAVISION_PLUGIN STD_string result; if(type==parx_passval) result=equiv.name+"="+get_label()+";\n"; return result; #else return ""; #endif } STD_string JcampDxClass::get_parx_def_string(const STD_string type, unsigned int dim) const { #ifdef PARAVISION_PLUGIN STD_string retstring; STD_string typelabel(type); if(typelabel.find("bit")!=STD_string::npos) typelabel="int"; retstring+=typelabel + " parameter {\n"; retstring+=" display_name \""+STD_string(get_label())+ "\";\n"; // retstring+=" relations method_relations;\n"; retstring+="} "+STD_string(get_label()); retstring+=n_times("[]",dim); retstring+=";\n\n\n"; return retstring; #else return ""; #endif } bool JcampDxClass::parse(STD_string& parstring) { Log odinlog(this,"parse"); if(parstring.find("\n##")==STD_string::npos) parstring+="\n##"; // make sure we have a trailing ## STD_string stringdummy="##"+extract(parstring,"##","\n##"); // extract string between two ## stringdummy=rmblock(stringdummy,"##","=",true,true,false,false); // remove line with label bool result=parsevalstring(stringdummy); // pass string to underlying data type parstring=rmblock(parstring,"##","##",true,false,false,false); // remove me from parstring return result; } int JcampDxClass::load(const STD_string& filename) { JcampDxBlock block; block.append(*this); return block.load(filename); } int JcampDxClass::write(const STD_string &filename) const { JcampDxClass* cc=create_copy(); JcampDxBlock block; block.append(*cc); int retval=block.write(filename); delete cc; return retval; } STD_string JcampDxClass::get_jdx_prefix() const { STD_string result("##"); if(isUserDefParameter()) result+="$"; result+=get_label(); result+="="; return result; } odin-1.8.5/odinpara/jdxblock.h0000644000175000017500000001672411322062341013151 00000000000000/*************************************************************************** jdxblock.h - description ------------------- begin : Sun Jun 6 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXBLOCK_H #define JDXBLOCK_H #include #include #include #include /** * @addtogroup jcampdx * @{ */ typedef List JDXList; // alias /** * * This class represents a block of parameters. Parameters can be * added or removed from the list of parameters within the block. * The whole block may be written to or read from a file. */ class JcampDxBlock : public virtual JcampDxClass, public JDXList, public StaticHandler { public: /** * * Constructs an empty block of parameters with the label 'title' and the specified mode */ JcampDxBlock(const STD_string& title="Parameter List",compatMode mode=notBroken); /** * * Copy constructor */ JcampDxBlock(const JcampDxBlock& block); /** * * Destructor */ ~JcampDxBlock(); /** * * Assignment operator */ JcampDxBlock& operator = (const JcampDxBlock& block); /** * * Merges all parameters found in the specified 'block' into this block */ JcampDxBlock& merge(JcampDxBlock& block, bool onlyUserPars=true); /** * * Removes all parameters found in the specified 'block' from this block */ JcampDxBlock& unmerge(JcampDxBlock& block); /** * * Print the value of the parameter that has the label 'parameterName' as a formated string */ STD_string printval(const STD_string& parameterName) const; /** * * Set the value of the parameter that has the label 'parameterName' to 'value'. * Returns 'true' if sucessful. */ bool parseval(const STD_string& parameterName, const STD_string& value); /** * * Parse values of thius block from the string 'src' in JCAMP-DX format, * returns the number of parameters sucessfully parsed. */ int parseblock(const STD_string& source); /** * * Returns the current number of parameters in the block */ unsigned int numof_pars() const; /** * Returns a pointer to parameter 'label', or zero if not found */ JcampDxClass* get_parameter(const STD_string& ldrlabel); /** * * Returns true if a parameter with the given label already exists * in the block */ bool parameter_exists(const STD_string& ldrlabel) const; /** * * Prefixes all parameters labels with the given string. If the prefix * is already at the beginning of the label, it is not added again. */ JcampDxBlock& set_prefix(const STD_string& prefix); /** * * If embedded is true, the block's widget will be displayed in a subwidget * otherwise an 'Edit' button that will open a subdialog is generated */ JcampDxBlock& set_embedded(bool embedded) {embed=embedded; return *this;} /** * * Returns whether the block's widget will be displayed in a subwidget * or an 'Edit' button that will open a subdialog is generated */ bool is_embedded() const {return embed;} /** * Returns the i'th parameter in the block */ JcampDxClass& operator [] (unsigned int i); /** * Returns the const i'th parameter in the block */ const JcampDxClass& operator [] (unsigned int i) const; /** * Returns the first parameter in the block with the given 'id' */ JcampDxClass& get_parameter_by_id(int id); /** * Makes this become a copy of 'src', including its parameters by creating temporary objects. * These temporary objects will be deleted automatically upon destruction. */ JcampDxBlock& create_copy(const JcampDxBlock& src); /** * Appends a deep copy of src (not a reference). * This copy will be deleted automatically upon destruction. */ JcampDxBlock& append_copy(const JcampDxClass& src); /** * Copy parameter values from 'src' to the equivalent parameters in this block */ JcampDxBlock& copy_ldr_vals(const JcampDxBlock& src); /** * Compares 'rhs' with 'this' with respect to whether all parameters with * the same label mutually exist in the other block * and whether these parameters have the same type, label and value. */ bool operator == (const JcampDxBlock& rhs) const {return !( ((*this)* exclude=0, double accuracy=0.0) const; #ifndef NO_CMDLINE JcampDxBlock& parse_cmdline_options(int argc, char *argv[], bool modify=true); STD_map get_cmdline_options() const; STD_string get_cmdline_usage(const STD_string& lineprefix="") const; #endif // functions for StaticHandler static void init_static(); static void destroy_static(); // overwriting virtual functions from JcampDxClass STD_string print() const; JcampDxClass& set_compatmode(compatMode compat_mode); JcampDxClass& set_parmode(parameterMode parameter_mode); JcampDxClass& set_filemode(fileMode file_mode); STD_string get_parx_code(parxCodeType type, const ParxEquiv& equiv=ParxEquiv()) const; STD_ostream& print2stream(STD_ostream& os) const; bool parsevalstring (const STD_string&) {return true;} bool parse(STD_string& parstring); STD_string printvalstring() const {return "";} JcampDxClass* create_copy() const {JcampDxBlock* result=new JcampDxBlock; result->create_copy(*this); return result;} const char* get_typeInfo() const {return "JcampDxBlock";} JcampDxBlock* cast(JcampDxBlock*) {return this;} int load(const STD_string &filename); int write(const STD_string &filename) const; STD_string get_jdx_prefix() const {return "";} STD_string get_jdx_postfix() const {return "";} protected: /** * * Use this functions to append members of derived classes */ JcampDxBlock& append_member(JcampDxClass& ldr,const STD_string ldrlabel=""); private: friend class JDXwidget; static STD_string extract_parlabel(const STD_string& parstring); STD_string print_header() const; STD_string print_tail() const; JDXList::constiter ldr_exists(const STD_string& label) const; int parse_ldr_list(STD_string& parstring); STD_list* garbage; bool embed; }; /** @} */ #endif odin-1.8.5/odinpara/study.cpp0000644000175000017500000001215011322062341013041 00000000000000#include "study.h" #include // for current date/time #ifdef HAVE_TIME_H #include #endif void Study::format_date(STD_string& result, const STD_string& date) { Log odinlog("Study","format_date"); if(date.length()!=ODIN_DATE_LENGTH) { ODINLOG(odinlog,warningLog) << "Wrong length of date string >" << date << "<" << STD_endl; return; } // Parsing date/time manually since strptime is not available on all platforms (MinGW) result=itos(atoi(date.substr(0,4).c_str()),9999) + itos(atoi(date.substr(4,2).c_str()),12) + itos(atoi(date.substr(6,2).c_str()),31); } void Study::format_time(STD_string& result, const STD_string& time) { Log odinlog("Study","format_time"); if(time.length()!=ODIN_TIME_LENGTH) { ODINLOG(odinlog,warningLog) << "Wrong length of time string >" << time << "<" << STD_endl; return; } // Parsing date/time manually since strptime is not available on all platforms (MinGW) result=itos(atoi(time.substr(0,2).c_str()),24) + itos(atoi(time.substr(2,2).c_str()),60) + itos(atoi(time.substr(4,2).c_str()),60); } Study::Study(const STD_string& label) : JcampDxBlock(label) { set_timestamp(); // set current date/time ScanDate.set_cmdline_option("date").set_unit("yyyymmdd").set_description("Date of scan"); ScanTime.set_cmdline_option("time").set_unit("hhmmss").set_description("Time of scan"); PatientId="Unknown"; PatientId.set_cmdline_option("pid").set_description("Unique patient identifier"); PatientName="Unknown"; PatientName.set_cmdline_option("pname").set_description("Full patient name"); PatientBirthDate=STD_string(ODIN_DATE_LENGTH,'0'); PatientBirthDate.set_cmdline_option("pbirth").set_unit("yyyymmdd").set_description("Patients date of birth"); PatientSex.add_item("M"); PatientSex.add_item("F"); PatientSex.add_item("O"); PatientSex.set_cmdline_option("psex").set_description("Patients sex"); PatientWeight=50.0; PatientWeight.set_cmdline_option("pweight").set_unit("kg").set_description("Patients weight"); Description="Unknown"; Description.set_cmdline_option("stud").set_description("Study Description"); ScientistName="Unknown"; ScientistName.set_cmdline_option("scient").set_description("Scientist Name"); SeriesDescription="Unknown"; SeriesDescription.set_cmdline_option("serd").set_description("Series Description"); SeriesNumber=1; SeriesNumber.set_cmdline_option("serno").set_description("Series Number"); append_all_members(); } Study::Study(const Study& s) { Study::operator = (s); } Study& Study::operator = (const Study& s) { JcampDxBlock::operator = (s); append_all_members(); // copy only visible members of JcampDxBlock copy_ldr_vals(s); return *this; } Study& Study::set_DateTime(const STD_string& date, const STD_string& time) { format_date(ScanDate,date); format_time(ScanTime,time); return *this; } void Study::get_DateTime(STD_string& date, STD_string& time) const { date=ScanDate; time=ScanTime; } void Study::set_timestamp() { ScanDate=STD_string(ODIN_DATE_LENGTH,'0'); ScanTime=STD_string(ODIN_TIME_LENGTH,'0'); #if defined(HAVE_TIME_H) && defined(HAVE_STRFTIME) time_t tt=time(NULL); char datebuff[ODIN_DATE_LENGTH+1]; if(strftime(datebuff, ODIN_DATE_LENGTH+1, ODIN_DATE_FORMAT, localtime(&tt))) ScanDate=datebuff; char timebuff[ODIN_TIME_LENGTH+1]; if(strftime(timebuff, ODIN_TIME_LENGTH+1, ODIN_TIME_FORMAT, localtime(&tt))) ScanTime=timebuff; #endif } Study& Study::set_Patient(const STD_string& id, const STD_string& full_name, const STD_string& birth_date, char sex, float weight) { PatientId=id; PatientName=full_name; format_date(PatientBirthDate,birth_date); PatientSex=STD_string(1,toupper(sex)); PatientWeight=weight; return *this; } void Study::get_Patient(STD_string& id, STD_string& full_name, STD_string& birth_date, char& sex, float& weight) const { id=PatientId; full_name=PatientName; birth_date=PatientBirthDate; sex=PatientSex.JDXenum::operator STD_string()[0]; weight=PatientWeight; } Study& Study::set_Context(const STD_string& description, const STD_string& scientist) { Description=description; ScientistName=scientist; return *this; } void Study::get_Context(STD_string& description, STD_string& scientist) const { description=Description; scientist=ScientistName; } Study& Study::set_Series(const STD_string& description, int number) { SeriesDescription=description; SeriesNumber=number; return *this; } void Study::get_Series(STD_string& description, int& number) const { description=SeriesDescription; number=SeriesNumber; } void Study::append_all_members() { JcampDxBlock::clear(); append_member(ScanDate,"ScanDate"); append_member(ScanTime,"ScanTime"); append_member(PatientId,"PatientId"); append_member(PatientName,"PatientName"); append_member(PatientBirthDate,"PatientBirthDate"); append_member(PatientSex,"PatientSex"); append_member(PatientWeight,"PatientWeight"); append_member(Description,"Description"); append_member(ScientistName,"ScientistName"); append_member(SeriesDescription,"SeriesDescription"); append_member(SeriesNumber,"SeriesNumber"); } odin-1.8.5/odinpara/Makefile.am0000644000175000017500000000162511322062341013226 00000000000000 INCLUDES = $(all_includes) lib_LTLIBRARIES = libodinpara.la libodinpara_la_LDFLAGS = -no-undefined -release $(VERSION) libodinpara_la_LIBADD = ../tjutils/libtjutils.la library_includedir=$(includedir)/odinpara library_include_HEADERS = \ jdxarrays.h \ jdxbase.h \ jdxblock.h \ jdxfilter.h \ jdxfunction.h \ jdxnumbers.h \ jdxtypes.h \ odinpara.h \ protocol.h \ geometry.h \ reco.h \ sample.h \ seqpars.h \ study.h \ system.h 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installcheck-am \ installdirs maintainer-clean maintainer-clean-generic \ mostlyclean mostlyclean-compile mostlyclean-generic \ mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \ uninstall-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/odinpara/protocol.cpp0000644000175000017500000000642011665172216013552 00000000000000#include "protocol.h" #include Protocol::Protocol(const STD_string& label) : JcampDxBlock(label), system(label+"_system"), geometry(label+"_geometry"), seqpars(label+"_seqpars"), methpars(label+"_methpars"), study(label+"_study") { append_all_members(); } Protocol& Protocol::operator = (const Protocol& p) { JcampDxBlock::operator = (p); system=p.system; geometry=p.geometry; seqpars=p.seqpars; methpars.create_copy(p.methpars); study=p.study; append_all_members(); return *this; } bool Protocol::operator < (const Protocol& rhs) const { STD_list exclude; exclude.push_back("AcquisitionStart"); exclude.push_back("offsetSlice"); exclude.push_back("Datatype"); // account for different TRs in gated mode if(seqpars.get_PhysioTrigger() || rhs.seqpars.get_PhysioTrigger()) { exclude.push_back("PhysioTrigger"); exclude.push_back("RepetitionTime"); exclude.push_back("ExpDuration"); } double accuracy=0.01; // This will make geometries equal which are approximately the same return JcampDxBlock::compare(rhs,&exclude,accuracy); } void Protocol::append_all_members() { JcampDxBlock::clear(); merge(study); merge(system); merge(geometry); merge(seqpars); merge(methpars); } /////////////////////////////////////////////////////////////////////// #ifndef NO_UNIT_TEST class ProtocolTest : public UnitTest { public: ProtocolTest() : UnitTest("Protocol") {} private: bool check() const { Log odinlog(this,"check"); // Testing == operator (of JcampDxBlock) Protocol p1; Protocol p2; if(!(p1==p2)) { ODINLOG(odinlog,errorLog) << "Protocol::operator == (equal) failed: p1=" << p1 << "p2=" << p2 << STD_endl; return false; } p1.seqpars.set_AcquisitionStart(123); // should still be equal if(!(p1==p2)) { ODINLOG(odinlog,errorLog) << "Protocol::operator == (AcquisitionStart) failed: p1=" << p1 << "p2=" << p2 << STD_endl; return false; } p1.seqpars.set_RepetitionTime(12345); if(p1==p2) { ODINLOG(odinlog,errorLog) << "Protocol::operator == (unequal) failed: p1=" << p1 << "p2=" << p2 << STD_endl; return false; } if(p1cast(intdummy); if( !intdummy ) { ODINLOG(odinlog,errorLog) << "Protocol::operator = methpars.testint cannot be casted" << STD_endl; return false; } if( (*intdummy)!=7 ) { ODINLOG(odinlog,errorLog) << "Protocol::operator = intdummy=" << (*intdummy) << STD_endl; return false; } return true; } }; void alloc_ProtocolTest() {new ProtocolTest();} // create test instance #endif odin-1.8.5/odinpara/reco.h0000644000175000017500000004143211455553536012315 00000000000000/*************************************************************************** reco.h - Parameters for image reconstruction ------------------- begin : Thu May 06 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECO_H #define RECO_H #include #include /** * @addtogroup odinpara * @{ */ // some limits #define MAX_NUMOF_READOUT_SHAPES 10 #define MAX_NUMOF_KSPACE_TRAJS 10 #define MAX_NUMOF_ADC_WEIGHTING_VECTORS 10 #define PROTOCOL_BLOCK_LABEL "Protocol" /** * Flags(bits) to mark ADCs: * - recoLastInChunkBit: last ADC in a collection of consecutive ADCs generated by the system, an undefined number of zeroes may follow * - recoReflectBit: ADC is reflected * - recoEpiNavPolarityBit: Indicates that first echo in EPI navigator readout is reflected */ enum recoFlags { recoLastInChunkBit =1, recoReflectBit =2, recoEpiNavPolarityBit =4, recoAllBits =255 }; /////////////////////////////////////////////////////////// /** * Dimensions of acquired data, order is reversed for easy indexing of C-style arrays * - userdef: Extra dimension which can be used by the sequence programmer * - te: Echo-time index in a multi-echo acquistion, e.g. for field-map calculation * - dti: Direction index for diffusion-tensor imaging * - average: Average index to add up ADCs * - cycle: Cycle index (spiral imaging, PROPELLER blades) * - slice: Slice index * - line3d: 3D phase encoding index * - line: 2D phase encoding index * - echo: Echo index in a multi-echo readout, e.g. an CPMG or EPI echo train * - epi: Index of EPI readout train, e.g. in a 3D sequence * - templtype: Type of template prescan * - navigator: Type of navigator scan * - freq: Frequency offset (will be used by multi-frequency reconstruction in odinreco) * - channel: Channel index of phased-array coil * - readout: Readout index * - repetition: Repetition dimension * */ enum recoDim { userdef=0, te, dti, average, cycle, slice, line3d, line, echo, epi, templtype, navigator, freq, channel, readout, repetition, n_recoDims}; static const char* recoDimLabel[]={"userdef", "te","dti","average","cycle","slice","line3d","line","echo","epi","templtype","navigator","freq","channel","readout","repetition"}; static const int n_recoIndexDims=templtype+1; // only the first dims are required for indexing of ADCs, the remaining are used only by odinreco /////////////////////////////////////////////////////////// /** * * Enum to distinguish between different types of template prescan ADCs: * - no_template: Not a template ADC * - phasecorr_template: Template ADC for 1D phase correction * - fieldmap_template: Template to calculate fieldmap, the echo dimension will index the different TEs * - grappa_template: Training data to calculate GRAPPA weights */ enum templateType {no_template=0, phasecorr_template, fieldmap_template, grappa_template, n_templateTypes}; static const char templateTypeChar[]={'N', 'P', 'F', 'G'}; /////////////////////////////////////////////////////////// /** * * Enum to distinguish between different types of navigator ADCs: * - no_navigator: Not a navigator ADC * - epi_navigator: Siemens EPI phase correction navigator */ enum navigatorType {no_navigator=0, epi_navigator, n_navigatorTypes}; static const char navigatorTypeChar[]={'n', 'e'}; /////////////////////////////////////////////////////////// /** * * This struct holds the k-space position of one ADC */ struct kSpaceCoord { kSpaceCoord() {reset2defaults();} // for STD_list bool operator == (const kSpaceCoord& ri) const; bool operator < (const kSpaceCoord& ri) const; static int string2index(const STD_string& str, recoDim dim); static STD_string index2string(int index, recoDim dim, int numof=0); STD_string printcoord(const unsigned short* numof_cache) const; // friend STD_ostream& operator << (STD_ostream& s,const kSpaceCoord& kcoord) { return s << kcoord.printcoord();} bool parsecoord(const STD_string& str); void reset2defaults(); static STD_string print_header(const unsigned short* numof_cache); mutable unsigned int number; // unique index of the ADC unsigned int reps; // number of times this ADC is repeated unsigned short adcSize; // size with oversampling unsigned char channels; // coil channels unsigned short preDiscard; // points to discard at the beginning of an ADC unsigned short postDiscard; // points to discard at the end of an ADC unsigned short concat; // number of concatenated acquisition this ADC is composed of float oversampling; // oversampling factor float relcenter; // relative position of k-space center short readoutIndex; // index of the readout shape to be used for ramp-sampling correction, -1 if none short trajIndex; // index of the used k-space trajectory, -1 if none short weightIndex; // index of the used ADC weighting vector, -1 if none short dtIndex; // index of the dwell time used unsigned short index[n_recoIndexDims]; // multi-dimensional reco index to locate ADC in k-space unsigned char flags; // recoFlags private: friend class JDXkSpaceCoords; static void assign_parsepos(const STD_string& header); static int parsepos_number; static int parsepos_reps; static int parsepos_adcSize; static int parsepos_channels; static int parsepos_preDiscard; static int parsepos_postDiscard; static int parsepos_concat; static int parsepos_oversampling; static int parsepos_relcenter; static int parsepos_readoutIndex; static int parsepos_trajIndex; static int parsepos_weightIndex; static int parsepos_dtIndex; static int parsepos_index[n_recoIndexDims]; static int parsepos_lastinchunk; static int parsepos_reflect; static int max_parsepos; }; ////////////////////////////////////////////////////////////////////// /** * * This class holds the assignment of consecutive ADCs to k-space positions */ class JDXkSpaceCoords : public JcampDxClass { enum JDXkSpaceCoords_state {coords_in_list, has_vec_cache, has_vec_alloc}; public: JDXkSpaceCoords(); ~JDXkSpaceCoords() {clear();} unsigned int size() const {create_vec_cache(); return vec_cache.size();} const kSpaceCoord& operator [] (unsigned int i) const {create_vec_cache(); return *(vec_cache[i]);} void clear(); // clear list before retrieving k-space ordering from sequence JDXkSpaceCoords& append_coord(const kSpaceCoord& coord); private: friend class RecoPars; void create_vec_cache() const; // overwriting virtual functions from JcampDxClass bool parsevalstring (const STD_string& parstring); STD_string printvalstring() const; STD_ostream& print2stream(STD_ostream& os) const; const char* get_typeInfo() const {return "kSpaceCoords";} JcampDxClass* create_copy() const {return new JDXkSpaceCoords(*this);} mutable STD_list coordlist; mutable JDXkSpaceCoords_state state; mutable STD_vector vec_cache; // use pointers for better performance mutable unsigned short numof_cache[n_recoIndexDims]; }; ////////////////////////////////////////////////////////////////////// /** * * Structure to return ordering of k-space data while traversing the sequence tree */ struct RecoValList : public ValList { RecoValList(const STD_string& object_label="unnamedRecoValList", unsigned int repetitions=1) : ValList(object_label,repetitions) {} }; ////////////////////////////////////////////////////////////////////// /** * * This class holds the assignment of consecutive ADCs to k-space positions */ class JDXrecoValList : public RecoValList, public JcampDxClass { public: JDXrecoValList(const STD_string& ldrlabel="unnamedJDXrecoValList"); JDXrecoValList(const JDXrecoValList& jdrvl) {JDXrecoValList::operator = (jdrvl);} JDXrecoValList& operator = (const JDXrecoValList& jdrvl); JDXrecoValList& operator = (const RecoValList& rvl); // for assignment from get_recovallist in SeqMethod // overwriting virtual functions from JcampDxClass bool parsevalstring (const STD_string& parstring); STD_string printvalstring() const; STD_ostream& print2stream(STD_ostream& os) const; const char* get_typeInfo() const {return "RecoValList";} JcampDxClass* create_copy() const {return new JDXrecoValList(*this);} }; ////////////////////////////////////////////////////////////////////// /** * This class is used to hold all information about the reconstruction */ class RecoPars : public JcampDxBlock { public: /** * Constructs a RecoPars with the given label */ RecoPars(const STD_string& label="unnamedRecoPars"); /** * Constructs a copy of 'sr' */ RecoPars(const RecoPars& sr); /** * Assignment operator */ RecoPars& operator = (const RecoPars& sr); /** * Returns the scan protocol. */ const Protocol& get_protocol() const {return prot;} /** * Returns the const assignment of ADC indices to k-space lines (for odinreco) */ const JDXkSpaceCoords& get_kSpaceCoords() const {return kSpaceCoords;} /** * Returns the data type of the acquired ADCs */ const STD_string& get_DataFormat() const {return DataFormat;} /** * Returns whether the of the acquired ADCs is little endian */ bool is_LittleEndian() const {return LittleEndian;} /** * Returns the file name of raw data */ const STD_string& get_RawFile() const {return RawFile;} /** * Returns the header size of raw data */ unsigned int get_RawHeaderSize() const {return RawHeaderSize;} /** * Returns the relative offset which should be added by the reco */ const fvector& get_RelativeOffset() const {return RelativeOffset;} /** * Extra command-line arguments for processing of final images */ const STD_string& get_ImageProc() const {return ImageProc;} /** * Returns the value vector attached to reco dimension 'dim' */ const dvector& get_DimValues(recoDim dim) const {return DimValues[dim];} /** * Returns the scaling factors for ADC channels */ fvector get_ChannelScales() const {return ChannelScaling;} /** * Returns the i'th dwell time (including oversampling) */ double get_DwellTime(unsigned int i) const; /** * Returns the number of ADC chunks, a chunk is a collection of * one or more ADCs stored by the system in one block. It can be * followed by an arbitrary number of zeroes. */ int get_NumOfAdcChunks() const; /** * Attaches a vector 'vals' of values to each step in the given dimension 'dim' */ RecoPars& set_DimValues(recoDim dim, const dvector& vals); /** * Appends a new ADC readout-gradient shape and its target grid size. Returns its index */ int append_readout_shape(const fvector& shape, unsigned int dstsize); /** * Appends a new k-space trajectory and returns its index */ int append_kspace_traj(const farray& kspace_traj); /** * Appends a new ADC weighting vector and returns its index */ int append_adc_weight_vec(const cvector& weightvec); /** * Appends a new ADC dwell time (including oversampling) and returns its index */ int append_dwell_time(double dt); /** * Returns the i'th ADC readout-gradient and its target grid size */ void get_ReadoutShape(unsigned int i, fvector& shape, unsigned int& dstsize) const; /** * Returns the number of k-space trajectories */ unsigned int numof_kSpaceTraj() const; /** * Returns the i'th k-space trajectory */ const farray& get_kSpaceTraj(unsigned int i) const; /** * Returns the i'th complex weighting vector with which the corresponding ADCs will be multiplied */ const cvector& get_AdcWeightVector(unsigned int i) const; /** * Returns the total number of ADC samples, if 'discard' is set to 'true' * only the effective ADC size is returned, i.e. without 'preDiscard' and * 'postDiscard' */ LONGEST_INT get_TotalNumOfSamples(bool discard=false) const; /** * Returns the total number of ADCs */ unsigned int numof_adcs() const {return kSpaceOrdering.size();} /** * Returns the i'th ADC of the sequence */ const kSpaceCoord& get_kSpaceCoord(unsigned int i) const; /** * Set a string describing the reconstruction pipeline (chain of steps/functors). */ RecoPars& set_Recipe(const STD_string& recipe) {Recipe=recipe; return *this;} /** * Returns a string describing the reconstruction pipeline (chain of steps/functors). */ STD_string get_Recipe() const {return Recipe;} /** * The extra chain of reconstruction steps (functors) described by 'recipe' * wil be performed after 3D reconstruction (including channel combination) but * before data is stored on disk. */ RecoPars& set_PostProc3D(const STD_string& recipe) {PostProc3D=recipe; return *this;} /** * Returns the extra chain of reconstruction steps (functors) which will be * performed after 3D reconstruction (including channel combination) but before * data is stored on disk. */ STD_string get_PostProc3D() const {return PostProc3D;} /** * The extra chain of reconstruction steps (functors) described by 'recipe' * wil be performed after 3D FFT but before channel combination. */ RecoPars& set_PreProc3D(const STD_string& recipe) {PreProc3D=recipe; return *this;} /** * Returns the extra chain of reconstruction steps (functors) described by 'recipe' * wil be performed after 3D FFT but before channel combination. */ STD_string get_PreProc3D() const {return PreProc3D;} /** * Extra command-line options for the reco. */ RecoPars& set_CmdLineOpts(const STD_string& opts) {CmdLineOpts=opts; return *this;} /** * Returns the extra chain of reconstruction steps (functors) which will be * performed after 3D reconstruction before data is stored on disk. */ STD_string get_CmdLineOpts() const {return CmdLineOpts;} private: friend class SeqAcq; friend class SeqEpiDriverParavision; friend class SeqMethod; void common_init(); void reset(); void create_cache() const; void append_all_members(); Protocol prot; JDXstring DataFormat; JDXbool LittleEndian; JDXstring RawFile; JDXint RawHeaderSize; JDXtriple RelativeOffset; JDXstring ImageProc; JDXfloatArr ChannelScaling; JDXdoubleArr DwellTime; JDXfloatArr ReadoutShape[MAX_NUMOF_READOUT_SHAPES]; JDXintArr ReadoutDstSize; JDXfloatArr kSpaceTraj[MAX_NUMOF_KSPACE_TRAJS]; JDXcomplexArr AdcWeightVector[MAX_NUMOF_ADC_WEIGHTING_VECTORS]; JDXdoubleArr DimValues[n_recoIndexDims]; JDXstring Recipe; JDXstring PreProc3D; JDXstring PostProc3D; JDXstring CmdLineOpts; JDXkSpaceCoords kSpaceCoords; JDXrecoValList kSpaceOrdering; mutable STD_vector kSpaceOrdering_cache; // fast cache of ADC indices mutable bool cache_is_up2date; }; ////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// /** * Class to hold complex sensitivity */ class CoilSensitivity : public JcampDxBlock { public: /** * Constructs a CoilSensitivity with the given label */ CoilSensitivity(const STD_string& label="unnamedCoilSensitivity"); /** * Constructs a copy of 'cs' */ CoilSensitivity(const CoilSensitivity& cs); /** * Assignment operator */ CoilSensitivity& operator = (const CoilSensitivity& cs); /** * Accepts a 4-dim complex array 'sens_map' with the dimensions * (coil,z,y,x) and the corresponding FOVs */ CoilSensitivity& set_sensitivity_map(const carray& sens_map, float FOVx, float FOVy, float FOVz); /** * Returns complex sensitivity value for the given channel and spatial position, * uses trilinear interpolation */ STD_complex get_sensitivity_value(unsigned int channel, float x, float y, float z) const; /** * Returns the number of channels of the coil */ unsigned int get_numof_channels() const {return SensitivityMap.get_extent()[0];} private: void append_all_members(); JDXtriple FOV; JDXcomplexArr SensitivityMap; }; ////////////////////////////////////////////////////////////////////// /** @} */ #endif odin-1.8.5/odinpara/system.h0000644000175000017500000002321711712547771012712 00000000000000/*************************************************************************** system.h - description ------------------- begin : Wed Jun 29 2005 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef SYSTEM_H #define SYSTEM_H #include #include #include #include #include // defaults for systemInfo #define _DEFAULT_B0_ 3000 // 3 Tesla #define _DEFAULT_MAX_SYSTEM_GRADIENT_ 0.04 #define _DEFAULT_MAX_SYSTEM_SLEWRATE_ 0.2 /** * @ingroup odinpara * This enum is used to specify the scanner system type */ enum odinPlatform {standalone=0, paravision, numaris_4, epic, numof_platforms}; /** * @ingroup odinpara * This enum is used to distinguish different properties of sequence objects according to * their category. Examples are minimum duration or rastertime. */ enum objCategory {unknownObj=0,delayObj,pulsObj,gradObj,loopObj,acqObj,freqObj,syncObj,endObj}; ///////////////////////////////////////////////////////////////////////// /** * @ingroup odinpara * This class is a small database which maps nuclei names to gyromagnetic ratios. */ class Nuclei { public: Nuclei(); /** * Returns the gyromagnetic ratio of the nucleus with name 'nucName' */ double get_gamma(const STD_string& nucName) const; /** * Returns the base frequency of the nucleus with name 'nucName' in a static field with the strength 'B0' */ double get_nuc_freq(const STD_string& nucName,float B0) const; /** * Returns an enum with all registered nuclei as entries */ JDXenum get_nuc_enum() const; private: typedef STD_pair Nucleus; typedef STD_list NucList; // do not use std::map since we do not want unsorted list NucList nuclist; }; ///////////////////////////////////////////////////////////////////////// /** * @ingroup odinpara * * \brief System proxy * * This class is used to hold all information/configuration of the spectrometer */ class System : public JcampDxBlock { public: /** * Constructs a System with the given label */ System(const STD_string& object_label="unnamedSystem"); /** * Copy constructor */ System(const System& s) {System::operator = (s);} /** * Assignment operator */ System& operator = (const System& s); /** * Returns the platform identifier for the scanner, works only in the context of sequence programming */ odinPlatform get_platform() const; /** * Returns a string identifying the platform */ STD_string get_platform_str() const {return platformstr;} /** * Returns a string identifying the transmit coil */ STD_string get_transmit_coil_name() const {return transmit_coil_name;} /** * Sets the transmit coil name */ System& set_transmit_coil_name(const STD_string& tcname); /** * Returns the current main nucleus of the sequence, i.e. the nucleus for which both, excitation and acquisition, will be performed */ STD_string get_main_nucleus() const {return main_nucleus;} /** * Specifies the current main nucleus of the scanner, i.e. the nucleus for which both, excitation and acquisition, will be performed */ System& set_main_nucleus(const STD_string& nucname); /** * Returns the maximum gradient strength of the scanner */ float get_max_grad() const {return max_grad;} /** * Returns the maximum slew rate */ float get_max_slew_rate() const {return max_slew_rate;} /** * Returns the time required to change the gradient strength by the specified amount */ float get_grad_switch_time(float graddiff) const; /** * Returns the minimum time gap between two gradient commands */ float get_inter_grad_delay() const {return inter_grad_delay;} /** * Sets the directory where the experimental data files of the current scans are stored */ System& set_scandir(const STD_string& dir); /** * Returns the directory where the experimental data files of the current scans are stored */ STD_string get_scandir() const; /** * Returns the time shift between RF and gradient channel */ float get_grad_shift_delay() const {return grad_shift;} /** * Returns the field strength of the static magnetic field */ double get_B0() const {return B0;} /** * Returns the field strength of the static magnetic field */ System& set_B0(double b0) {B0=b0; return *this;} /** * Specifies the field strength of the static magnetic field by giving the resonance frequency * for the specified nucleus */ System& set_B0_from_freq(double freq, const STD_string& nucName=""); /** * Returns the gyromagnetic ratio of the given nucleus, default returns the ratio of protons */ double get_gamma(const STD_string& nucName="") const; /** * Sets the reference gain in dB */ System& set_reference_gain(float refgain); /** * Returns the reference gain in dB */ float get_reference_gain() const {return reference_gain;} /** * Returns the resonance for the given nucleus */ double get_nuc_freq(const STD_string& nucName="") const; /** * Returns an enum with all registered nuclei as entries */ JDXenum get_nuc_enum() const; /** * Returns the minimum duration for the given object category */ double get_min_duration(objCategory c) const {return min_duration[c];} /** * Returns the minimum gradient raster time */ double get_min_grad_rastertime() const {return min_grad_rastertime;} /** * Returns the raster time for the given object category, if no such time exists, it returns 0 */ double get_rastertime(objCategory cat) const; /** * Returns the rastered time for the given object type and non-rastered time point/period */ double get_rasteredtime(objCategory cat, double time) const; /** * Returns the maximum number of samples per RF pulse */ int get_max_rf_samples() const {return max_rf_samples;} /** * Returns the maximum number of samples per gradient waveform */ int get_max_grad_samples() const {return max_grad_samples;} /** * Sets the data represention type of the image data */ System& set_data_type(const STD_string& type) {datatype=type; return *this;} /** * Returns the data represention type of the image data */ STD_string get_data_type() const {return datatype;} /** * Returns 'true' if gradient switching frequency 'freq' does not cause * acoustic resonance, otherwise, 'low' and 'upp' will contain the next * possible lower and upper frequencies, respectively. */ bool allowed_grad_freq(double freq, double& low, double& upp) const; private: friend class SeqMethod; friend class SeqIdea; friend class SeqParavision; friend class SeqStandAlone; friend class SeqEpic; // overwriting virtual functions from JcampDxClass int load(const STD_string &filename); int append_all_members(); Nuclei nuc; JDXstring platformstr; JDXenum main_nucleus; JDXdouble max_grad; JDXdouble max_slew_rate; JDXdouble grad_shift; JDXdouble inter_grad_delay; JDXdouble B0; JDXdouble reference_gain; JDXstring transmit_coil_name; JDXdouble delay_rastertime; JDXdouble rf_rastertime; JDXdouble grad_rastertime; JDXdouble min_grad_rastertime; JDXdouble acq_rastertime; JDXint max_rf_samples; JDXint max_grad_samples; JDXstring datatype; JDXdoubleArr grad_reson_center; JDXdoubleArr grad_reson_width; STD_string scandir; dvector min_duration; }; ////////////////////////////////////////////////////////////////////////////// /** * @ingroup odinpara * An interface class that makes the global systemInfo look like a pointer, * but requests will be delegated to the actual System object in the platform object */ class SystemInterface : public StaticHandler { public: SystemInterface() {} System& operator * () {return *get_sysinfo_ptr();} const System& operator * () const {return *get_const_sysinfo_ptr();} System* operator -> () {return get_sysinfo_ptr();} const System* operator -> () const {return get_const_sysinfo_ptr();} // functions to initialize/delete static members by the StaticHandler template class static void init_static(); static void destroy_static(); static void set_current_pf(odinPlatform pf); static odinPlatform get_current_pf() { // make it inline to speed up driver access if(current_pf) return odinPlatform(current_pf->operator int ()); // else STD_cerr << "ERROR: SystemInterface::get_current_pf: current_pf not yet initialized" << STD_endl; return odinPlatform(0); } private: // friend class System; friend class SeqIdea; friend class SeqParavision; friend class SeqStandAlone; friend class SeqEpic; // friend class SeqPlatformInstances; static System* get_sysinfo_ptr(); static const System* get_const_sysinfo_ptr(); // the actual platform static SingletonHandler current_pf; // separate systemInfo for each platform static SingletonHandler* systemInfo_platform; }; #endif odin-1.8.5/odinpara/jdxfunction.cpp0000644000175000017500000002332211322062341014227 00000000000000#include "jdxfunction.h" JDXfunctionPlugIn& JDXfunctionPlugIn::register_function(funcType type, funcMode mode) { JDXfunctionEntry entry(this,type,mode); JDXfunction dummy(type,"dummy"); // make sure that JDXfunction::init_static is called once dummy.registered_functions->push_back(entry); return *this; } kspace_coord JDXfunctionPlugIn::coord_retval; //shape_vals JDXfunctionPlugIn::shape_retval; shape_info JDXfunctionPlugIn::shape_info_retval; traj_info JDXfunctionPlugIn::traj_info_retval; //////////////////////////////////////// bool JDXfunctionEntry::operator == (const JDXfunctionEntry& jfe) const { bool result=true; if(plugin!=jfe.plugin) result=false; if(type!=jfe.type) result=false; if(mode!=jfe.mode) result=false; return result; } bool JDXfunctionEntry::operator < (const JDXfunctionEntry& jfe) const { bool result=true; if(!(plugin odinlog(jdxlabel.c_str(),"JDXfunction(funcType ...)"); set_label(jdxlabel); set_function(0); } JDXfunction::JDXfunction(const JDXfunction& jf) : allocated_function(0), type(jf.type) { Log odinlog(this,"JDXfunction(const JDXfunction&)"); JDXfunction::operator = (jf); } JDXfunction& JDXfunction::operator = (const JDXfunction& jf) { JcampDxClass::operator = (jf); Log odinlog(this,"operator = (...)"); if(jf.type!=type) { ODINLOG(odinlog,normalDebug) << "wrong functype" << STD_endl; return *this; } mode=jf.mode; if(jf.allocated_function) { JDXfunctionPlugIn* pi=jf.allocated_function->clone(); pi->copy_ldr_vals(*jf.allocated_function); new_plugin(pi); } return *this; } JDXfunction& JDXfunction::set_function_mode(funcMode newmode) { if(mode==newmode) return *this; mode=newmode; new_plugin(0); set_function(0); return *this; } svector JDXfunction::get_alternatives() const { svector result; for(STD_list::const_iterator it=registered_functions->begin(); it!=registered_functions->end(); ++it) { if( it->type==type && it->mode==mode ) result.push_back(it->plugin->get_label()); } return result; } JDXfunction& JDXfunction::set_function(const STD_string& funclabel) { Log odinlog(this,"set_function"); if( allocated_function && (funclabel==allocated_function->get_label())) { ODINLOG(odinlog,normalDebug) << "function " << funclabel << " already set" << STD_endl; return *this; } STD_list::const_iterator it; for(it=registered_functions->begin(); it!=registered_functions->end(); ++it) { JDXfunctionPlugIn* plugin_template=it->plugin; ODINLOG(odinlog,normalDebug) << "checking " << funclabel << "/" << plugin_template->get_label() << STD_endl; if( it->type==type && it->mode==mode ) { ODINLOG(odinlog,normalDebug) << "type and mode match" << STD_endl; if(funclabel==plugin_template->get_label()) { ODINLOG(odinlog,normalDebug) << "label match" << STD_endl; new_plugin(plugin_template->clone()); break; } } } return *this; } static STD_string nofunc("none"); const STD_string& JDXfunction::get_function_label(unsigned int index) const { Log odinlog(this,"get_function_label"); unsigned int i=0; for(STD_list::const_iterator it=registered_functions->begin(); it!=registered_functions->end(); ++it) { if( it->type==type && it->mode==mode ) { ODINLOG(odinlog,normalDebug) << "type and mode match" << STD_endl; if(i==index) { ODINLOG(odinlog,normalDebug) << "index match" << STD_endl; return it->plugin->get_label(); } i++; } } return nofunc; } JDXfunction& JDXfunction::set_function(unsigned int index) { Log odinlog(this,"set_function"); if( allocated_function && index==get_function_index() ) { return *this; ODINLOG(odinlog,normalDebug) << "function " << index << " already set" << STD_endl; } unsigned int i=0; for(STD_list::const_iterator it=registered_functions->begin(); it!=registered_functions->end(); ++it) { JDXfunctionPlugIn* plugin_template=it->plugin; ODINLOG(odinlog,normalDebug) << "checking " << index << "/" << plugin_template->get_label() << STD_endl; if( it->type==type && it->mode==mode ) { ODINLOG(odinlog,normalDebug) << "type and mode match" << STD_endl; if(i==index) { ODINLOG(odinlog,normalDebug) << "index match" << STD_endl; new_plugin(plugin_template->clone()); break; } i++; } } return *this; } unsigned int JDXfunction::get_function_index() const { unsigned int result=0; unsigned int i=0; if(!allocated_function) return result; STD_list::const_iterator it; for(it=registered_functions->begin(); it!=registered_functions->end(); ++it) { if( it->type==type && it->mode==mode ) { if( STD_string(allocated_function->get_label()) == it->plugin->get_label() ) {result=i; break;} i++; } } return result; } JcampDxBlock* JDXfunction::get_funcpars_block() { Log odinlog(this,"get_funcpars_block"); if(allocated_function) ODINLOG(odinlog,normalDebug) << "allocated_function=" << allocated_function->get_label() << STD_endl; else ODINLOG(odinlog,normalDebug) << "allocated_function=0" << STD_endl; return allocated_function; } JDXfunction& JDXfunction::set_funcpars(const svector& funcpars) { Log odinlog(this,"set_funcpars"); if(funcpars.size()<1) return *this; set_function(funcpars[0]); if(allocated_function) { ODINLOG(odinlog,normalDebug) << "allocated_function=" << allocated_function->get_label() << STD_endl; unsigned int n_pars=allocated_function->JcampDxBlock::numof_pars(); unsigned int n_pars_min = funcpars.size()-1; if(n_pars odinlog(this,"get_funcpars"); svector funcpars; if(allocated_function) { unsigned int n_pars=allocated_function->JcampDxBlock::numof_pars(); ODINLOG(odinlog,normalDebug) << "n_pars=" << n_pars << STD_endl; funcpars.resize(n_pars+1); funcpars[0]=allocated_function->get_label(); for(unsigned int i=0;iJcampDxBlock::parseval(parameter_label,value); return false; } STD_string JDXfunction::get_parameter(const STD_string& parameter_label) const { STD_string result; if(allocated_function) result=allocated_function->JcampDxBlock::printval(parameter_label); return result; } STD_string JDXfunction::get_function_name() const { STD_string result("noFunction"); if(allocated_function) result=allocated_function->get_label(); return result; } const STD_string& JDXfunction::get_funcdescription() const { if(allocated_function) return allocated_function->get_description(); return JcampDxClass::get_description(); } bool JDXfunction::parsevalstring (const STD_string& parstring) { Log odinlog(this,"parsevalstring"); svector funcpars; STD_string argstring=extract(parstring,"(",")",true); if(argstring!="") { ODINLOG(odinlog,normalDebug) << "argstring=" << argstring << STD_endl; funcpars.push_back(extract(parstring,"","(")); argstring=shrink(argstring); svector args=tokens(argstring,',','(',')'); for(unsigned int i=0;i; } void JDXfunction::destroy_static() { // plugin might be used for different modes so we will make sure that delete is only called once for each pointer STD_list tobedeleted; for(STD_list::iterator it=registered_functions->begin(); it!=registered_functions->end(); ++it) { tobedeleted.push_back(it->plugin); } tobedeleted.sort(); tobedeleted.unique(); for(STD_list::iterator delit=tobedeleted.begin(); delit!=tobedeleted.end(); ++delit) { delete (*delit); } delete registered_functions; } void JDXfunction::new_plugin(JDXfunctionPlugIn* pi) { Log odinlog(this,"new_plugin"); if(allocated_function) delete allocated_function; if(pi) ODINLOG(odinlog,normalDebug) << "plugin=" << pi->get_label() << STD_endl; allocated_function=pi; } EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; STD_list* JDXfunction::registered_functions=0; odin-1.8.5/odinpara/seqpars.cpp0000644000175000017500000001246111725203122013355 00000000000000#include "seqpars.h" SeqPars::SeqPars(const STD_string& label) : JcampDxBlock(label) { ExpDuration.set_parmode(noedit); ExpDuration.set_description("The overall duration of the sequence"); ExpDuration.set_unit("min"); Sequence="Unknown"; Sequence.set_parmode(hidden); Sequence.set_description("The MR sequence used"); AcquisitionStart.set_filemode(exclude).set_parmode(hidden); AcquisitionStart.set_description("Starting time point of the sequence"); MatrixSizeRead=128; MatrixSizeRead.set_cmdline_option("nx").set_description("Number of points in read direction"); MatrixSizePhase=128; MatrixSizePhase.set_cmdline_option("ny").set_description("Number of points in phase direction"); MatrixSizeSlice=1; MatrixSizeSlice.set_cmdline_option("nz").set_description("Number of points in slice direction"); RepetitionTime=1000.0; RepetitionTime.set_unit(ODIN_TIME_UNIT).set_cmdline_option("tr").set_description("Time between consecutive excitations"); NumOfRepetitions=1; NumOfRepetitions.set_cmdline_option("nr").set_description("Number of consecutive measurements"); EchoTime=80.0; EchoTime.set_unit(ODIN_TIME_UNIT).set_cmdline_option("te").set_description("Time-to-echo of the sequence"); // AcqSweepWidth=25.6; // fails as default on Siemens AcqSweepWidth=25.0; AcqSweepWidth.set_unit(ODIN_FREQ_UNIT).set_description("Receiver bandwidth"); FlipAngle=90.0; FlipAngle.set_unit(ODIN_ANGLE_UNIT).set_description("Excitation flipangle"); ReductionFactor=1; ReductionFactor.set_description("Reduction factor for parallel imaging"); PartialFourier=0.0; PartialFourier.set_description("Partial Fourier acquisition in phase encoding direction (0.0 = full k-space, 1.0 = half k-space)"); RFSpoiling=true; RFSpoiling.set_description("RF Spoiling by phase cycling"); GradientIntro=true; GradientIntro.set_description("Gradient intro which will be played out prior to sequence"); PhysioTrigger=false; PhysioTrigger.set_description("Pysiological triggering"); append_all_members(); } SeqPars& SeqPars::set_MatrixSize(direction dir,unsigned int size,parameterMode parmode) { Log odinlog(this,"set_MatrixSize"); switch(dir){ case readDirection: MatrixSizeRead=size; MatrixSizeRead.set_parmode(parmode);break; case phaseDirection: MatrixSizePhase=size; MatrixSizePhase.set_parmode(parmode);break; case sliceDirection: MatrixSizeSlice=size; MatrixSizeSlice.set_parmode(parmode);break; default: ODINLOG(odinlog,errorLog) << "Direction " << dir << " is not available." << STD_endl; } return *this; } unsigned int SeqPars::get_MatrixSize(direction dir) const { unsigned int result=0; if(dir==readDirection) result=MatrixSizeRead; if(dir==phaseDirection) result=MatrixSizePhase; if(dir==sliceDirection) result=MatrixSizeSlice; return result; } SeqPars& SeqPars::set_RepetitionTime(double time,parameterMode parmode) { RepetitionTime=time; RepetitionTime.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_NumOfRepetitions(unsigned int times,parameterMode parmode) { NumOfRepetitions=times; NumOfRepetitions.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_EchoTime(double time,parameterMode parmode) { EchoTime=time; EchoTime.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_AcqSweepWidth(double sw,parameterMode parmode) { AcqSweepWidth=sw; AcqSweepWidth.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_FlipAngle(double fa,parameterMode parmode) { FlipAngle=fa; FlipAngle.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_ReductionFactor(unsigned int factor, parameterMode parmode) { ReductionFactor=factor; ReductionFactor.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_PartialFourier(float factor, parameterMode parmode) { PartialFourier=factor; PartialFourier.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_RFSpoiling(bool flag, parameterMode parmode) { RFSpoiling=flag; RFSpoiling.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_GradientIntro(bool flag, parameterMode parmode) { GradientIntro=flag; GradientIntro.set_parmode(parmode); return *this; } SeqPars& SeqPars::set_PhysioTrigger(bool flag, parameterMode parmode) { PhysioTrigger=flag; PhysioTrigger.set_parmode(parmode); return *this; } SeqPars& SeqPars::operator = (const SeqPars& pars2) { JcampDxBlock::operator = (pars2); append_all_members(); // copy only visible members of JcampDxBlock copy_ldr_vals(pars2); return *this; } void SeqPars::append_all_members() { JcampDxBlock::clear(); append_member(ExpDuration,"ExpDuration"); append_member(Sequence,"Sequence"); append_member(AcquisitionStart,"AcquisitionStart"); append_member(MatrixSizeRead,"MatrixSizeRead"); append_member(MatrixSizePhase,"MatrixSizePhase"); append_member(MatrixSizeSlice,"MatrixSizeSlice"); append_member(RepetitionTime,"RepetitionTime"); append_member(NumOfRepetitions,"NumOfRepetitions"); append_member(EchoTime,"EchoTime"); append_member(AcqSweepWidth,"AcqSweepWidth"); append_member(FlipAngle,"FlipAngle"); append_member(ReductionFactor,"ReductionFactor"); append_member(PartialFourier,"PartialFourier"); append_member(RFSpoiling,"RFSpoiling"); append_member(GradientIntro,"GradientIntro"); append_member(PhysioTrigger,"PhysioTrigger"); } odin-1.8.5/odinpara/jdxfunction.h0000644000175000017500000001666311322062340013705 00000000000000/*************************************************************************** jdxfunction.h - description ------------------- begin : Mon Jun 24 2002 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXFUNCTION_H #define JDXFUNCTION_H #include /** * @addtogroup jcampdx * @{ */ enum funcType {shapeFunc=0, trajFunc, filterFunc}; /** * * Dimension Mode Enum: * * - zeroDeeMode : Only RF waveform will be calculated * - oneDeeMode : RF and gradient shape will be calculated according * to the selected shape/trajectory for 1D pulses * - twoDeeMode : RF and gradient shape will be calculated according * to the selected shape/trajectory for 2D pulses */ enum funcMode {zeroDeeMode=0,oneDeeMode,twoDeeMode,n_dimModes}; /////////////////////////////////////////// class OdinPulse; // forward declaration /////////////////////////////////////////// /** * * Structure to return k-space coordinates, gradient strengts and sampling density * compensations of trajectories. */ struct kspace_coord { kspace_coord() : index(-1), traj_s(0.0), kx(0), ky(0), kz(0), Gx(0), Gy(0), Gz(0), denscomp(1.0) {} /** * The current index in the array */ mutable int index; /** * The dimension-less time parameter which will be used for the shape and filter, ranging from 0 to 1 */ float traj_s; /** * The dimension-less x-coordinate in k-space, ranging from -1 to 1 */ float kx; /** * The dimension-less y-coordinate in k-space, ranging from -1 to 1 */ float ky; /** * The dimension-less z-coordinate in k-space, ranging from -1 to 1 */ float kz; /** * The dimension-less x-gradient, i.e. the derivative of kx by s (the dimension-less time parameter) */ float Gx; /** * The dimension-less y-gradient, i.e. the derivative of kx by s (the dimension-less time parameter) */ float Gy; /** * The dimension-less z-gradient, i.e. the derivative of kx by s (the dimension-less time parameter) */ float Gz; /** * Compensation for differing sampling density, RF shape or RF signal will be multiplied by this function */ float denscomp; }; /////////////////////////////////////////// struct shape_info { shape_info() : ref_x_pos(0), ref_y_pos(0), ref_z_pos(0), adiabatic(false), fixed_size(-1), spatial_extent(0.0) {} float ref_x_pos; // Reference position to adjust flip angle float ref_y_pos; float ref_z_pos; bool adiabatic; // Whether pulse is adiabatic int fixed_size; // Pulse has fixed size (for imported pulses) float spatial_extent; }; /////////////////////////////////////////// struct traj_info { traj_info() : rel_center(0), max_kspace_step(0) {} float rel_center; float max_kspace_step; }; /////////////////////////////////////////// class JDXfunctionPlugIn : public JcampDxBlock { public: JDXfunctionPlugIn(const STD_string& funclabel) : JcampDxBlock(funclabel) {} JDXfunctionPlugIn(const JDXfunctionPlugIn& jfp) : JcampDxBlock(jfp) {} virtual ~JDXfunctionPlugIn() {} JDXfunctionPlugIn& operator = (const JDXfunctionPlugIn& jfp) {JcampDxBlock::operator = (jfp); return *this;} JDXfunctionPlugIn& register_function(funcType type, funcMode mode); // virtual functions for pulse shapes virtual void init_shape() {} virtual STD_complex calculate_shape(const kspace_coord& coord ) const {return STD_complex(0.0);} virtual STD_complex calculate_shape(float s, float Tp) const {return STD_complex(0.0);} virtual const shape_info& get_shape_properties() const {return shape_info_retval;} // virtual functions for pulse trajectories virtual void init_trajectory(OdinPulse* pls) {} virtual const kspace_coord& calculate_traj(float s) const {return coord_retval;} virtual const traj_info& get_traj_properties() const {return traj_info_retval;} // virtual functions for filters virtual float calculate_filter(float rel_kradius) const {return 0;} // virtual constructor virtual JDXfunctionPlugIn* clone() const = 0; // local statics do not work on IDEA static kspace_coord coord_retval; // static shape_vals shape_retval; static shape_info shape_info_retval; static traj_info traj_info_retval; }; /////////////////////////////////////////// // Wrapper to bundle JDXfunctionPlugIn and funcType/funcMode together so it can be inserted into lists // multiple times with different funcTypes and funcModes struct JDXfunctionEntry { JDXfunctionEntry(JDXfunctionPlugIn* func_plugin, funcType func_type, funcMode func_mode) : plugin(func_plugin), type(func_type), mode(func_mode) {} JDXfunctionPlugIn* plugin; const funcType type; const funcMode mode; bool operator == (const JDXfunctionEntry& jfe) const; bool operator < (const JDXfunctionEntry& jfe) const; }; /////////////////////////////////////////// class JDXfunction : public JcampDxClass, public StaticHandler { public: ~JDXfunction() {new_plugin(0);} JDXfunction& set_function_mode(funcMode newmode); funcMode get_function_mode() const {return mode;} const STD_string& get_function_label(unsigned int index) const; JDXfunction& set_function(const STD_string& funclabel); JDXfunction& set_function(unsigned int index); unsigned int get_function_index() const; JcampDxBlock* get_funcpars_block(); JDXfunction& set_funcpars(const svector& funcpars); JDXfunction& set_funcpars(const STD_string& funcpars) {STD_string tt(funcpars); parsevalstring(tt); return *this;} svector get_funcpars() const; bool set_parameter(const STD_string& parameter_label, const STD_string& value); STD_string get_parameter(const STD_string& parameter_label) const; STD_string get_function_name() const; const STD_string& get_funcdescription() const; // overwriting virtual functions from JcampDxClass JDXfunction* cast(JDXfunction*) {return this;} bool parsevalstring (const STD_string& parstring); STD_string printvalstring() const; svector get_alternatives() const; const char* get_typeInfo() const {return "function";} JcampDxClass* create_copy() const {return new JDXfunction(*this);} // stuff for StaticHandler static void init_static(); static void destroy_static(); protected: // Make it impossible to create/use instance of JDXfunction directly JDXfunction(funcType function_type, const STD_string& jdxlabel); JDXfunction(const JDXfunction& jf); JDXfunction& operator = (const JDXfunction& jf); funcMode mode; JDXfunctionPlugIn* allocated_function; private: friend class JDXfunctionPlugIn; void new_plugin(JDXfunctionPlugIn* pi); const funcType type; static STD_list* registered_functions; }; /** @} */ #endif odin-1.8.5/odinpara/jdxfilter.cpp0000644000175000017500000001304211363773555013712 00000000000000#include "jdxfilter.h" #include "jdxnumbers.h" class Gauss : public JDXfunctionPlugIn { JDXdouble filterwidth; public: Gauss() : JDXfunctionPlugIn("Gauss") { filterwidth=0.36169; filterwidth.set_minmaxval(0.1,1.0); append_member(filterwidth,"FilterWidth"); } private: float calculate_filter (float rel_kradius) const { float factor = (-1) * log (0.5) * secureInv( (filterwidth * filterwidth)) ; if(rel_kradius<0.0) rel_kradius=0.0; return exp(-(rel_kradius*rel_kradius)*factor); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Gauss;} }; /////////////////////////////////////////////////////////// class NoFilter : public JDXfunctionPlugIn { public: NoFilter() : JDXfunctionPlugIn("NoFilter") {} float calculate_filter (float rel_kradius) const { if(rel_kradius>1.0) return 0.0; return 1.0; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new NoFilter;} }; /////////////////////////////////////////////////////////// class Triangle : public JDXfunctionPlugIn { public: Triangle() : JDXfunctionPlugIn("Triangle") { } float calculate_filter (float rel_kradius) const { if(rel_kradius<0.0) rel_kradius=0.0; if(rel_kradius>1.0) rel_kradius=1.0; return 1.0-rel_kradius; } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Triangle;} }; /////////////////////////////////////////////////////////// class Hann : public JDXfunctionPlugIn { public: Hann() : JDXfunctionPlugIn("Hann") { } float calculate_filter (float rel_kradius) const { if(rel_kradius<0.0) rel_kradius=0.0; if(rel_kradius>1.0) rel_kradius=1.0; return 0.5*(1.0+cos(rel_kradius*PII)); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Hann;} }; /////////////////////////////////////////////////////////// class Hamming : public JDXfunctionPlugIn { public: Hamming() : JDXfunctionPlugIn("Hamming") { } float calculate_filter (float rel_kradius) const { if(rel_kradius<0.0) rel_kradius=0.0; if(rel_kradius>1.0) rel_kradius=1.0; return (0.53836+0.46164*cos(rel_kradius*PII)); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Hamming;} }; /////////////////////////////////////////////////////////// class CosSq : public JDXfunctionPlugIn { public: CosSq() : JDXfunctionPlugIn("CosSq") { } private: float calculate_filter (float rel_kradius) const { if(rel_kradius<0.0) rel_kradius=0.0; if(rel_kradius>1.0) rel_kradius=1.0; double value=pow(cos(rel_kradius*PII/2.0),2.0); return (value); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new CosSq;} }; /////////////////////////////////////////////////////////// class Blackman : public JDXfunctionPlugIn { public: Blackman() : JDXfunctionPlugIn("Blackman") { } float calculate_filter (float rel_kradius) const { if(rel_kradius<0.0) rel_kradius=0.0; if(rel_kradius>1.0) rel_kradius=1.0; return 0.42+0.5*cos(rel_kradius*PII)+0.08*cos(2.0*rel_kradius*PII); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Blackman;} }; /////////////////////////////////////////////////////////// class BlackmanNuttall : public JDXfunctionPlugIn { public: BlackmanNuttall() : JDXfunctionPlugIn("BlackmanNuttall") { } private: float calculate_filter (float rel_kradius) const { if(rel_kradius<0.0) rel_kradius=0.0; if(rel_kradius>1.0) rel_kradius=1.0; float step = PII*0.5*rel_kradius; float a0 = 0.3635819; float a1 = 0.4891775; float a2 = 0.1365995; float a3 = 0.0106411; double value=a0+a1*cos(2.0*step)+a2*cos(4.0*step)+a3*cos(6.0*step); return (value); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new BlackmanNuttall;} }; /////////////////////////////////////////////////////////// class Exp : public JDXfunctionPlugIn { JDXdouble filterwidth; public: Exp() : JDXfunctionPlugIn("Exp") { } private: float calculate_filter (float rel_kradius) const { return exp(-rel_kradius); } // implementing virtual function of JDXfunctionPlugIn JDXfunctionPlugIn* clone() const {return new Exp;} }; /////////////////////////////////////////////////////////// /* class Fermi : public JDXfunctionTemplate { public: Fermi() : JDXfunctionTemplate("Fermi") { } float calculate (float knorm, float kernel) const { float dummy=(knorm*kernel*2.0-8.0); return 1.0/(exp(dummy)+1.0); } }; */ /////////////////////////////////////////////////////////// void JDXfilter::init_static() { (new Gauss)->register_function(filterFunc, funcMode(0)); (new NoFilter)->register_function(filterFunc, funcMode(0)); (new Triangle)->register_function(filterFunc, funcMode(0)); (new Hann)->register_function(filterFunc, funcMode(0)); (new Hamming)->register_function(filterFunc, funcMode(0)); (new CosSq)->register_function(filterFunc, funcMode(0)); (new Blackman)->register_function(filterFunc, funcMode(0)); (new BlackmanNuttall)->register_function(filterFunc, funcMode(0)); (new Exp)->register_function(filterFunc, funcMode(0)); // (new Fermi)->register_function(filterFunc, funcMode(0)); } void JDXfilter::destroy_static() { // pulgins will be deleted by JDXfunction } EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; odin-1.8.5/odinpara/jdxfilter.h0000644000175000017500000000335611322062340013340 00000000000000/*************************************************************************** jdxfilter.h - description ------------------- begin : Thu Jul 6 2006 copyright : (C) 2002 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXFILTER_H #define JDXFILTER_H #include /** * @addtogroup jcampdx * @{ */ /** * * Wrapper class for pulse shape functions. */ class JDXfilter : public JDXfunction, public StaticHandler { public: JDXfilter(const STD_string& jdxlabel="unnamedJDXfilter") : JDXfunction(filterFunc,jdxlabel) {} JDXfilter(const JDXfilter& jf) : JDXfunction(jf) {} JDXfilter& operator = (const JDXfilter& jf) {JDXfunction::operator = (jf); return *this;} float calculate (float rel_kradius) const { if(allocated_function) return allocated_function->calculate_filter(rel_kradius); else return 0.0; } static void init_static(); static void destroy_static(); }; /** @} */ #endif odin-1.8.5/odinpara/reco.cpp0000644000175000017500000006136411455553536012656 00000000000000#include "reco.h" #include #include static const char* recoFlagTrue="X"; static const char* recoFlagFalse="-"; void kSpaceCoord::reset2defaults() { number=0; reps=1; adcSize=0; channels=1; preDiscard=0; postDiscard=0; concat=1; oversampling=1.0; relcenter=0.5; readoutIndex=-1; trajIndex=-1; weightIndex=-1; dtIndex=0; for(int i=0; i1) result+=STD_string(recoDimLabel[i])+","; } result+="lastinchunk,"; result+="reflect"; return result; } STD_string kSpaceCoord::printcoord(const unsigned short* numof_cache) const { STD_string result; STD_string tab(","); result+=itos(number)+tab; result+=itos(reps)+tab; result+=itos(adcSize)+tab; result+=itos(channels)+tab; result+=itos(preDiscard)+tab; result+=itos(postDiscard)+tab; result+=itos(concat)+tab; result+=ftos(oversampling)+tab; result+=ftos(relcenter)+tab; result+=itos(readoutIndex)+tab; result+=itos(trajIndex)+tab; result+=itos(weightIndex)+tab; result+=itos(dtIndex)+tab; for(int i=0; i1) result+=index2string(index[i], recoDim(i))+tab; } if(flags&recoLastInChunkBit) result+=recoFlagTrue+tab; else result+=recoFlagFalse+tab; if(flags&recoReflectBit) result+=recoFlagTrue; else result+=recoFlagFalse; return result; } int kSpaceCoord::string2index(const STD_string& str, recoDim dim) { int result=0; bool numeric_encoding=true; // Fallback: Convert string to int // Special treatment of template dimension which has characters to index different template types (for extensibility) if(dim==templtype) { if(str.size()) { char templchar=str[0]; if(templchar>='A' && templchar<='Z') { for(int itempl=0; itempl='a' && navchar<='z') { for(int inav=0; inav=0 && index=0 && index odinlog("kSpaceCoord","parsecoord"); reset2defaults(); svector toks(tokens(str,',')); int ntoks=toks.size(); if(ntoks=0) number=atoi(toks[parsepos_number].c_str()); if(parsepos_reps>=0) reps=atoi(toks[parsepos_reps].c_str()); if(parsepos_adcSize>=0) adcSize=atoi(toks[parsepos_adcSize].c_str()); if(parsepos_channels>=0) channels=atoi(toks[parsepos_channels].c_str()); if(parsepos_preDiscard>=0) preDiscard=atoi(toks[parsepos_preDiscard].c_str()); if(parsepos_postDiscard>=0) postDiscard=atoi(toks[parsepos_postDiscard].c_str()); if(parsepos_concat>=0) concat=atoi(toks[parsepos_concat].c_str()); if(parsepos_oversampling>=0) oversampling=atof(toks[parsepos_oversampling].c_str()); if(parsepos_relcenter>=0) relcenter=atof(toks[parsepos_relcenter].c_str()); if(parsepos_readoutIndex>=0) readoutIndex=atoi(toks[parsepos_readoutIndex].c_str()); if(parsepos_trajIndex>=0) trajIndex=atoi(toks[parsepos_trajIndex].c_str()); if(parsepos_weightIndex>=0) weightIndex=atoi(toks[parsepos_weightIndex].c_str()); if(parsepos_dtIndex>=0) dtIndex=atoi(toks[parsepos_dtIndex].c_str()); for(int i=0; i=0) { STD_string indexstr(toks[parsepos_index[i]]); index[i]=string2index(indexstr, recoDim(i)); } } if(parsepos_lastinchunk>=0) if(toks[parsepos_lastinchunk]==recoFlagFalse) flags=flags&(recoLastInChunkBit^recoAllBits); if(parsepos_reflect>=0) if(toks[parsepos_reflect] ==recoFlagTrue) flags=flags|recoReflectBit; return true; } int findval(const svector& strvec, const STD_string& val) { for(unsigned int i=0;i odinlog("kSpaceCoord","assign_parsepos"); svector toks(tokens(header,',')); max_parsepos=STD_max(max_parsepos,parsepos_number=findval(toks,"number")); max_parsepos=STD_max(max_parsepos,parsepos_reps=findval(toks,"reps")); max_parsepos=STD_max(max_parsepos,parsepos_adcSize=findval(toks,"adcSize")); max_parsepos=STD_max(max_parsepos,parsepos_channels=findval(toks,"channels")); max_parsepos=STD_max(max_parsepos,parsepos_preDiscard=findval(toks,"preDiscard")); max_parsepos=STD_max(max_parsepos,parsepos_postDiscard=findval(toks,"postDiscard")); max_parsepos=STD_max(max_parsepos,parsepos_concat=findval(toks,"concat")); max_parsepos=STD_max(max_parsepos,parsepos_oversampling=findval(toks,"oversampling")); max_parsepos=STD_max(max_parsepos,parsepos_relcenter=findval(toks,"relcenter")); max_parsepos=STD_max(max_parsepos,parsepos_readoutIndex=findval(toks,"readoutIndex")); max_parsepos=STD_max(max_parsepos,parsepos_trajIndex=findval(toks,"trajIndex")); max_parsepos=STD_max(max_parsepos,parsepos_weightIndex=findval(toks,"weightIndex")); max_parsepos=STD_max(max_parsepos,parsepos_dtIndex=findval(toks,"dtIndex")); for(int i=0; i odinlog(this,"clear"); if(state==has_vec_alloc) { for(unsigned int i=0; i::iterator it=coordlist.begin(); it!=coordlist.end(); ++it) { kSpaceCoord& coord=(*it); vec_cache[counter]=&coord; for(int j=0; j odinlog(this,"parsevalstring"); ODINLOG(odinlog,normalDebug) << "tokenizing ..." << STD_endl; svector toks(tokens(parstring)); ODINLOG(odinlog,normalDebug) << "toks.size()=" << toks.size() << STD_endl; if(!toks.size()) return true; kSpaceCoord::assign_parsepos(toks[0]); unsigned int n_lines=toks.size()-1; ODINLOG(odinlog,normalDebug) << "parsing " << n_lines << " lines" << STD_endl; clear(); vec_cache.resize(n_lines); bool result=true; ODINLOG(odinlog,normalDebug) << "parsing sinle tokens ..." << STD_endl; for(unsigned int i=0; iparsecoord(toks[i+1])) result=false; for(int j=0; jindex[j]+1)); } state=has_vec_alloc; ODINLOG(odinlog,normalDebug) << "size()=" << size() << STD_endl; return result; } STD_string JDXkSpaceCoords::printvalstring() const { create_vec_cache(); STD_string result(kSpaceCoord::print_header(numof_cache)+"\n"); for(unsigned int i=0; i odinlog(ldrlabel.c_str(), "JDXrecoValList(label)"); set_label(ldrlabel); } JDXrecoValList& JDXrecoValList::operator = (const JDXrecoValList& jdrvl) { RecoValList::operator = (jdrvl); JcampDxClass::operator = (jdrvl); return *this; } JDXrecoValList& JDXrecoValList::operator = (const RecoValList& rvl) { STD_string label_backup(get_label()); RecoValList::operator = (rvl); set_label(label_backup); return *this; } bool JDXrecoValList::parsevalstring (const STD_string& parstring) { Log odinlog(this,"parsevalstring"); STD_string sting4vallist(rmblock(parstring,"(",")",true,true)); return ValList::parsevallist(sting4vallist); } STD_string JDXrecoValList::printvalstring() const { return "("+itos(size())+")\n"+tokenstring(tokens(ValList::printvallist())); // nice formatting } STD_ostream& JDXrecoValList::print2stream(STD_ostream& os) const { os << "(" << itos(size()) << ")\n"; ValList::print2stream(os); return os; } ////////////////////////////////////////////////////////////////// void RecoPars::common_init() { Log odinlog(this,"common_init"); cache_is_up2date=false; ReadoutDstSize.resize(MAX_NUMOF_READOUT_SHAPES); } RecoPars::RecoPars(const STD_string& label) : JcampDxBlock(label) { Log odinlog(this,"RecoPars(label)"); common_init(); if(little_endian_byte_order()) LittleEndian=true; else LittleEndian=false; ODINLOG(odinlog,normalDebug) << "LittleEndian=" << bool(LittleEndian) << STD_endl; append_all_members(); } RecoPars::RecoPars(const RecoPars& sr) { common_init(); RecoPars::operator = (sr); } RecoPars& RecoPars::operator = (const RecoPars& sr) { JcampDxBlock::operator = (sr); append_all_members(); // copy only visible members of JcampDxBlock copy_ldr_vals(sr); return (*this); } RecoPars& RecoPars::set_DimValues(recoDim dim, const dvector& vals) { Log odinlog(this,"set_DimValues"); if(dim odinlog(this,"append_all_members"); int i; clear(); append_member(prot,PROTOCOL_BLOCK_LABEL); append_member(DataFormat,"DataFormat"); append_member(LittleEndian,"LittleEndian"); append_member(RawFile,"RawFile"); append_member(RawHeaderSize,"RawHeaderSize"); append_member(RelativeOffset,"RelativeOffset"); append_member(ImageProc,"ImageProc"); append_member(ChannelScaling,"ChannelScaling"); append_member(DwellTime,"DwellTime"); for(i=0; i odinlog(this,"get_sensitivity_value"); STD_complex result(0); ndim nn=SensitivityMap.get_extent(); int nx=nn[3]; int ny=nn[2]; int nz=nn[1]; int nchans=nn[0]; if(int(channel) >= nchans) return result; float xDelta=secureDivision(FOV[0],nx); float yDelta=secureDivision(FOV[1],ny); float zDelta=secureDivision(FOV[2],nz); // indices of the grid square which contain the desired point float fx=(x+0.5*FOV[0])/xDelta; float fy=(y+0.5*FOV[1])/yDelta; float fz=(z+0.5*FOV[2])/zDelta; int ixlow=int(floor(fx-0.5)); int ixupp=int(floor(fx+0.5)); int iylow=int(floor(fy-0.5)); int iyupp=int(floor(fy+0.5)); int izlow=int(floor(fz-0.5)); int izupp=int(floor(fz+0.5)); if(nx<=1) ixlow=ixupp=0; if(ny<=1) iylow=iyupp=0; if(nz<=1) izlow=izupp=0; if(ixlow==-1) ixlow=0; if(iylow==-1) iylow=0; if(izlow==-1) izlow=0; if(ixupp==nx) ixupp=nx-1; if(iyupp==ny) iyupp=ny-1; if(izupp==nz) izupp=nz-1; if(ixlow<0) return result; if(iylow<0) return result; if(izlow<0) return result; if(ixupp>=nx) return result; if(iyupp>=ny) return result; if(izupp>=nz) return result; ODINLOG(odinlog,normalDebug) << "ixlow/iylow/izlow(" << x << "," << y << "," << z << ")=" << ixlow << "/" << iylow << "/" << izlow << STD_endl; ODINLOG(odinlog,normalDebug) << "ixupp/iyupp/izupp(" << x << "," << y << "," << z << ")=" << ixupp << "/" << iyupp << "/" << izupp << STD_endl; float xlow=-0.5*FOV[0]+(float(ixlow)+0.5)*xDelta; float ylow=-0.5*FOV[1]+(float(iylow)+0.5)*yDelta; float zlow=-0.5*FOV[2]+(float(izlow)+0.5)*zDelta; // relative positions within the grid square float sx=(x-xlow)/xDelta; if(sx<0.0) sx=0.0; if(sx>1.0) sx=1.0; float sy=(y-ylow)/yDelta; if(sy<0.0) sy=0.0; if(sy>1.0) sy=1.0; float sz=(z-zlow)/zDelta; if(sz<0.0) sz=0.0; if(sz>1.0) sz=1.0; ODINLOG(odinlog,normalDebug) << "sx/sy/sz(" << x << "," << y << "," << z << ")=" << sx << "/" << sy << "/" << sz << STD_endl; result=STD_complex((1.0-sz)*(1.0-sy)*(1.0-sx))*SensitivityMap(channel,izlow,iylow,ixlow) +STD_complex((1.0-sz)*(1.0-sy)*( sx))*SensitivityMap(channel,izlow,iylow,ixupp) +STD_complex((1.0-sz)*( sy)*(1.0-sx))*SensitivityMap(channel,izlow,iyupp,ixlow) +STD_complex((1.0-sz)*( sy)*( sx))*SensitivityMap(channel,izlow,iyupp,ixupp) +STD_complex(( sz)*(1.0-sy)*(1.0-sx))*SensitivityMap(channel,izupp,iylow,ixlow) +STD_complex(( sz)*(1.0-sy)*( sx))*SensitivityMap(channel,izupp,iylow,ixupp) +STD_complex(( sz)*( sy)*(1.0-sx))*SensitivityMap(channel,izupp,iyupp,ixlow) +STD_complex(( sz)*( sy)*( sx))*SensitivityMap(channel,izupp,iyupp,ixupp); return result; } void CoilSensitivity::append_all_members() { clear(); SensitivityMap.redim(1,1,1,1); SensitivityMap.set_filemode(compressed); append_member(FOV,"FOV"); append_member(SensitivityMap,"SensitivityMap"); } //////////////////////////////////////////////// #ifndef NO_UNIT_TEST class CoilSensitivityTest : public UnitTest { public: CoilSensitivityTest() : UnitTest("CoilSensitivity") {} private: bool check() const { Log odinlog(this,"check"); unsigned int i; int testsize=10; float testfov=200.0; CoilSensitivity sens; carray testmap(1,1,testsize,testsize); ndim nn=testmap.get_extent(); ndim ii; float center=0.5*float(testsize-1); for(i=0; i1.0) { ODINLOG(odinlog,errorLog) << "mean1=" << mean1 << STD_endl; ODINLOG(odinlog,errorLog) << "mean2=" << mean2 << STD_endl; return false; } return true; } }; void alloc_CoilSensitivityTest() {new CoilSensitivityTest();} // create test instance #endif odin-1.8.5/odinpara/jdxnumbers.h0000644000175000017500000001075711322062341013532 00000000000000/*************************************************************************** jdxnumbers.h - description ------------------- begin : Mon Jul 12 2004 copyright : (C) 2001 by Thies H. Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef JDXNUMBERS_H #define JDXNUMBERS_H #include #include /** * @addtogroup jcampdx * @{ */ ////////////////////////////////////////////////////////////////// /** * * JCAMP-DX template class for representing built-in numbers */ template class JDXnumber : public virtual JcampDxClass { public: /** * Default constructor */ JDXnumber() {set_defaults();} /** * Constructor with the following arguments: * - v: Initial value for the number * - name: The label of the JCAMP-DX parameter * - userParameter: Whether this is a user defined JCAMP-DX parameter * - mode: Mode for ASCII representation of strings or arrays of strings * - parameter_mode: Mode for GUI accesibility of the parameter * - parx_equivalent: Equivalent parameter in PARX to which this parameter will be assigned * - parx_assign_factor: Scaling factor when assigning to the equivalent parameter in PARX * - parx_assign_offset: Offset when assigning to the equivalent parameter in PARX */ JDXnumber(T v, const STD_string& name="",bool userParameter=true, compatMode mode=notBroken,parameterMode parameter_mode=edit, const STD_string& parx_equivalent="", float parx_assign_factor=1.0,float parx_assign_offset=0.0); /** * Copy constructor */ JDXnumber(const JDXnumber& bi) {JDXnumber::operator = (bi);} /** * Assignment operator from a built-in number */ JDXnumber& operator = (T v) {val=v; return *this;} /** * Copy assignment */ JDXnumber& operator = (const JDXnumber& bi); // code to make the number appear like a built-in number operator T () const {return val;} T operator += (T rhsval) {val+=rhsval; return *this;} T operator -= (T rhsval) {val-=rhsval; return *this;} T operator *= (T rhsval) {val*=rhsval; return *this;} T operator /= (T rhsval) {val/=rhsval; return *this;} T operator ++ () {val=val+(T)1; return val;} // prefix T operator ++ (int) {T tmp=val; val=val+(T)1; return tmp;} // postfix T operator -- () {val=val-(T)1; return val;} // prefix T operator -- (int) {T tmp=val; val=val-(T)1; return tmp;} // postfix /** * Specifies the minimum and maximum allowed value for this number. * Only useful when editing the parameter in a GUI */ JDXnumber& set_minmaxval(double min,double max) {minval=min; maxval=max; return *this;} // overwriting virtual functions from JcampDxClass STD_string printvalstring() const; bool parsevalstring (const STD_string& parstring); STD_string get_parx_code(parxCodeType type, const ParxEquiv& equiv) const; ParxEquiv get_parx_equiv() const {return parx_equiv;} double get_minval() const {return minval;} double get_maxval() const {return maxval;} const char* get_typeInfo() const {return TypeTraits::type2label(val);} JcampDxClass* create_copy() const {return new JDXnumber(*this);} T* cast(T*) {return &val;} private: void set_defaults(); T val; mutable ParxEquiv parx_equiv; double minval,maxval; }; ///////////////////////////////////////////////////////////////////////////// // // Aliases: /** * An integer number */ typedef JDXnumber JDXint; /** * An single-precision floating point number */ typedef JDXnumber JDXfloat; /** * An double-precision floating point number */ typedef JDXnumber JDXdouble; /** * Complex number */ typedef JDXnumber JDXcomplex; /** @} */ #endif odin-1.8.5/odinpara/jdxblock.cpp0000644000175000017500000004617611363773555013535 00000000000000#include "jdxblock.h" #include #ifdef HAVE_LOCALE_H #include #endif void set_c_locale() { Log odinlog("JcampDxBlock","set_c_locale"); #ifdef HAVE_LOCALE_H // set locale to default before reading/writing blocks // to get decimal point on all platforms const char* retval=setlocale(LC_NUMERIC, "C"); ODINLOG(odinlog,normalDebug) << "LC_NUMERIC=" << retval << STD_endl; #endif } JcampDxBlock::JcampDxBlock(const STD_string& title,compatMode mode) : garbage(0), embed(true) { Log odinlog(title.c_str(),"JcampDxBlock(title)"); set_label(title); JcampDxBlock::set_compatmode(mode); // Do NOT call virtual function in constructor! } JcampDxBlock::JcampDxBlock(const JcampDxBlock& block) : garbage(0) { JcampDxBlock::operator = (block); } JcampDxBlock::~JcampDxBlock() { Log odinlog(this,"~JcampDxBlock"); if(garbage) { ODINLOG(odinlog,normalDebug) << "Removing " << JDXList::size() << " parameters from block" << STD_endl; JDXList::clear(); // remove before deleting ODINLOG(odinlog,normalDebug) << "Deleting " << garbage->size() << " parameters in garbage" << STD_endl; for(STD_list::iterator it=garbage->begin(); it!=garbage->end(); ++it) { ODINLOG(odinlog,normalDebug) << "Deleting >" << (*it)->get_label() << "<" << STD_endl; delete (*it); } delete garbage; } } JcampDxBlock& JcampDxBlock::operator = (const JcampDxBlock& block) { Log odinlog(this,"JcampDxBlock::operator = "); JcampDxClass::operator = (block); // JDXList::operator = (block); // Unneccessary since the copied list would be cleared in the next line JDXList::clear(); // start with empty block so that members are copied by value and not by pointer (as done in List) embed=block.embed; return *this; } JDXList::constiter JcampDxBlock::ldr_exists(const STD_string& label) const { Log odinlog(this,"ldr_exists"); for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { ODINLOG(odinlog,normalDebug) << "comparing LDR >" << label << "< and >" << (*it)->get_label() << "<" << STD_endl; if( (*it)->get_label()==label ) { ODINLOG(odinlog,normalDebug) << "LDR found" << STD_endl; return it; } } ODINLOG(odinlog,normalDebug) << "LDR not found" << STD_endl; return get_const_end(); } STD_string JcampDxBlock::extract_parlabel(const STD_string& parstring) { STD_string parlabel(extract(parstring,"##","=")); if (parlabel[0]=='$') { parlabel+="="; parlabel=extract(parlabel,"$","="); } if(parlabel=="TITLE") { parlabel=extract(parstring,"##TITLE=","\n"); } return parlabel; } int JcampDxBlock::parse_ldr_list(STD_string& parstring) { Log odinlog(this,"parse_ldr_list"); parstring+="##"; // set mark at end so rmblock(parstring,"##","##",... always works ODINLOG(odinlog,normalDebug) << "parstring=>" << parstring << "<" << STD_endl; // get 1st parameter before starting while loop STD_string parlabel(extract_parlabel(parstring)); constiter ldr_it=get_const_begin(); int n_parsed=0; while(parlabel!="") { if( (ldr_it=ldr_exists(parlabel) )!=get_const_end() ) { if(!(*ldr_it)->parse(parstring)) { ODINLOG(odinlog,normalDebug) << "parsing of >" << parlabel << "< failed" << STD_endl; return -1; } else { ODINLOG(odinlog,normalDebug) << "parsing of >" << parlabel << "< successful" << STD_endl; n_parsed++; } } else { parstring=rmblock(parstring,"##","##",true,false,false,false); } // get next parameter parlabel=extract_parlabel(parstring); } return n_parsed; } bool JcampDxBlock::parse(STD_string& parstring) { Log odinlog(this,"parse"); if(parseblock(parstring)<0) return false; ODINLOG(odinlog,normalDebug) << "parstring(pre)=>" << parstring << "<" << STD_endl; // eat up my part from parstring parstring+="##END="; // make sure we have an end tag which might got lost STD_string blockbody(extract(parstring,"##TITLE=","##END=",true)); parstring=replaceStr(parstring,"##TITLE="+blockbody+"##END=",""); ODINLOG(odinlog,normalDebug) << "parstring(post)=>" << parstring << "<" << STD_endl; return true; } STD_string JcampDxBlock::print_header() const { STD_string result="##TITLE="+get_label()+"\n"; result+="##JCAMPDX=4.24\n"; result+="##DATATYPE=Parameter Values\n"; return result; } STD_string JcampDxBlock::print_tail() const { return "##END=\n"; } STD_string JcampDxBlock::print() const { Log odinlog(this,"print"); STD_string retstring(print_header()); ODINLOG(odinlog,normalDebug) << "printing " << numof_pars() << " parameters" << STD_endl; for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { retstring+=(*it)->print(); } retstring+=print_tail(); return retstring; } STD_ostream& JcampDxBlock::print2stream(STD_ostream& os) const { os << print_header(); for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if((*it)->get_filemode()!=exclude) { os << (*it)->get_jdx_prefix(); (*it)->print2stream(os); os << (*it)->get_jdx_postfix(); } } return os << print_tail(); } STD_string JcampDxBlock::printval(const STD_string& parameterName) const { Log odinlog(this,"printval"); STD_string retstring; constiter it=ldr_exists(parameterName); if(it!=get_const_end()) { retstring=(*it)->printvalstring(); } return retstring; } bool JcampDxBlock::parseval(const STD_string& parameterName, const STD_string& value) { Log odinlog(this,"parseval"); bool result=false; constiter it=ldr_exists(parameterName); if(it!=get_const_end()) { STD_string valdummy=value; result=(*it)->parsevalstring(valdummy); } return result; } STD_string JcampDxBlock::get_parx_code(parxCodeType type, const ParxEquiv& equiv) const { #ifdef PARAVISION_PLUGIN STD_string result=JcampDxClass::get_parx_code(type,equiv); if(type==parx_def) { for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if((*it)->isUserDefParameter()) result+=(*it)->get_parx_code(parx_def,(*it)->get_parx_equiv()); } } if(type==parx_parclass_def) { result="parclass {\n"; for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if((*it)->isUserDefParameter()) result+=STD_string((*it)->get_label())+";\n"; } result+="} "+STD_string(get_label())+";\n"; } if(type==parx_parclass_init) { STD_string visabilityString; result="PARX_hide_class (NOT_HIDDEN, \""+STD_string(get_label())+"\");\n"; for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if((*it)->isUserDefParameter()) { if( (*it)->get_parmode() == hidden) visabilityString="HIDDEN"; else visabilityString="NOT_HIDDEN"; result+="PARX_hide_pars ("+visabilityString+", \""+(*it)->get_label()+"\");\n"; result+="PARX_hide_pars (HIDE_IN_FILE, \""+STD_string((*it)->get_label())+"\");\n"; if( (*it)->get_parmode() == noedit) { result+="PARX_noedit (TRUE, \""+STD_string((*it)->get_label())+"\");\n"; } } } } if(type==parx_parclass_passval) { for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if((*it)->isUserDefParameter() && (*it)->get_parx_equiv().name!="" ) { result+=(*it)->get_parx_code(parx_passval_head,(*it)->get_parx_equiv()); } } // result+="PARX_read_file(\""+STD_string(get_label())+"\",\""+equiv.name+"\");\n"; result+="ParxRelsReadClass(\""+STD_string(get_label())+"\","+equiv.name+");\n"; for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if((*it)->isUserDefParameter() && (*it)->get_parx_equiv().name!="" ) { result+=(*it)->get_parx_code(parx_passval,(*it)->get_parx_equiv()); } } } return result; #else return ""; #endif } int JcampDxBlock::load(const STD_string &filename) { Log odinlog(this,"load"); set_c_locale(); // Make sure we have right locale STD_string blockstr; int retval=::load(blockstr,filename); ODINLOG(odinlog,normalDebug) << "retval(" << filename << ")=" << retval << STD_endl; if(retval) return -1; return parseblock(dos2unix(blockstr)); } int JcampDxBlock::parseblock(const STD_string& source) { Log odinlog(this,"parseblock"); STD_string blocklabel; int result=-1; STD_string parlabel=extract(source,"##","="); if(parlabel=="TITLE") { STD_string source_without_comments=rmblock(source, "\n$$", "\n", true, false); // Remove single-line comments source_without_comments=rmblock(source_without_comments, "$$", "\n", true, false); // Remove remaining end-line comments blocklabel=extract(source_without_comments,"##TITLE=","\n"); set_label(blocklabel); STD_string blockbody(extract(source_without_comments,"##TITLE=","##END=",true)); // Extract body of parameter block, regarding nested structure (blocks within blocks) // blockbody=replaceStr(blockbody,blocklabel+"\n",""); // This seems to be unecessary result=parse_ldr_list(blockbody); } return result; } int JcampDxBlock::write(const STD_string &filename) const { Log odinlog(this,"write"); set_c_locale(); // Make sure we have right locale STD_ofstream outfile(filename.c_str()); JcampDxBlock::print2stream(outfile); outfile.close(); return 0; } unsigned int JcampDxBlock::numof_pars() const { Log odinlog(this,"numof_pars"); unsigned int n=0; ODINLOG(odinlog,normalDebug) << "size()=" << size() << STD_endl; for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { ODINLOG(odinlog,normalDebug) << "trying to count parameter ..." << STD_endl; if((*it)->isUserDefParameter()) n++; ODINLOG(odinlog,normalDebug) << "counted parameter >" << (*it)->get_label() << "<" << STD_endl; } return n; } JcampDxBlock& JcampDxBlock::merge(JcampDxBlock& block, bool onlyUserPars) { Log odinlog(this,"merge"); for(iter it=block.get_begin(); it!=block.get_end(); ++it) { if( onlyUserPars ) { if( (*it)->isUserDefParameter() ) append(**it); } else append(**it); } return *this; } JcampDxBlock& JcampDxBlock::unmerge(JcampDxBlock& block) { Log odinlog(this,"unmerge"); for(iter it=block.get_begin(); it!=block.get_end(); ++it) { remove(**it); } return *this; } JcampDxClass* JcampDxBlock::get_parameter(const STD_string& ldrlabel) { Log odinlog(this,"get_parameter"); for(iter it=get_begin(); it!=get_end(); ++it) { if( (*it)->get_label()==ldrlabel ) { return (*it); } } return 0; } bool JcampDxBlock::parameter_exists(const STD_string& ldrlabel) const { Log odinlog(this,"parameter_exists"); bool result=false; if(ldr_exists(ldrlabel)!=get_const_end()) result=true; return result; } JcampDxBlock& JcampDxBlock::set_prefix(const STD_string& prefix) { Log odinlog(this,"set_prefix"); if( STD_string(get_label()).find(prefix) == STD_string::npos ) set_label(prefix+"_"+get_label()); for(iter it=get_begin(); it!=get_end(); ++it) { if((*it)->isUserDefParameter()) { if( STD_string((*it)->get_label()).find(prefix) != 0 ) (*it)->set_label(prefix+"_"+(*it)->get_label()); } } return *this; } JcampDxClass& JcampDxBlock::set_compatmode(compatMode compat_mode) { JcampDxClass::set_compatmode(compat_mode); for(iter it=get_begin(); it!=get_end(); ++it) (*it)->set_compatmode(compat_mode); return *this; } JcampDxClass& JcampDxBlock::set_parmode(parameterMode parameter_mode) { JcampDxClass::set_parmode(parameter_mode); for(iter it=get_begin(); it!=get_end(); ++it) (*it)->set_parmode(parameter_mode); return *this; } JcampDxClass& JcampDxBlock::set_filemode(fileMode file_mode) { JcampDxClass::set_filemode(file_mode); for(iter it=get_begin(); it!=get_end(); ++it) (*it)->set_filemode(file_mode); return *this; } JcampDxClass& JcampDxBlock::operator [] (unsigned int i) { Log odinlog(this,"operator []"); unsigned int n=numof_pars(); if(i>=n) return *this; unsigned int j=0; for(iter it=get_begin(); it!=get_end(); ++it) { if((*it)->isUserDefParameter()) { if(j==i) return *(*it); j++; } } return *this; } const JcampDxClass& JcampDxBlock::operator [] (unsigned int i) const { Log odinlog(this,"operator [] const"); unsigned int n=numof_pars(); if(i>=n) return *this; unsigned int j=0; for(constiter it=get_const_begin(); it!=get_const_end(); ++it) { if((*it)->isUserDefParameter()) { if(j==i) return *(*it); j++; } } return *this; } JcampDxClass& JcampDxBlock::get_parameter_by_id(int id) { for(iter it=get_begin(); it!=get_end(); ++it) { if((*it)->get_parameter_id()==id) return *(*it); } return *this; } JcampDxBlock& JcampDxBlock::append_copy(const JcampDxClass& src) { if(!garbage) garbage=new STD_list; JcampDxClass* ldrcopy=src.create_copy(); garbage->push_back(ldrcopy); append(*ldrcopy); return *this; } JcampDxBlock& JcampDxBlock::create_copy(const JcampDxBlock& src) { JcampDxBlock::operator = (src); if(!garbage) garbage=new STD_list; for(constiter ldr_it=src.get_const_begin(); ldr_it!=src.get_const_end(); ++ldr_it) { if((*ldr_it)->isUserDefParameter()) append_copy(**ldr_it); } return *this; } JcampDxBlock& JcampDxBlock::copy_ldr_vals(const JcampDxBlock& src) { Log odinlog(this,"copy_ldr_vals"); for(constiter ldr_it=src.get_const_begin(); ldr_it!=src.get_const_end(); ++ldr_it) { ODINLOG(odinlog,normalDebug) << "copying " << (*ldr_it)->get_label() << STD_endl; constiter it; if( (it=ldr_exists((*ldr_it)->get_label()))!=get_const_end() ) { STD_string valstring((*ldr_it)->printvalstring()); ODINLOG(odinlog,normalDebug) << "valstring=" << valstring << STD_endl; (*it)->parsevalstring(valstring); } } return *this; } bool JcampDxBlock::compare(const JcampDxBlock& rhs, const STD_list* exclude, double accuracy) const { Log odinlog(this,"compare"); unsigned int mynpars=numof_pars(); unsigned int rhnpars=rhs.numof_pars(); ODINLOG(odinlog,normalDebug) << "mynpars/rhnpars=" << mynpars << "/" << rhnpars << STD_endl; if(mynpars!=rhnpars) return mynpars::const_iterator exclude_begin,exclude_end; if(exclude) { exclude_begin=exclude->begin(); exclude_end=exclude->end(); } for(constiter rh_it=rhs.get_const_begin(); rh_it!=rhs.get_const_end(); ++rh_it) { STD_string parlabel((*rh_it)->get_label()); my_it=ldr_exists(parlabel); if( exclude && (STD_find(exclude_begin, exclude_end, parlabel) != exclude_end ) ) { ODINLOG(odinlog,normalDebug) << "Excluding " << parlabel << " from comparison" << STD_endl; } else { if(my_it==get_const_end()) return true; // 'this' does not include all pars of 'rhs' -> it is 'smaller' // check for type STD_string mytype=(*my_it)->get_typeInfo(); STD_string rhtype=(*rh_it)->get_typeInfo(); ODINLOG(odinlog,normalDebug) << "mytype/rhtype(" << parlabel << ")=" << mytype << "/" << rhtype << STD_endl; if( mytype!=rhtype ) return mytypecast(dumfloat)) ) {myfloat=(*dumfloat); my_is_float=true;} if( (dumdouble=(*my_it)->cast(dumdouble)) ) {myfloat=(*dumdouble); my_is_float=true;} if( (dumfloat=(*rh_it)->cast(dumfloat)) ) {rhfloat=(*dumfloat); rh_is_float=true;} if( (dumdouble=(*rh_it)->cast(dumdouble)) ) {rhfloat=(*dumdouble); rh_is_float=true;} ODINLOG(odinlog,normalDebug) << "my_is_float/rh_is_float(" << parlabel << ")=" << my_is_float << "/" << rh_is_float << STD_endl; if(my_is_float && rh_is_float) { ODINLOG(odinlog,normalDebug) << "myfloat/rhfloat(" << parlabel << ")=" << myfloat << "/" << rhfloat << STD_endl; if(fabs(myfloat-rhfloat)>accuracy) { // Otherwise, values are considered equal ODINLOG(odinlog,normalDebug) << "Unequal myfloat/rhfloat(" << parlabel << ")=" << myfloat << "/" << rhfloat << STD_endl; return myfloatprintvalstring(); STD_string rhval=(*rh_it)->printvalstring(); ODINLOG(odinlog,normalDebug) << "myval/rhval(" << parlabel << ")=" << myval << "/" << rhval << STD_endl; if( myval!=rhval) { ODINLOG(odinlog,normalDebug) << "Unequal myval/rhval(" << parlabel << ")=" << myval << "/" << rhval << STD_endl; return myval odinlog(this,"append_member"); if(ldrlabel!=STD_string("")) ldr.set_label(ldrlabel); append(ldr); return *this; } #ifndef NO_CMDLINE JcampDxBlock& JcampDxBlock::parse_cmdline_options(int argc, char *argv[], bool modify) { char optval[ODIN_MAXCHAR]; for(constiter ldr_it=get_const_begin(); ldr_it!=get_const_end(); ++ldr_it) { STD_string opt((*ldr_it)->get_cmdline_option()); if(opt!="") { STD_string optstr("-"+opt); bool* booldummy=(*ldr_it)->cast(booldummy=NULL); if(booldummy) { if(isCommandlineOption(argc,argv,optstr.c_str())) (*booldummy)=true; } else { if(getCommandlineOption(argc,argv,optstr.c_str(),optval,ODIN_MAXCHAR,modify)) (*ldr_it)->parsevalstring(optval); } } } return *this; } STD_map JcampDxBlock::get_cmdline_options() const { STD_map result; for(constiter ldr_it=get_const_begin(); ldr_it!=get_const_end(); ++ldr_it) { STD_string opt((*ldr_it)->get_cmdline_option()); if(opt!="") { STD_string descr=(*ldr_it)->get_description(); STD_string unit=(*ldr_it)->get_unit(); if(unit!="") descr+=" ["+unit+"]"; // Exclude default value for Boolean types STD_string defval; bool* booldummy=(*ldr_it)->cast(booldummy=0); if(!booldummy) defval=(*ldr_it)->printvalstring(); svector alt=(*ldr_it)->get_alternatives(); if(defval!="" || alt.size()) { descr+=" ("; if(alt.size()) descr+="options="+tokenstring(alt,0)+", "; if(defval!="") descr+="default="+defval+unit; descr+=")"; } result[opt]=descr; } } return result; } STD_string JcampDxBlock::get_cmdline_usage(const STD_string& lineprefix) const { STD_string result; STD_map optmap=get_cmdline_options(); for(STD_map::const_iterator it=optmap.begin(); it!=optmap.end(); ++it) { result += lineprefix+"-"+it->first+": "+it->second+"\n"; } return result; } #endif void JcampDxBlock::init_static() { Log odinlog("JcampDxBlock","init_static"); set_c_locale(); } void JcampDxBlock::destroy_static() { Log odinlog("JcampDxBlock","destroy_static"); } EMPTY_TEMPL_LIST bool StaticHandler::staticdone=false; // Template instantiations template class ListItem; template class List; odin-1.8.5/odinreco/0000755000175000017500000000000011735135552011270 500000000000000odin-1.8.5/odinreco/refgain.cpp0000644000175000017500000001316311322062351013317 00000000000000#include "refgain.h" #include "data.h" #include "controller.h" #include #define _BRIM_POW_ 10 struct RefgainFunction : public ModelFunction { fitpar gain0; double A,C; double start_gain,brim_gain_delta; float evaluate_f(float x) const { return A * ( fabs( sin( C * pow( 10.0, -(x-gain0.val)/20.0 ) ) ) + pow((gain0.val-start_gain)/brim_gain_delta,_BRIM_POW_) ); } fvector evaluate_df(float x) const { fvector result(numof_fitpars()); double power=pow( 10.0, -(x-gain0.val)/20.0 ); double sinus=sin( C * power ); double cosinus=cos( C * power ); result[0] = A *( C*log(10.0)/(20.0) * power * cosinus * sinus + 1.0/(_BRIM_POW_*brim_gain_delta) * pow((gain0.val-start_gain)/brim_gain_delta,_BRIM_POW_-1) )/fabs(sinus); return result; } unsigned int numof_fitpars() const {return 1;} fitpar& get_fitpar(unsigned int i) { if(i==0) return gain0; return dummy_fitpar; } }; /////////////////////////////////////////////////////////////////////////// int first_max_index(const Array& vec, float thresh) { int n=vec.numElements(); if(n==0) return 0; float max=vec(0); int maxindex=n-1; bool maxfound=false; int i; for(i=1;i<(n-1);i++) { if(vec(i)>max && vec(i+1)thresh) { maxfound=true; break; } } if(maxfound) maxindex=i; else maxindex=n-1; return maxindex; } /////////////////////////////////////////////////////////////////////////// int first_min_index(const Array& vec, float thresh) { int n=vec.numElements(); if(n==0) return 0; float min=vec(0); int minindex=n-1; bool minfound=false; int i; for(i=1;i<(n-1);i++) { if(vec(i)vec(i) && vec(i)>thresh) { minfound=true; break; } } if(minfound) minindex=i; else minindex=n-1; return minindex; } /////////////////////////////////////////////////////////////////////////// void RecoRefGain::init() { pulsedur=0.0; pulsedur.set_description("Pulse duration"); append_arg(pulsedur,"pulsedur"); pulsegain=0.0; pulsegain.set_description("Pulse gain"); append_arg(pulsegain,"pulsegain"); } #define NOISELEVEL_FIRSTMAX 0.2 #define BRIM_REFGAIN 3.0 #define MIN_REFGAIN -1000.0 #define MAX_REFGAIN 1000.0 #define _REFERENCE_GAIN_BP_PARAVISION_ 0.9 bool RecoRefGain::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); Data magn(cabs(indata)); TinyVector inshape=indata.shape(); float noiselevel=0.2*max(magn); int nrefg=inshape(0); int nline3d=inshape(1); int nline=inshape(2); int nread=inshape(3); ODINLOG(odinlog,normalDebug) << "nrefg/nline3d/nline/nread=" << nrefg << "/" << nline3d << "/" << nline << "/" << nread << STD_endl; RefgainFunction refgf; FunctionFit refgfit(refgf,nrefg,10000,0.001); refgf.C=pulsedur*0.5*PII; int anglecounter; double refgain; double absval; double weightsum=0.0; double refgsum=0.0; dvector attenuations=controller.dim_values(userdef); if(int(attenuations.size())!=nrefg) { ODINLOG(odinlog,errorLog) << "attenuations.size()=" << attenuations.size() << " does not match nrefg=" << nrefg << STD_endl; return false; } Data pixel(nrefg); Data yvals(nrefg); Data xvals(nrefg); for(int i=0; i refgmap(nline3d,nline,nread); for(int iline3d=0; iline3d noiselevel ) { pixel=magn(all,iline3d,j,i); int minmaxindex=0; int prevminmaxindex=0; int firstmaxindex=0; anglecounter=0; // find the first maximum above the noise threshhold float threshhold=NOISELEVEL_FIRSTMAX*max(pixel); minmaxindex=first_max_index(pixel,threshhold); xvals(anglecounter)=pow(10.0,-attenuations[minmaxindex]/20.0); yvals(anglecounter)=(double)(anglecounter+1); anglecounter++; prevminmaxindex=minmaxindex; firstmaxindex=minmaxindex; // if only one max is found, calculate refgain according to a 90deg pulse refgain=0.0; if(anglecounter==1) { refgain=attenuations[firstmaxindex]+20.0*log10(secureInv(pulsedur))-pulsegain; } // non-linear fit refgf.A=pixel(firstmaxindex); refgf.start_gain=refgain+pulsegain; refgf.brim_gain_delta=BRIM_REFGAIN; refgf.gain0.val=refgain+pulsegain; refgfit.fit(pixel,Array(0),xvals); refgain=refgf.gain0.val-pulsegain; if(refgainMAX_REFGAIN) refgain=0.0; if(refgain!=0.0) { double fitweight=secureInv(refgf.gain0.err); refgsum+=refgain*fitweight; weightsum+=fitweight; } refgmap(iline3d,j,i)=refgain+_REFERENCE_GAIN_BP_PARAVISION_; } else { refgmap(iline3d,j,i)=0.0; } } } } double avrefgain=secureDivision(refgsum,weightsum); ODINLOG(odinlog,infoLog) << "average refgain=" << avrefgain << STD_endl; STD_string valfile=STD_string(secure_getenv("HOME"))+"/.odin/opdir/odin_refgain"; ::write(ftos(avrefgain),valfile); system(("chmod 666 "+valfile).c_str()); ComplexData<3>& outdata=rd.data(Rank<3>()); outdata.resize(nline3d,nline,nread); outdata=float2real(refgmap); return execute_next_step(rd,controller); } odin-1.8.5/odinreco/fieldmap.cpp0000644000175000017500000002722011713467630013501 00000000000000#include "fieldmap.h" #include "data.h" #include "controller.h" #include #include bool RecoFieldMap::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); TinyVector inshape=indata.shape(); TinyVector outshape(inshape(1), inshape(2), inshape(3)); ODINLOG(odinlog,normalDebug) << "inshape/outshape=" << inshape << "/" << outshape << STD_endl; dvector tes=controller.dim_values(te); ODINLOG(odinlog,normalDebug) << "tes=" << tes.printbody() << STD_endl; if(int(tes.size())!=inshape(0)) { ODINLOG(odinlog,errorLog) << "TE size mismatch: " << tes.size() << "!=" << inshape(0) << STD_endl; return false; } if(inshape(0)<2) { ODINLOG(odinlog,errorLog) << "too few number of TEs: " << inshape(0) << STD_endl; return false; } bool oddeven=(inshape(0)>2); // Assume odd and even echoes (EPI-type readtout) for more than 2 TEs int npol=1; if(oddeven) npol=2; int ntes[npol]; if(oddeven) { ntes[0]=ntes[1]=inshape(0)/2; if(inshape(0)%2) ntes[0]++; } else { ntes[0]=inshape(0); } ODINLOG(odinlog,normalDebug) << "oddeven/inshape(0)/npol/ntes[0]/ntes[1]=" << oddeven << "/" << inshape(0) << "/" << npol << "/" << ntes[0] << "/" << ntes[1] << STD_endl; // regroup odd and even data ComplexData<4> tedata[2]; Data pixel[2]; Data magn[2]; ComplexData<1> pixel_complex[2]; Data sigma[2]; Data tevals[2]; for(int ipol=0; ipol(cabs(tedata[ipol])).autowrite("cabs_"+idstr+".nii"); Data(phase(tedata[ipol])).autowrite("phase_"+idstr+".nii"); } */ Data reliability(outshape); reliability(all,all,all)=cabs(indata(0,all,all,all)); // Take 1st echo for reliability based on image magnitude float noiselevel=0.6*mean(reliability); indata.free(); Data fieldmap(outshape); fieldmap=0.0; // ComplexData<3> cplxphase(outshape); cplxphase=STD_complex(0.0); LinearFunction linf; for(int ipol=0; ipol srcshape=it->second.shape(); if(srcshape!=dstshape) { ODINLOG(odinlog,errorLog) << "shape mismatch: srcshape" << srcshape << "!=dstshape" << dstshape << STD_endl; return false; } fieldmap.reference(it->second.copy()); // Deep copy for multi-threaded access calc_fmap=false; } fmapmutex.unlock(); if(calc_fmap) { if(!controller.data_announced(posted_fmap_str)) { ODINLOG(odinlog,errorLog) << "fieldmap not available" << STD_endl; return false; } RecoData rdfieldmap(fmapcoord); rdfieldmap.coord().index[cycle] = 0; // reset to 0 to only get initial (not rotated) field map if(!controller.inquire_data(posted_fmap_str, rdfieldmap)) return false; float os_fmap = rdfieldmap.coord().overSamplingFactor; float os_user = fmapcoord.overSamplingFactor; // float osFactor = secureDivision(os_user, os_fmap); ODINLOG(odinlog,normalDebug) << "os_fmap/os_user=" << os_fmap << "/" << os_user << STD_endl; Data fmreal(creal(rdfieldmap.data(Rank<3>()))); TinyVector fmshape(fmreal.shape()); ODINLOG(odinlog,normalDebug) << "fmshape/dstshape=" << fmshape << "/" << dstshape << STD_endl; // spatial shifting TinyVector reloffset=controller.reloffset(); reloffset(0) = 0; // set zero to only shift in phase and readout direction, shifting in slice direction is not necessary because no rotation is done in slice direction reloffset(2)/=os_fmap; bool do_shift=false; if(max(abs(reloffset))>0.0) do_shift=true; // create mask for weighting Data mask(fmshape); mask=where(Array(fmreal)!=0.0, float(1.0), float(0.0)); // mask.autowrite("mask_"+rdfieldmap.coord().print(RecoIndex::filename)+".nii"); // prepare shapes and vars for gridder STD_vector > src_coords(product(fmshape)); TinyVector image_center = 0.5 * (fmshape-1); // index of center in image space TinyVector srcfov; srcfov = 0.0; TinyVector dstfov; dstfov = 0.0; if (fmshape(0) > 1) srcfov(0) = controller.protocol().geometry.get_FOV(sliceDirection); if (dstshape(0) > 1) dstfov(0) = controller.protocol().geometry.get_FOV(sliceDirection); // Only regridding in line3d direction if dimension > 1 srcfov(1) = dstfov(1) = controller.protocol().geometry.get_FOV(phaseDirection); srcfov(2) = os_fmap*controller.protocol().geometry.get_FOV(readDirection); dstfov(2) = os_user*controller.protocol().geometry.get_FOV(readDirection); ODINLOG(odinlog,normalDebug) << "srcfov=" << srcfov << STD_endl; ODINLOG(odinlog,normalDebug) << "dstfov=" << dstfov << STD_endl; bool hasBlades = (fmapcoord.index[cycle].get_numof() > 1); int iblade = fmapcoord.index[cycle]; dvector angles; if (hasBlades) { angles = controller.dim_values(cycle); ODINLOG(odinlog,normalDebug) << "angles=" << angles.printbody() << STD_endl; hasBlades = (angles.length() == fmapcoord.index[cycle].get_numof()); // check for spiral or propeller } ODINLOG(odinlog,normalDebug) << "hasBlades=" << hasBlades << STD_endl; int isrc = 0; TinyVector coord; for (int islice = 0; islice < fmshape(0); islice++) { for (int iphase = 0; iphase < fmshape(1); iphase++) { for (int iread = 0; iread < fmshape(2); iread++) { TinyVector index3d(islice, iphase, iread); coord = (index3d - image_center) / fmshape * srcfov; double angle_rad = 0.0; if(hasBlades) angle_rad = angles[iblade]; // not reversed rotation... GriddingPoint<3>& src_point=src_coords[isrc]; src_point.coord = coord; src_point.weight = mask(islice,iphase,iread); if(angle_rad) { TinyVector coord_min = -image_center / fmshape * srcfov; TinyVector coord_max = image_center / fmshape * srcfov; if (do_shift) { // Shift to center src_point.coord -= reloffset * srcfov; if (src_point.coord(1) < coord_min(1)) src_point.coord(1) = coord_max(1) - (coord_min(1) - src_point.coord(1)); if (src_point.coord(2) < coord_min(2)) src_point.coord(2) = coord_max(2) - (coord_min(2) - src_point.coord(2)); if (src_point.coord(1) >= coord_max(1)) src_point.coord(1) = coord_min(1) + (src_point.coord(1) - coord_max(1)); if (src_point.coord(2) >= coord_max(2)) src_point.coord(2) = coord_min(2) + (src_point.coord(2) - coord_max(2)); } // Rotation float si=sin(angle_rad); float co=cos(angle_rad); TinyVector coord_temp = src_point.coord; src_point.coord(0)=coord_temp(0); src_point.coord(1)=co*coord_temp(1)-si*coord_temp(2); src_point.coord(2)=si*coord_temp(1)+co*coord_temp(2); if (do_shift) { // Shift back TinyVector reloffset_rot; reloffset_rot(0)=reloffset(0); reloffset_rot(1)=co*reloffset(1)-si*reloffset(2); reloffset_rot(2)=si*reloffset(1)+co*reloffset(2); src_point.coord += reloffset_rot * srcfov; if (src_point.coord(1) < coord_min(1)) src_point.coord(1) = coord_max(1) - (coord_min(1) - src_point.coord(1)); if (src_point.coord(2) < coord_min(2)) src_point.coord(2) = coord_max(2) - (coord_min(2) - src_point.coord(2)); if (src_point.coord(1) >= coord_max(1)) src_point.coord(1) = coord_min(1) + (src_point.coord(1) - coord_max(1)); if (src_point.coord(2) >= coord_max(2)) src_point.coord(2) = coord_min(2) + (src_point.coord(2) - coord_max(2)); } } isrc++; } } } JDXfilter gridkernel; gridkernel.set_function("Gauss"); float kwidth = 1.5*max(dstfov/dstshape); ODINLOG(odinlog,normalDebug) << "kwidth=" << kwidth << STD_endl; Gridding gridder; gridder.init(dstshape, dstfov, src_coords, gridkernel, kwidth); fieldmap.reference(gridder(fmreal)); fmapmutex.lock(); fmap[fmapcoord].reference(fieldmap); fmapmutex.unlock(); } return true; } void RecoFieldMapUser::modify4fieldmap(RecoCoord& coord) { for(int idim=0; idim& adc); const STD_vector& get_coords() const; dvector dim_values(recoDim dim) const {return recoInfo.get_DimValues(dim);} const TinyVector& reloffset() const {return reloffset_cache;} STD_string image_proc() const {return image_proc_cache;} const TinyVector& image_size() const {return size_cache;} const Protocol& protocol() const {return prot_cache;} STD_string seqrecipe() const {return recoInfo.get_Recipe();} STD_string postProc3D() const {return recoInfo.get_PostProc3D();} STD_string preProc3D() const {return recoInfo.get_PreProc3D();} STD_string cmdline_opts() const {return recoInfo.get_CmdLineOpts();} void kcoord2coord(const kSpaceCoord& kcoord, RecoCoord& coord) const; static bool concat_data(STD_string& rawfile, const STD_string& scandir, const STD_string& fnameprefix); template bool read_block(T2 dummy, ComplexData<2>& block); JDXstring fifoFile; JDXbool padZero; // read only in fetch() unsigned int nadc; int zeroesPerChunk; unsigned int rawtypesize; // cached values unsigned int nChannels_cache; TinyVector reloffset_cache; STD_string image_proc_cache; TinyVector size_cache; Protocol prot_cache; ReadoutShape readoutShape_cache[MAX_NUMOF_READOUT_SHAPES]; KspaceTraj kspaceTraj_cache[MAX_NUMOF_KSPACE_TRAJS]; ComplexData<1> weightVec_cache[MAX_NUMOF_ADC_WEIGHTING_VECTORS]; Data channelFactors; // data used during reco RecoPars recoInfo; STD_string dataformat; ComplexData<2> rawdata; // cache rawdata because all channels are loaded at once STD_string rawdata_filename; FILE* rawdata_fileptr; unsigned int index; // counter for indexing ADCs (each channel increments this counter) unsigned int ri_index; // index for ADCs in recoInfo kSpaceCoord kcoord_cache; // cache num of channels and crop size of current ADC unsigned int chancount; // counter for channels mutable STD_vector coord_vec_cache; }; /** @} */ #endif odin-1.8.5/odinreco/bladegrid.h0000644000175000017500000000310611363773557013310 00000000000000/*************************************************************************** bladegrid.h - description ------------------- begin : Fri Jan 07 2009 copyright : (C) 2009 by Martin Krämer email : MartinKraemer@gmx.net ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef BLADEGRID_H #define BLADEGRID_H #include #include #include "odinreco.h" class BladeGrid { public: bool init(const TinyVector& inshape, const TinyVector fov, const TinyVector image_size, const float os_factor, const JDXfilter& filterkernel); ComplexData<4> operator () (const ComplexData<4>& src, const dvector& angles) const; private: Data filtermask_center; TinyVector dstextent; TinyVector dstshape; TinyVector kmax; }; #endif odin-1.8.5/odinreco/fmri.cpp0000644000175000017500000000500211322062351012632 00000000000000#include "fmri.h" #include "data.h" #include "controller.h" #include void RecoFMRI::init() { stimsize=0; stimsize.set_description("Number of repetitions during stimulation"); append_arg(stimsize,"stimsize"); restsize=0; restsize.set_description("Number of repetitions during rest"); append_arg(restsize,"restsize"); } bool RecoFMRI::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); if(!stimsize || !restsize) { ODINLOG(odinlog,errorLog) << "stimsize/restsize=" << stimsize << "/" << restsize << STD_endl; return false; } ComplexData<4>& indata=rd.data(Rank<4>()); Data magn(cabs(indata)); TinyVector inshape=indata.shape(); TinyVector outshape(inshape(1), inshape(2), inshape(3)); int nrep=inshape(0); int blocksize=stimsize+restsize; Data design(nrep); design=0.0; for(int irep=0; irep overlay(outshape); for(int iphase3d=0; iphase3d tcourse(nrep); for(int iphase3d=0; iphase3d()).free(); rd.data(Rank<3>()).resize(outshape); rd.data(Rank<3>())=float2real(overlay); rd.coord().index[repetition]=0; return execute_next_step(rd,controller); } odin-1.8.5/odinreco/phasecourse.cpp0000644000175000017500000000307411734622163014237 00000000000000#include "phasecourse.h" #include "data.h" #include bool RecoPhaseCourse::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<5>& indata=rd.data(Rank<5>()); TinyVector inshape=indata.shape(); int nchan=inshape(0); int nrep=inshape(1); int nline3d=inshape(2); int nphase=inshape(3); int nread =inshape(4); TinyVector outshape(nrep, nline3d, nphase, nread); ODINLOG(odinlog,normalDebug) << "outshape=" << outshape << STD_endl; Data outdata(outshape); Data unwrapped(nrep); ComplexData<1> cplx1d(nrep); ComplexData<1> cplxsum(nrep); LinearFunction linf; for(int iline3d=0; iline3d()).reference(float2real(outdata)); return execute_next_step(rd,controller); } odin-1.8.5/odinreco/phasecourse.h0000644000175000017500000000324311322062351013670 00000000000000/*************************************************************************** phasecourse.h - description ------------------- begin : Thu May 28 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOPHASECOURSE_H #define RECOPHASECOURSE_H #include "step.h" class RecoPhaseCourse : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "phasecourse";} STD_string description() const {return "Combine phase timecourse from multi-channel data";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,channel,repetition,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single,channel);} RecoStep* allocate() const {return new RecoPhaseCourse;} void init() {} }; #endif odin-1.8.5/odinreco/b1fit.h0000644000175000017500000000333711322062351012360 00000000000000/*************************************************************************** b1fit.h - description ------------------- begin : Tue Oct 16 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOB1FIT_H #define RECOB1FIT_H #include "step.h" class RecoB1Fit : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "b1fit";} STD_string description() const {return "B1-mapping method based on: Fast, Accurate, and Precise Mapping of the RF Field In Vivo Using the 180 Signal Null. Dowell et al., Magn Reson Med 58 (2007).";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,userdef,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single,userdef);} RecoStep* allocate() const {return new RecoB1Fit;} void init() {} }; #endif odin-1.8.5/odinreco/conjphase.h0000644000175000017500000000330611322062351013321 00000000000000/*************************************************************************** conjphase.h - description ------------------- begin : Wed Jun 6 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOCONJPHASE_H #define RECOCONJPHASE_H #include "fieldmap.h" class RecoConjPhaseFT : public RecoFieldMapUser { // implementing virtual functions of RecoStep STD_string label() const {return "conjphase";} STD_string description() const {return "Discrete Fourier transform with conjugate-phase correction according to field map";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected, readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::collected, line3d, line);} RecoStep* allocate() const {return new RecoConjPhaseFT;} void init() {} Mutex trajmutex; }; #endif odin-1.8.5/odinreco/messer.h0000644000175000017500000000315511322062351012647 00000000000000/*************************************************************************** messer.h - description ------------------- begin : Thu Apr 9 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOMESSER_H #define RECOMESSER_H #include "step.h" class RecoMesser : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "messer";} STD_string description() const {return "Postprocessing for MESSER sequence";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,userdef,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::separate,userdef);} RecoStep* allocate() const {return new RecoMesser;} void init() {} }; #endif odin-1.8.5/odinreco/measindex.cpp0000644000175000017500000000003011322062351013646 00000000000000#include "measindex.h" odin-1.8.5/odinreco/switch.cpp0000644000175000017500000001404611322062351013206 00000000000000#include "switch.h" #include "controller.h" #include "data.h" void RecoSwitch::init() { brancharg.set_description("A semicolon-separated list of entries in the form 'dim=value {sub-pipeline}' where 'dim' can \ be any of the dimensions in recoDim, 'value' is an integer number (or character from templateTypeChar) \ and 'sub-pipeline' is a pipeline to be executed when the index of the input in dimension 'dim' matches 'value'. \ If the 'dim=value' is omitted, the pipeline will be executed for each incoming data."); append_arg(brancharg,"brancharg"); } bool RecoSwitch::pipeline_init(const RecoController& controller, const RecoCoord& input_coord) { Log odinlog(c_label(),"pipeline_init"); svector branchstr(tokens(brancharg,';','{','}')); for(unsigned int ibranch=0; ibranch > class RecoMeasIndex { public: /** * Initialize with coordinate 'coord' in this branch of the pipeline using 'controller'. */ bool init(const RecoCoord& coord, const RecoController& controller) { Log odinlog("RecoMeasIndex","init"); RecoCoord coord4count(coord); prep_coord(coord4count); coord4count.set_mode(RecoIndex::separate, dim); const CoordCountMap* countmap=controller.create_count_map(coord4count); if(!countmap) return false; init_countmap=(*countmap); // create deep copy because countmap may be deleted by controller after prep return create_measmap(init_countmap); } /** * Update cache of measured/interpolated coords by adding 'extra' to the initial coordinates. */ bool update(const CoordCountMap& extra) { Log odinlog("RecoMeasIndex","update"); if(!extra.size()) return true; CoordCountMap countmap_copy(init_countmap); ODINLOG(odinlog,normalDebug) << "countmap_copy/extra.size()=" << countmap_copy.size() << "/" << extra.size() << STD_endl; for(CoordCountMap::const_iterator it=extra.begin(); it!=extra.end(); ++it) countmap_copy[it->first]+=it->second; return create_measmap(countmap_copy); } /** * Returns the list of indices for coordinate 'coord'. */ ivector get_indices(const RecoCoord& coord) const { Log odinlog("RecoMeasIndex","get_indices"); ivector result; RecoCoord coord4meas(coord); prep_coord(coord4meas); coord4meas.set_mode(RecoIndex::ignore,dim); MeasMap::const_iterator it=measmap.find(coord4meas); if(it==measmap.end()) { ODINLOG(odinlog,normalDebug) << "<" << recoDimLabel[dim] << ">: No indices for coordinate " << coord4meas.print() << STD_endl; } else { result=it->second; ODINLOG(odinlog,normalDebug) << "coord4meas/it=" << coord4meas.print() << "/" << it->first.print() << STD_endl; ODINLOG(odinlog,normalDebug) << "result=" << result.printbody() << STD_endl; } return result; } private: static void prep_coord(RecoCoord& coord) { Ignore::modify(RecoIndex::ignore, coord); Separate::modify(RecoIndex::separate, coord); } bool create_measmap(const CoordCountMap& countmap) { Log odinlog("RecoMeasIndex","create_measmap"); STD_map > indexlist; for(CoordCountMap::const_iterator it=countmap.begin(); it!=countmap.end(); ++it) { RecoCoord coord4indexlist(it->first); coord4indexlist.set_mode(RecoIndex::ignore, dim); // collapse index, indices will be stored in the index vectors of measmap indexlist[coord4indexlist].push_back(it->first.index[dim]); } for(STD_map >::iterator lstit=indexlist.begin(); lstit!=indexlist.end(); ++lstit) { STD_list& lstref=lstit->second; lstref.sort(); lstref.unique(); measmap[lstit->first]=list2vector(lstref); } for(MeasMap::const_iterator mapit=measmap.begin(); mapit!=measmap.end(); ++mapit) { ODINLOG(odinlog,normalDebug) << "measmap[" << mapit->first.print() << "]=" << mapit->second.printbody() << STD_endl; } return true; } CoordCountMap init_countmap; typedef STD_map MeasMap; MeasMap measmap; // will be initialized during init }; #endif odin-1.8.5/odinreco/data.cpp0000644000175000017500000000167311734622163012632 00000000000000#include "data.h" #include RecoData::~RecoData() { if (prof) delete prof; } RecoData& RecoData::copy_meta(const RecoData& rd) { kcoord=rd.kcoord; override_protocol=rd.override_protocol; mode=rd.mode; interpolated=rd.interpolated; return *this; } RecoData& RecoData::free(int dim) { if(dim==1) data1.free(); if(dim==2) data2.free(); if(dim==3) data3.free(); if(dim==4) data4.free(); if(dim==5) data5.free(); if(dim==6) data6.free(); return *this; } RecoData& RecoData::operator = (const RecoData& rd) { data1.reference(rd.data1.copy()); data2.reference(rd.data2.copy()); data3.reference(rd.data3.copy()); data4.reference(rd.data4.copy()); data5.reference(rd.data5.copy()); data6.reference(rd.data6.copy()); return copy_meta(rd); } void RecoData::new_profiler(const STD_string& steplabel) { #ifdef ODIN_DEBUG if(prof) delete prof; prof=new Profiler("RecoStep->"+steplabel); #endif } odin-1.8.5/odinreco/qualitycontrol.h0000644000175000017500000000342311725203123014441 00000000000000/*************************************************************************** qualitycontrol.h - description ------------------- begin : Tue Feb 28 2011 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef QUALITYCONTROL_H #define QUALITYCONTROL_H #include "step.h" class RecoQualityControlSpike : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "qcspike";} STD_string description() const {return "Check for spikes in data";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoQualityControlSpike;} void init() {} STD_map spikecount; // separately for each channel Mutex spikemutex; LONGEST_INT total_acqpts; Mutex totalmutex; }; #endif odin-1.8.5/odinreco/circmask.h0000644000175000017500000000310311322062351013136 00000000000000/*************************************************************************** circmask.h - description ------------------- begin : Thu Sep 3 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOCIRCMASK_H #define RECOCIRCMASK_H #include "step.h" class RecoCircMask : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "circmask";} STD_string description() const {return "Cut out central circular region.";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoCircMask;} void init() {} }; #endif odin-1.8.5/odinreco/adc.h0000644000175000017500000000760711455553545012127 00000000000000/*************************************************************************** adc.h - description ------------------- begin : Mon Jan 22 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOADC_H #define RECOADC_H #include "step.h" class RecoAdcReflect : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "adc_reflect";} STD_string description() const {return "Reflect ADC if recoReflectBit is set";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoAdcReflect;} void init() {} }; //////////////////////////////////////////////////////// class RecoAdcGridPrep : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "adc_gridprep";} STD_string description() const {return "Prepare ADC for gridding (ramp sampling)";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoAdcGridPrep;} void init() {} KspaceTraj traj; // caching trajectory Mutex trajmutex; }; //////////////////////////////////////////////////////// class RecoAdcWeight : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "adc_weight";} STD_string description() const {return "Weight ADC using weightVec";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoAdcWeight;} void init() {} Mutex weightMutex; // to protect global Blitz array which contains weightVec }; //////////////////////////////////////////////////////// class RecoAdcBaseline : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "adc_baseline";} STD_string description() const {return "Baseline correction of ADCs";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoAdcBaseline;} void init() {} }; ///////////////////////////////////////////////////////////////// class RecoAdcPad : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "adc_pad";} STD_string description() const {return "Pad missing points by zeroes";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoAdcPad;} void init() {} }; #endif odin-1.8.5/odinreco/dti.h0000644000175000017500000000302711322062351012127 00000000000000/*************************************************************************** dti.h - description ------------------- begin : Thu Oct 29 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECODTI_H #define RECODTI_H #include "step.h" class RecoDTI : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "dti";} STD_string description() const {return "DTI preprocessing";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoDTI;} void init() {} }; #endif odin-1.8.5/odinreco/fft.h0000644000175000017500000000305511322062351012127 00000000000000/*************************************************************************** fft.h - description ------------------- begin : Sat Dec 30 2006 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOFFT_H #define RECOFFT_H #include "step.h" class RecoFFT : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "fft";} STD_string description() const {return "Fast Fourier Transform";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoFFT;} void init(); JDXbool forward; }; #endif odin-1.8.5/odinreco/mip.h0000644000175000017500000000311011322062351012125 00000000000000/*************************************************************************** mip.h - description ------------------- begin : Tue Dec 4 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOMIP_H #define RECOMIP_H #include "step.h" class RecoMip : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "mip";} STD_string description() const {return "Maximum intensity projection in slice direction";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoMip;} void init(); JDXint neighbors; }; #endif odin-1.8.5/odinreco/grappa.h0000644000175000017500000001044511363773557012651 00000000000000/*************************************************************************** grappa.h - description ------------------- begin : Fri Feb 2 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOGRAPPA_H #define RECOGRAPPA_H #include "step.h" #include "measindex.h" /////////////////////////////////////////////////////////////////////////////////////////////////////////// // NOTE: Dimensions of the weights are: dstchannel * reduction index * srcchannel * phase * read template > class RecoGrappaWeights : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const { STD_string result="grappaweights"; if(Ignore::dim()>0) result+="templ"; if(interpolDim==line3d) result+="3d"; return result; } STD_string description() const {return "Calculate GRAPPA weights in dimension '"+STD_string(recoDimLabel[interpolDim])+"' and post them on the blackboard with the label 'grappaweights_"+recoDimLabel[interpolDim]+"'.";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,channel,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoGrappaWeights;} void init(); JDXint reduction_factor; JDXint neighbours_read; JDXint neighbours_phase; JDXfloat svd_trunc; JDXfloat discard_level; // helper functions ivector acl_lines(const RecoCoord& coord, int numof_neighb, int ired) const; bool calc_weights(ComplexData<5>& weights, const RecoCoord& trainingcoord, const ComplexData<4>& trainingdata); // Instance of RecoMeasIndex to get k-space sampling pattern, // i.e. hase-encoding lines actually measured, // by assuming the same for channel, freq, repetition and separate // schemes for the orthogonal phase-encoding direction RecoMeasIndex, RecoDim<1,orthoDim> > measlines; }; /////////////////////////////////////////////////////////////////////////////////////////////////////////// template class RecoGrappa : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {if(interpolDim==line3d) return "grappa3d"; else return "grappa";} STD_string description() const {return "Perform GRAPPA interpolation in dimension '"+STD_string(recoDimLabel[interpolDim])+"'";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,channel,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoGrappa;} void init(); JDXint reduction_factor; JDXbool keep_shape; // helper functions int reduction_index(const ivector& indexvec, int sizePhase, int iphase) const; bool correct_shape(RecoData& rdkspace, const RecoController& controller) const; // Instance of RecoMeasIndex to get k-space sampling pattern, // i.e. hase-encoding lines actually measured, // by assuming the same for channel, freq, repetition and separate // schemes for the orthogonal phase-encoding direction RecoMeasIndex, RecoDim<1,orthoDim> > measlines; }; #endif odin-1.8.5/odinreco/sum.h0000644000175000017500000000460111322062351012152 00000000000000/*************************************************************************** sum.h - description ------------------- begin : Thu Mar 8 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSUM_H #define RECOSUM_H #include "step.h" /* * Template class to sum up data in one or more dimensions. * The rank of the unmodified collected data dimensions is is given by 'Nunmod'. * The particular unmodified dimension are given in 'Unmod' by a specialization of 'RecoDim'. * The numer of dimensions to sum up is given in 'Nsum' and specified in 'Sum' by * a specialization of 'RecoDim'. * The dimensions to sum up are expected leftmost in the input data array. * The optional parameter 'Magn' specifies whether only the magnitude will * be accumulated instead of the complex values. */ template class RecoSum : public RecoStep, public Labeled { public: RecoSum(const STD_string& sum_label) : Labeled(sum_label) {} private: // implementing virtual functions of RecoStep STD_string label() const {return get_label();} STD_string description() const {return "Sum up data in one or more dimensions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {RecoCoord result=Unmod::preset_coord(RecoIndex::collected); Sum::modify(RecoIndex::collected,result); return result;} void modify_coord(RecoCoord& coord) const {Sum::modify(RecoIndex::single,coord);} RecoStep* allocate() const {return new RecoSum(get_label());} void init() {} }; #endif odin-1.8.5/odinreco/swi.h0000644000175000017500000000304711322062351012153 00000000000000/*************************************************************************** swi.h - description ------------------- begin : Fri Sep 14 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSWI_H #define RECOSWI_H #include "step.h" class RecoSwi : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "swi";} STD_string description() const {return "Susceptibility weighted imaging";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoSwi;} void init() {} }; #endif odin-1.8.5/odinreco/messer.cpp0000644000175000017500000001154711363773557013234 00000000000000#include "messer.h" #include "data.h" #include "controller.h" #include #define NOISELEVEL 0.3 #define MAXT2 1000.0 bool RecoMesser::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); TinyVector inshape=indata.shape(); TinyVector outshape(inshape(1), inshape(2), inshape(3)); Protocol prot(controller.protocol()); // Local copy of protocol, used for override_protocol float TEse=prot.seqpars.get_EchoTime(); dvector tes=controller.dim_values(userdef); ODINLOG(odinlog,normalDebug) << "tes=" << tes.printbody() << STD_endl; int ntes=inshape(0); if(ntes!=int(tes.size())) { ODINLOG(odinlog,errorLog) << "ntes=" << ntes << " does not match tes.size()=" << tes.size() << STD_endl; return false; } int nfid=0; int nser=0; for(int ite=0; ite fidlog(nfid); Data fidsigma(nfid); Data fidte(nfid); Data serlog(nser); Data sersigma(nser); Data serte(nser); int ite=0; for(int i=0; i pixel(ntes); Data T2(outshape); T2=0.0; Data T2star(outshape); T2star=0.0; Data S0(outshape); S0=0.0; Data SE(outshape); SE=0.0; for(int iphase3d=0; iphase3dnoiselevel) { ite=0; float R2star=0.0; float R2minus=0.0; float s0=0.0; float se=0.0; // signal at Spin-Echo // fit FID part if(nfid) { for(int i=0; i(t2, 0.0, MAXT2); check_range(t2star, 0.0, MAXT2); T2star(iphase3d,iphase,iread)=t2star; T2(iphase3d,iphase,iread)=t2; S0(iphase3d,iphase,iread)=s0; SE(iphase3d,iphase,iread)=se; } } } } // modify coordinate rd.coord().index[userdef].set_numof(ntes+4); int iuserdef=0; rd.override_protocol=&prot; STD_string series; int number; prot.study.get_Series(series, number); // feed echoes separately into rest of pipeline for(ite=0; ite()).resize(outshape); rdecho.data(Rank<3>())=indata(ite,all,all,all); rdecho.coord().index[userdef]=iuserdef; prot.study.set_Series(series+"_TE"+ftos(tes[ite]),number); if(!execute_next_step(rdecho,controller)) return false; iuserdef++; } // feed T2star into rest of pipeline RecoData rdT2star(rd); rdT2star.data(Rank<3>()).resize(outshape); rdT2star.data(Rank<3>())=float2real(T2star); rdT2star.coord().index[userdef]=iuserdef; prot.study.set_Series(series+"_T2star",number); if(!execute_next_step(rdT2star,controller)) return false; iuserdef++; // feed T2 into rest of pipeline RecoData rdT2(rd); rdT2.data(Rank<3>()).resize(outshape); rdT2.data(Rank<3>())=float2real(T2); rdT2.coord().index[userdef]=iuserdef; prot.study.set_Series(series+"_T2",number); if(!execute_next_step(rdT2,controller)) return false; iuserdef++; // feed S0 into rest of pipeline RecoData rdS0(rd); rdS0.data(Rank<3>()).resize(outshape); rdS0.data(Rank<3>())=float2real(S0); rdS0.coord().index[userdef]=iuserdef; prot.study.set_Series(series+"_S0",number); if(!execute_next_step(rdS0,controller)) return false; iuserdef++; // feed SE into rest of pipeline RecoData rdSE(rd); rdSE.data(Rank<3>()).resize(outshape); rdSE.data(Rank<3>())=float2real(SE); rdSE.coord().index[userdef]=iuserdef; prot.study.set_Series(series+"_SE",number); if(!execute_next_step(rdSE,controller)) return false; iuserdef++; return true; } odin-1.8.5/odinreco/splitter_code.h0000644000175000017500000000445311322062351014213 00000000000000#include "splitter.h" #include "data.h" template bool RecoSplitter::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); // create new view of input data ComplexData& indata=rd.data(Rank()); TinyVector splitshape; for(int i=0; i outshape; for(int i=0; i outshape_padded=1; for(unsigned int i=0; i lowin=0; TinyVector uppin=outshape_padded-1; TinyVector lowout=0; TinyVector uppout=outshape_padded-1; // output domain, the same for each dataset RectDomain outdomain(lowout,uppout); ComplexData outdata_padded(outshape_padded); ComplexData outdata(outshape); for(int isplit=0; isplit splitindex=index2extent(splitshape, isplit); // set input inidices for(unsigned int i=0; i indomain(lowin,uppin); outdata_padded(outdomain)=indata(indomain); outdata_padded.convert_to(outdata); // bring to output shape // set data and index and feed data into rest of pipeline RecoData rdout; // separate data object since indata is just a reference rdout.copy_meta(rd); // Use all meta data from indata Split::modify(RecoIndex::separate, rdout.coord()); Split::set_index(splitindex, rdout.coord()); rdout.data(Rank()).reference(outdata); if(!execute_next_step(rdout,controller)) return false; } return true; } odin-1.8.5/odinreco/fieldmap.h0000644000175000017500000000411011322062351013122 00000000000000/*************************************************************************** fieldmap.h - description ------------------- begin : Mon Feb 25 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOFIELDMAP_H #define RECOFIELDMAP_H #include "step.h" static const char* posted_fmap_str="fieldmap"; class RecoFieldMap : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "fieldmap";} STD_string description() const {return "Calculate fieldmap";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,te,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single, te);} RecoStep* allocate() const {return new RecoFieldMap;} void init() {} }; ////////////////////////////////////////////////////////////// class RecoFieldMapUser : public RecoStep { public: bool get_fmap(Data& fieldmap, const TinyVector& dstshape, const RecoCoord& fmapcoord, RecoController& controller); static void modify4fieldmap(RecoCoord& coord); private: // cache interpolated fieldmaps typedef STD_map > FieldMap; FieldMap fmap; Mutex fmapmutex; }; #endif odin-1.8.5/odinreco/phasecorr.h0000644000175000017500000000542011322062351013334 00000000000000/*************************************************************************** phasecorr.h - description ------------------- begin : Mon Jan 24 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOPHASECORR_H #define RECOPHASECORR_H #include "step.h" class RecoPhaseMap : public RecoStep { public: static void modify(RecoCoord& coord) { // to be used in query() coord.set_mode(RecoIndex::ignore, line, line3d); // dimensions irrelevant to phase correction coord.set_mode(RecoIndex::separate, echo); // override collected mode } static void modify4blackboard(RecoCoord& coord) { // index for blackboard modify(coord); coord.set_mode(RecoIndex::separate, epi); // no longer ignore EPI index coord.set_mode(RecoIndex::ignore, repetition, dti, line3d, templtype, freq); // re-use phasemap for all repetitions, etc. } private: // implementing virtual functions of RecoStep STD_string label() const {return "phasemap";} STD_string description() const {return "Calculate and post phasemap for echo-by-echo phase correction";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,echo,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoPhaseMap;} void init() {} bool odd_even_echoes; }; ////////////////////////////////////////////////////////////// class RecoPhaseCorr : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "phasecorr";} STD_string description() const {return "Apply echo-by-echo phase correction";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoPhaseCorr;} void init() {} }; #endif odin-1.8.5/odinreco/b1fit.cpp0000644000175000017500000000631611322062351012713 00000000000000#include "b1fit.h" #include "data.h" #include "controller.h" #include bool RecoB1Fit::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); TinyVector inshape=indata.shape(); TinyVector outshape(inshape(1), inshape(2), inshape(3)); ComplexData<3>& outdata=rd.data(Rank<3>()); outdata.resize(outshape); outdata=STD_complex(0.0); dvector flips=controller.dim_values(userdef); ODINLOG(odinlog,normalDebug) << "flips=" << flips.printbody() << STD_endl; int nflips=flips.size(); if(nflips!=inshape(0)) { ODINLOG(odinlog,errorLog) << "size mismatch" << STD_endl; return false; } Data magn(cabs(indata)); float masklevel=0.2; float noiselevel=masklevel*mean(magn(0,all,all,all)); LinearFunction linf; Data pixel4fit(nflips); Data flipwinkel(nflips); for ( int icount = 0; icount < nflips; icount++ ) { flipwinkel(icount)=flips[icount]; } Data pixel4fitcalc(nflips-2); Data ysigmacalc(nflips-2); ysigmacalc=1.0; Data flipwinkelcalc(nflips-2); for(int iphase3d=0; iphase3dnoiselevel) { pixel4fit=magn(all,iphase3d,iphase,iread); int checkmin = minIndex(pixel4fit)(0); if ( (checkmin == 0) || (checkmin == 1) ) { flipwinkelcalc(0) = flipwinkel(0); flipwinkelcalc(1) = flipwinkel(1); flipwinkelcalc(2) = flipwinkel(2); pixel4fitcalc(0) = pixel4fit(0); pixel4fitcalc(1) = pixel4fit(1); pixel4fitcalc(2) = pixel4fit(2); } if ( checkmin == 2 ) { flipwinkelcalc(0) = flipwinkel(1); flipwinkelcalc(1) = flipwinkel(2); flipwinkelcalc(2) = flipwinkel(3); pixel4fitcalc(0) = pixel4fit(1); pixel4fitcalc(1) = pixel4fit(2); pixel4fitcalc(2) = pixel4fit(3); } if ( (checkmin == 3) || (checkmin == 4) ) { flipwinkelcalc(0) = flipwinkel(2); flipwinkelcalc(1) = flipwinkel(3); flipwinkelcalc(2) = flipwinkel(4); pixel4fitcalc(0) = pixel4fit(2); pixel4fitcalc(1) = pixel4fit(3); pixel4fitcalc(2) = pixel4fit(4); } linf.fit(pixel4fitcalc,ysigmacalc,flipwinkelcalc); float error_ppp = linf.m.err; float m_ppp = linf.m.val; float c_ppp = linf.c.val; pixel4fitcalc(2) = -pixel4fitcalc(2); linf.fit(pixel4fitcalc,ysigmacalc,flipwinkelcalc); float error_ppm = linf.m.err; float m_ppm = linf.m.val; float c_ppm = linf.c.val; pixel4fitcalc(1) = -pixel4fitcalc(1); linf.fit(pixel4fitcalc,ysigmacalc,flipwinkelcalc); float error_pmm = linf.m.err; float m_pmm = linf.m.val; float c_pmm = linf.c.val; float B1; if ( error_ppp < error_ppm && error_ppp < error_pmm ) { B1 = fabs(secureDivision(m_ppp*180.0,c_ppp)); } else if ( error_ppm < error_pmm ) { B1 = fabs(secureDivision(m_ppm*180.0,c_ppm)); } else { B1 = fabs(secureDivision(m_pmm*180.0,c_pmm)); } if ( B1 > 1.8 ) { B1 = 0; } check_range(B1, 0.4, 1.6); outdata(iphase3d,iphase,iread)=B1; } } } } return execute_next_step(rd,controller); } odin-1.8.5/odinreco/reader_custom.h0000644000175000017500000000453411322062351014207 00000000000000/*************************************************************************** reader_custom.h - description ------------------- begin : Thu Oct 18 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOREADERCUSTOM_H #define RECOREADERCUSTOM_H #include "reader.h" /** * @addtogroup odinreco * @{ */ /** * Raw-data reader template to implement custom readers. */ class RecoReaderCustom : public virtual RecoReaderInterface { public: RecoReaderCustom(JcampDxBlock&) {} private: // Implementing virtual functions of RecoReaderInterface bool init(const STD_string& input_filename); bool fetch(RecoCoord& coord, ComplexData<1>& adc); const STD_vector& get_coords() const {return coord_vec_cache;} dvector dim_values(recoDim dim) const; const TinyVector& reloffset() const {return reloffset_cache;} STD_string image_proc() const {return "";} const TinyVector& image_size() const {return size_cache;} const Protocol& protocol() const {return prot_cache;} STD_string seqrecipe() const {return "";} // Let controller generate recipe automatically STD_string postProc3D() const {return "";} STD_string preProc3D() const {return "";} STD_string cmdline_opts() const; // Cached values TinyVector reloffset_cache; TinyVector size_cache; Protocol prot_cache; ComplexData<2> rawdata; // synthetic raw data mutable STD_vector coord_vec_cache; // Vector to hold reco coordinates (indices) unsigned int count; // counter for ADCs }; /** @} */ #endif odin-1.8.5/odinreco/conjphase.cpp0000644000175000017500000000660311322062351013657 00000000000000#include "conjphase.h" #include "data.h" #include "controller.h" bool RecoConjPhaseFT::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); ComplexData<1>& indata=rd.data(Rank<1>()); ComplexData<3>& outdata=rd.data(Rank<3>()); int nsample=indata.size(); int ncycle=rd.coord().numof(cycle); ODINLOG(odinlog,normalDebug) << "nsample/ncycle=" << nsample << "/" << ncycle << STD_endl; TinyVector outsize=controller.image_size(); outdata.resize(outsize); outdata=STD_complex(0.0); ODINLOG(odinlog,normalDebug) << "outsize=" << outsize << STD_endl; // local fast cache of trajectories and weight TinyVector ktraj[nsample]; float kweight[nsample]; trajmutex.lock(); const KspaceTraj* traj=rd.coord().kspaceTraj; // access is protected by mutex if(!traj) { ODINLOG(odinlog,errorLog) << "Trajectory missing" << STD_endl; trajmutex.unlock(); return false; } int nseg=traj->extent(0); int npts=traj->extent(1); if(nseg!=ncycle) { ODINLOG(odinlog,errorLog) << "Size mismatch: nseg(" << nseg << ")!=ncycle(" << ncycle << ")" << STD_endl; trajmutex.unlock(); return false; } if(npts!=nsample) { ODINLOG(odinlog,errorLog) << "Size mismatch: npts(" << npts << ")!=nsample(" << nsample << ")" << STD_endl; trajmutex.unlock(); return false; } int icycle=rd.coord().index[cycle]; for(int isample=0; isample& gp=(*traj)(icycle,isample); ktraj[isample]=gp.coord; kweight[isample]=gp.weight; } trajmutex.unlock(); // local fast cache of indata STD_complex signal[nsample]; for(int isample=0; isample fieldmap; bool has_fieldmap=false; if(controller.data_announced(posted_fmap_str)) { RecoCoord fmapcoord=rd.coord(); RecoFieldMapUser::modify4fieldmap(fmapcoord); if(!get_fmap(fieldmap, outsize, fmapcoord, controller)) return false; has_fieldmap=true; } double dt=rd.coord().dwellTime; ODINLOG(odinlog,normalDebug) << "dt=" << dt << STD_endl; Protocol prot(controller.protocol()); // get FOV TinyVector fov; fov(0)=0.0; //prot.geometry.get_FOV(sliceDirection); only 2D FT yet fov(1)=prot.geometry.get_FOV(phaseDirection); fov(2)=prot.geometry.get_FOV(readDirection); ODINLOG(odinlog,normalDebug) << "fov=" << fov << STD_endl; TinyVector extent; extent=outsize; ODINLOG(odinlog,normalDebug) << "extent=" << extent << STD_endl; TinyVector reloffset=controller.reloffset(); for(int i=0; i index=outdata.create_index(i); bool reconstruct_voxel=true; float deltaOmega_dt=0.0; if(has_fieldmap) { deltaOmega_dt=dt*fieldmap(index); if(!deltaOmega_dt) reconstruct_voxel=false; } TinyVector spatcoord= fov * (index/extent - 0.5 + reloffset); STD_complex voxel(0.0); if(reconstruct_voxel) { for(int isample=0; isample; template class RecoGrid<2>; template class RecoDeapodize<1>; template class RecoDeapodize<2>; odin-1.8.5/odinreco/offset.h0000644000175000017500000000313211322062351012632 00000000000000/*************************************************************************** offset.h - description ------------------- begin : Wed Feb 7 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOOFFSET_H #define RECOOFFSET_H #include "step.h" class RecoOffset : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "offset";} STD_string description() const {return "Create phase gradient in k-space so that image is shifted after FFT";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoOffset;} void init() {} }; #endif odin-1.8.5/odinreco/dti.cpp0000644000175000017500000000131711322062351012462 00000000000000#include "dti.h" #include "controller.h" bool RecoDTI::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Protocol prot(controller.protocol()); // Local copy of protocol, used for override_protocol rd.override_protocol=&prot; STD_string series; int number; prot.study.get_Series(series, number); int idti=rd.coord().index[dti]; dvector bvals=controller.dim_values(dti); JDXtriple bvector(bvals[3*idti], bvals[3*idti+1], bvals[3*idti+2], "Diffusion_bVector"); bvector*=1000.0; // in s/mm^2 prot.study.set_Series("b"+replaceStr(bvector.printbody()," ","_"),number); prot.methpars.append_copy(bvector); return execute_next_step(rd,controller); } odin-1.8.5/odinreco/switch.h0000644000175000017500000000440711322062351012653 00000000000000/*************************************************************************** switch.h - description ------------------- begin : Mon Jan 22 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSWITCH_H #define RECOSWITCH_H #include "step.h" class RecoSwitch : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "switch";} STD_string description() const {return "Branch off different flows through reconstruction pipeline";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::any();} void modify_coord(RecoCoord& coord) const {} // irrelevant since pipeline ends here RecoStep* allocate() const {return new RecoSwitch;} bool pipeline_init(const RecoController& controller, const RecoCoord& input_coord); bool query(RecoQueryContext& context); void init(); JDXstring brancharg; struct BranchKey { // BranchKey(recoDim branchdim, unsigned int branchindex) : dim(branchdim), val(branchindex) {} // does not work with GCC 3.5 recoDim dim; unsigned short val; bool operator < (const BranchKey& bs) const { if(dim!=bs.dim) return (dim BranchMap; BranchMap branches; STD_list unconditional; }; #endif odin-1.8.5/odinreco/oversampling.cpp0000644000175000017500000000200111322062351014377 00000000000000#include "oversampling.h" #include "data.h" bool RecoOversampling::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); float os_factor=rd.coord().overSamplingFactor; if(os_factor>1.0) { Range all=Range::all(); ComplexData<3>& indata=rd.data(Rank<3>()); TinyVector inshape=indata.shape(); TinyVector outshape=inshape; int insize=inshape(2); int outsize=int(float(insize)/os_factor+0.5); outshape(2)=outsize; int offset=insize/2-outsize/2; // Make zero-frequency column is zero-frequency column after cropping ODINLOG(odinlog,normalDebug) << "insize/outsize/offset=" << insize << "/" << outsize << "/" << offset << STD_endl; ComplexData<3> outdata(outshape); outdata(all,all,all)=indata(all,all,Range( offset, offset+outsize-1 )); rd.data(Rank<3>()).reference(outdata); } rd.coord().overSamplingFactor=1.0; // inidicate that oversampling has been removed return execute_next_step(rd,controller); } odin-1.8.5/odinreco/channel.h0000644000175000017500000000330511665172216012772 00000000000000/*************************************************************************** channel.h - description ------------------- begin : Sat Dec 30 2006 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOCHANNEL_H #define RECOCHANNEL_H #include "step.h" class RecoChannelSum : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "chansum";} STD_string description() const {return "Combine images from different channels";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,channel,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single, channel);} // reduce all channles to one RecoStep* allocate() const {return new RecoChannelSum;} void init(); JDXbool phasecomb; JDXfloat magnexp; }; #endif odin-1.8.5/odinreco/homodyne.cpp0000644000175000017500000000032511455553545013543 00000000000000#include "homodyne.h" #include "homodyne_code.h" // Instantiations used in step.cpp template class RecoHomodyne; template class RecoHomodyne; template class RecoHomodyne; odin-1.8.5/odinreco/slidingwindow.h0000644000175000017500000000305111322062351014225 00000000000000/*************************************************************************** slidingwindow.h - description ------------------- begin : Tue Sep 8 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSLIDINGWINDOW_H #define RECOSLIDINGWINDOW_H #include "step.h" class RecoSlidingWindow : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "slidingwindow";} STD_string description() const {return "Generate sliding window data";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::any();} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoSlidingWindow;} void init() {} }; #endif odin-1.8.5/odinreco/sum_code.h0000644000175000017500000000434311322062351013147 00000000000000#include "sum.h" #include "data.h" template bool RecoSum::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); // create new view of input data ComplexData& indata=rd.data(Rank()); TinyVector inshape(indata.shape()); TinyVector sumshape; for(int i=0; i outshape; for(int i=0; i outshape_padded=1; for(unsigned int i=0; i lowin=0; TinyVector uppin=outshape_padded-1; TinyVector lowout=0; TinyVector uppout=outshape_padded-1; // output domain, the same for each dataset RectDomain outdomain(lowout,uppout); ComplexData outdata_padded(outshape_padded); outdata_padded=STD_complex(0.0); for(int isum=0; isum sumindex=index2extent(sumshape, isum); // set input inidices for(unsigned int i=0; i indomain(lowin,uppin); if(Magn) outdata_padded(outdomain)+=float2real(cabs(indata(indomain))); else outdata_padded(outdomain)+=indata(indomain); } ComplexData outdata(outshape); outdata_padded.convert_to(outdata); // bring to output shape rd.data(Rank()).reference(outdata); ODINLOG(odinlog,normalDebug) << " outshape=" << outshape << STD_endl; modify_coord(rd.coord()); if(Magn) rd.mode=RecoData::real_data; if(!execute_next_step(rd,controller)) return false; return true; } odin-1.8.5/odinreco/zerofill.h0000644000175000017500000000322511322062351013175 00000000000000/*************************************************************************** zerofill.h - description ------------------- begin : Wed Oct 10 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOZEROFILL_H #define RECOZEROFILL_H #include "step.h" class RecoZeroFill : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "zerofill";} STD_string description() const {return "Fill k-space with zeroes to match matrix size of protocol";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoZeroFill;} void init(); JDXint minread; JDXint minphase; JDXint minslice; }; #endif odin-1.8.5/odinreco/grappa_code.h0000644000175000017500000005105411455553545013637 00000000000000#include "grappa.h" #include "data.h" #include "controller.h" #include STD_string grappa_postlabel(recoDim dim) { return STD_string("grappaweights_")+recoDimLabel[dim]; } /////////////////////////////////////////////////////// ivector next_neighbours_offset(unsigned int reductionFactor, int numof_neighb, int ired) { Log odinlog("","next_neighbours_offset"); ivector result(numof_neighb); int negfirst=(ired<(reductionFactor/2)); // determine initial direction for(int i=0; i void RecoGrappaWeights::init() { reduction_factor=0; reduction_factor.set_description("Reduction factor"); append_arg(reduction_factor,"reduction_factor"); neighbours_read=5; neighbours_read.set_cmdline_option("gr").set_description("Number of neigbours in read direction used for GRAPPA interpolation"); append_arg(neighbours_read,"neighbours_read"); neighbours_phase=2; neighbours_phase.set_cmdline_option("gp").set_description("Number of neigbouring measured k-space lines used for GRAPPA interpolation"); append_arg(neighbours_phase,"neighbours_phase"); svd_trunc=0.001; svd_trunc.set_cmdline_option("gs").set_description("Truncation value of SVD (i.e. regularization) when calculating GRAPPA weights"); append_arg(svd_trunc,"svd_trunc"); discard_level=0.01; discard_level.set_cmdline_option("gd").set_description("Fraction of k-psace points to discard in auto-calibration lines because of high residuals"); append_arg(discard_level,"discard_level"); } /////////////////////////////////////////////////////// template bool RecoGrappaWeights::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); RecoCoord coordcopy(rd.coord()); // local copy to modify coord according to ignored dims Ignore::modify(RecoIndex::ignore, coordcopy); RecoData rdweights(coordcopy); if(!calc_weights(rdweights.data(Rank<5>()), coordcopy, rd.data(Rank<4>()))) return false; controller.post_data(grappa_postlabel(interpolDim), rdweights); ODINLOG(odinlog,normalDebug) << "Posted rdweights=" << rdweights.coord().print() << STD_endl; return execute_next_step(rd,controller); } /////////////////////////////////////////////////////// template bool RecoGrappaWeights::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { context.controller.announce_data(grappa_postlabel(interpolDim)); RecoCoord coordcopy(context.coord); Ignore::modify(RecoIndex::ignore, coordcopy); if(!measlines.init(coordcopy, context.controller)) return false; } return RecoStep::query(context); } /////////////////////////////////////////////////////// template bool RecoGrappaWeights::calc_weights(ComplexData<5>& weights, const RecoCoord& trainingcoord, const ComplexData<4>& trainingdata) { Log odinlog(c_label(),"calc_weights"); Range all=Range::all(); ODINLOG(odinlog,normalDebug) << "neighbours_read/neighbours_phase=" << neighbours_read << "/" << neighbours_phase << STD_endl; TinyVector inshape=trainingdata.shape(); int nChannels=inshape(0); int sizeOrtho=inshape(1+orthoIndex); int sizeInterpol=inshape(1+interpolIndex); int sizeRead=inshape(3); ODINLOG(odinlog,normalDebug) << "nChannels/sizeOrtho/sizeInterpol/sizeRead/reduction_factor=" << nChannels << "/" << sizeOrtho << "/" << sizeInterpol << "/" << sizeRead << "/" << reduction_factor << STD_endl; // Shape for 3D volumes TinyVector shape3d(inshape(1),inshape(2),inshape(3)); // shape to calculate index vector within interpolation net TinyVector netshape(nChannels, neighbours_phase, neighbours_read); int ncols=product(netshape); // Size of the interpolation net ComplexData<1> weights_net_vec(ncols); // Interpolation net around a particular root node weights.resize(nChannels, reduction_factor-1, nChannels, neighbours_phase, neighbours_read); // the result weights=STD_complex(0.0); for(int ired=0; ired<(reduction_factor-1); ired++) { // loop over (R-1) missing lines // Mask for the root nodes available to calculate the weights Data acl_mask(inshape); acl_mask=0; RecoCoord aclcoord(trainingcoord); for(int iortho=0; iorthonrows) { ODINLOG(odinlog,errorLog) << "Not enough auto-calibration data for " << netshape << " interpolation net" << STD_endl; return false; } // fill acl_signal_vec with signal values from ACLs ComplexData<1> acl_signal_vec(nrows); // Will hold root node data of a particular channel Array,1> maskindex(nrows); // cache for coordinates of signal values contributing to SVD int irow=0; for(int i=0; i rowindex=index2extent(acl_signal_shape, i); TinyVector aclindex(ichan_dst, rowindex(0), rowindex(1), rowindex(2)); if(acl_mask(aclindex)) { maskindex(irow)=rowindex; STD_complex aclval=trainingdata(aclindex); if(cabs(aclval)==0.0) { ODINLOG(odinlog,warningLog) << "Zero acl at " << aclindex << STD_endl; } acl_signal_vec(irow)=aclval; irow++; } } // fill Matrix for SVD ComplexData<2> Matrix(nrows,ncols); for(int irow=0; irow aclindex=maskindex(irow); for(int icol=0; icol windex=index2extent(netshape,icol); int ichan_src=windex(0); int ipoloffset=neighboffset[windex(1)]; int readoffset=windex(2)-neighbours_read/2; // symmetrical about root node TinyVector trainingindex; trainingindex(0)=ichan_src; trainingindex(1)=aclindex(0); trainingindex(2)=aclindex(1); trainingindex(3)=aclindex(2)+readoffset; trainingindex(1+interpolIndex)+=ipoloffset; // take neighbour in interpolation direction STD_complex trainingval=trainingdata(trainingindex); if(cabs(trainingval)==0.0) { ODINLOG(odinlog,warningLog) << "Zero trainingdata at " << trainingindex << STD_endl; } Matrix(irow,icol)=trainingval; } } // solve system of linear equations using complex SVD weights_net_vec=solve_linear(Matrix, acl_signal_vec, svd_trunc); // Use residuals to eliminate noisy ACLs (Huo et al., JMRI 2008, 27:1412) if(discard_level>0.0) { Data residuals(cabs(matrix_product(Matrix, weights_net_vec)-acl_signal_vec)); int ndiscard=int(discard_level*nrows+0.5); if(ncols>(nrows-ndiscard)) { ODINLOG(odinlog,warningLog) << "Limiting ndiscard to " << ndiscard << " for sufficient auto-calibration data" << STD_endl; ndiscard=nrows-ncols; } for(int i=0; i windex=index2extent(netshape,icol); weights(ichan_dst, ired, windex(0), windex(1), windex(2))=weights_net_vec(icol); } } // end loop over channels } // end loop over reduction inidices ODINLOG(odinlog,normalDebug) << "cabs(sum(weights" << trainingcoord.print() << "))=" << cabs(sum(weights)) << STD_endl; return true; } /////////////////////////////////////////////////////// template ivector RecoGrappaWeights::acl_lines(const RecoCoord& coord, int numof_neighb, int ired) const { Log odinlog(c_label(),"acl_lines"); ivector neighboffset=next_neighbours_offset(reduction_factor, numof_neighb, ired); ODINLOG(odinlog,normalDebug) << "neighboffset=" << neighboffset.printbody() << STD_endl; ivector indexvec=measlines.get_indices(coord); ODINLOG(odinlog,normalDebug) << "indexvec(" << coord.print() << ")=" << indexvec.printbody() << STD_endl; STD_list indexlist; for(unsigned int i=0; i void RecoGrappa::init() { reduction_factor=0; reduction_factor.set_description("Reduction factor"); append_arg(reduction_factor,"reduction_factor"); keep_shape=false; keep_shape.set_description("Do not correct shape of interpolated k-space according to image space size"); append_arg(keep_shape,"keep_shape"); } template bool RecoGrappa::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); if(!controller.data_announced(grappa_postlabel(interpolDim))) { ODINLOG(odinlog,errorLog) << "GRAPPA weights not available" << STD_endl; return false; } ODINLOG(odinlog,normalDebug) << "reduction_factor=" << reduction_factor << STD_endl; if(!keep_shape) { if(!correct_shape(rd, controller)) return false; // adjust shape to account for incomplete sampling at end of k-space } ODINLOG(odinlog,normalDebug) << "Requesting weights for " << rd.coord().print() << STD_endl; RecoData rdweights(rd.coord()); if(!controller.inquire_data(grappa_postlabel(interpolDim), rdweights)) return false; ODINLOG(odinlog,normalDebug) << "Retrieved weights with " << rdweights.coord().print() << STD_endl; const ComplexData<5>& weights=rdweights.data(Rank<5>()); ODINLOG(odinlog,normalDebug) << "cabs(sum(weights(" << rdweights.coord().print() << ")))=" << cabs(sum(weights)) << STD_endl; ComplexData<4>& kspace=rd.data(Rank<4>()); TinyVector kspaceshape=kspace.shape(); int nChannels=kspaceshape(0); int sizeOrtho=kspaceshape(1+orthoIndex); int sizeInterpol=kspaceshape(1+interpolIndex); int sizeRead=kspaceshape(3); ODINLOG(odinlog,normalDebug) << "nChannels/sizeOrtho/sizeInterpol/sizeRead/reduction_factor=" << nChannels << "/" << sizeOrtho << "/" << sizeInterpol << "/" << sizeRead << "/" << reduction_factor << STD_endl; int neighbours_phase=weights.extent(3); int neighbours_read=weights.extent(4); ODINLOG(odinlog,normalDebug) << "neighbours_phase/neighbours_read=" << neighbours_phase << "/" << neighbours_read << STD_endl; CoordCountMap interpolated_coords; if(rd.interpolated) { measlines.update(*(rd.interpolated)); // take previously interpolated coords into account interpolated_coords=(*(rd.interpolated)); // merge previously interpolated coords } // shape to calculate index vector within interpolation net TinyVector netshape(nChannels, neighbours_phase, neighbours_read); // separate array for interpolated values to avoid recursive summation ComplexData<4> kspace_interpol(kspaceshape); kspace_interpol=STD_complex(0.0); for(int iortho=0; iortho kspaceindex; kspaceindex(0)=ichan; kspaceindex(1+orthoIndex)=iortho; kspaceindex(1+interpolIndex)=ipol; kspaceindex(3)=iread; STD_complex interpolval(0.0); // iterate over 3D interpolation net to accumulate signal value at root node for(int i=0; i netindex=index2extent(netshape,i); // index within net int jchan=netindex(0); int jphase=netindex(1); int jread=netindex(2); int offset_ipol=neighboffset[jphase]; int offset_read=jread-neighbours_read/2; // symmetrical about root node int src_ipol =ipol+offset_ipol; int src_iread =iread+offset_read; if(src_ipol>=0 && src_ipol=0 && src_iread srcindex; srcindex(0)=jchan; srcindex(1+orthoIndex)=iortho; // Use only src points from the same partition in orthogonal direction srcindex(1+interpolIndex)=src_ipol; srcindex(3)=src_iread; STD_complex srcval=kspace(srcindex); if(cabs(srcval)==0.0) { ODINLOG(odinlog,warningLog) << "Zero srcval at " << srcindex << " while interpolating " << kspaceindex << STD_endl; } interpolval += srcval * weights(ichan,ired,jchan,jphase,jread); // linear interpolation of kspace } } kspace_interpol(kspaceindex)=interpolval; } } } } } } } kspace=kspace+kspace_interpol; rd.interpolated=&interpolated_coords; // Inform subsequent steps about the interpolated coordinates return execute_next_step(rd,controller); } /////////////////////////////////////////////////////// template bool RecoGrappa::correct_shape(RecoData& rdkspace, const RecoController& controller) const { Log odinlog(c_label(),"correct_shape"); Range all=Range::all(); ComplexData<4>& inkspace=rdkspace.data(Rank<4>()); TinyVector inshape=inkspace.shape(); int nlines_dst=controller.image_size()(interpolIndex); int nlines_src=inshape(1+interpolIndex); if(nlines_dst==nlines_src) return true; if(nlines_dst outshape(inshape); outshape(1+interpolIndex)=nlines_dst; ODINLOG(odinlog,normalDebug) << "inshape/outshape=" << inshape << "/" << outshape << STD_endl; ComplexData<4> outkspace(outshape); outkspace=STD_complex(0.0); Range srcrange(0,nlines_src-1); if(interpolDim==line) outkspace(all,all,srcrange,all)=inkspace(all,all,srcrange,all); if(interpolDim==line3d) outkspace(all,srcrange,all,all)=inkspace(all,srcrange,all,all); rdkspace.data(Rank<4>()).reference(outkspace); return true; } /////////////////////////////////////////////////////// template bool RecoGrappa::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { if(!measlines.init(context.coord, context.controller)) return false; } return RecoStep::query(context); } /////////////////////////////////////////////////////// template int RecoGrappa::reduction_index(const ivector& indexvec, int sizePhase, int iphase) const { Log odinlog(c_label(),"reduction_index"); ODINLOG(odinlog,normalDebug) << "reduction_factor/sizePhase/iphase=" << reduction_factor << "/" << sizePhase << "/" << iphase << STD_endl; int posnext=-1; int negnext=-1; // search for next scanned line in positive direction for(int i=iphase; i=0; i--) { if(measured_line(indexvec, i)) { negnext=iphase-i; break; } } ODINLOG(odinlog,normalDebug) << "posnext/negnext(" << iphase << ")=" << posnext << "/" << negnext << STD_endl; if(posnext<0 || negnext<0) return -1; // Measured line is missing in one or more directions -> Line is not surrounded by measured lines return negnext-1; } odin-1.8.5/odinreco/homodyne.h0000644000175000017500000000406411455553545013214 00000000000000/*************************************************************************** homodyne.h - description ------------------- begin : Mon Apr 2 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOHOMODYNE_H #define RECOHOMODYNE_H #include "step.h" #include "measindex.h" template class RecoHomodyne : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const { STD_string result="homodyne"; if(interpolDim==line3d) result+="3d"; if(interpolDim==readout) result+="read"; return result; } STD_string description() const {return "Homodyne reconstruction of partial Fourier data in dimension '"+STD_string(recoDimLabel[interpolDim])+"'";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoHomodyne;} void init() {} // Phase-encoding lines actually measured RecoMeasIndex > measlines; }; #endif odin-1.8.5/odinreco/slicetime.cpp0000644000175000017500000000267711322062351013672 00000000000000#include "slicetime.h" #include "data.h" #include "controller.h" bool RecoSliceTime::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); dvector sliceorder=controller.dim_values(slice); ODINLOG(odinlog,normalDebug) << "sliceorder=" << sliceorder.printbody() << STD_endl; ComplexData<5>& indata=rd.data(Rank<5>()); TinyVector inshape=indata.shape(); int nrep=inshape(0); int nslices=inshape(1); if(nrep>1 && nslices>1) { dvector sliceshift(nslices); sliceshift=0.0; if(nslices==int(sliceorder.size())) { for(int islice=0; islice" << STD_endl; STD_cout << "Options:" << STD_endl; STD_cout << opts.get_cmdline_usage("\t"); STD_cout << "\t" << LogBase::get_usage() << STD_endl; STD_cout << "\t" << helpUsage() << STD_endl; } int main(int argc,char* argv[]) { if(LogBase::set_log_levels(argc,argv)) return 0; Log odinlog("","main"); JcampDxBlock opts; RecoController controller(opts); RecoReaderOdin reader_odin(opts); RecoReaderCustom reader_custom(opts); #ifdef IDEA_PLUGIN RecoReaderTwix reader_twix(opts); #endif if(isCommandlineOption(argc,argv,"-manual")){ STD_cout << controller.stepmanual() << STD_endl; return 0; } if(hasHelpOption(argc,argv)) {usage(opts);return 0;} // Select reader by autodetection RecoReaderInterface* reader=0; char optval[ODIN_MAXCHAR]; JDXfileName input_filename=STD_string("./recoInfo"); // default is odin data if(getCommandlineOption(argc,argv,"-r",optval,ODIN_MAXCHAR)) input_filename=optval; if(input_filename.get_basename()=="recoInfo") reader=&reader_odin; if(input_filename.get_suffix()=="smp") reader=&reader_custom; #ifdef IDEA_PLUGIN if(input_filename.get_suffix()=="dat") reader=&reader_twix; #endif if(!reader) { ODINLOG(odinlog,errorLog) << "Unable to initialize reader for input file " << input_filename << STD_endl; return -1; } opts.parse_cmdline_options(argc,argv,false); // Parse reader options if(!reader->init(input_filename)) return -1; if(!controller.init(reader,opts,argc,argv)) return -1; if(!controller.start()) return -1; Profiler::dump_final_result(); return 0; } odin-1.8.5/odinreco/fft.cpp0000644000175000017500000000056111322062351012461 00000000000000#include "fft.h" #include "data.h" void RecoFFT::init() { forward=true; forward.set_description("Forward (true) or backward (false) FFT"); append_arg(forward,"forward"); } bool RecoFFT::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); rd.data(Rank<3>()).fft(forward); return execute_next_step(rd,controller); } odin-1.8.5/odinreco/offset.cpp0000644000175000017500000000166611455553545013220 00000000000000#include "offset.h" #include "controller.h" #include "data.h" bool RecoOffset::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<3>& data=rd.data(Rank<3>()); float os_factor=rd.coord().overSamplingFactor; // should be set to 1.0 by prior functors if oversampling has already been removed float grid_factor=rd.coord().gridScaleFactor; // spatial shifting TinyVector reloffset=controller.reloffset(); reloffset(2)/=os_factor * grid_factor; reloffset(1)/=grid_factor; bool do_shift=false; if(max(abs(reloffset))>0.0) do_shift=true; if(do_shift) { // data.fft(false); // backward FFT ODINLOG(odinlog,normalDebug) << "shifting with reloffset=" << reloffset << STD_endl; data.modulate_offset(reloffset); // data.fft(true); // forward FFT for correct sign of modulated offset } return execute_next_step(rd,controller); } odin-1.8.5/odinreco/filter.h0000644000175000017500000000322611322062351012635 00000000000000/*************************************************************************** filter.h - description ------------------- begin : Fri Sep 14 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOFILTER_H #define RECOFILTER_H #include "step.h" #include class RecoFilter : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "filter";} STD_string description() const {return "Lowpass filter in k-space with plateau at the center";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoFilter;} void init(); JDXfilter filter; JDXfloat plateau; }; #endif odin-1.8.5/odinreco/mip.cpp0000644000175000017500000000506711322062351012475 00000000000000#include "mip.h" #include "data.h" #include "controller.h" void RecoMip::init() { neighbors=4; neighbors.set_cmdline_option("mn").set_description("In sliding-window maximum-intensity projection, use this number of neighbors in each direction"); append_arg(neighbors,"neighbors"); } /////////////////////////////////////////////////////////////////////////// bool RecoMip::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<3>& indata=rd.data(Rank<3>()); TinyVector shape=indata.shape(); Array magn(cabs(indata)); // Sliding window maximum-intensity projection (MIP) Array mip(shape); mip=0.0; for(int iline=0; iline mipall[3]; mipall[0].resize(1,shape(0),shape(1)); mipall[1].resize(1,shape(0),shape(2)); mipall[2].resize(1,shape(1),shape(2)); for(int j=0; j()).reference(float2real(mip)); rdmip.coord().index[userdef]=1; prot.study.set_Series(series+"_mip",number); if(!execute_next_step(rdmip,controller)) return false; for(int idir=0; idir<3; idir++) { STD_string id; if(idir==0) id=recoDimLabel[readout]; if(idir==1) id=recoDimLabel[line]; if(idir==2) id=recoDimLabel[line3d]; // feed mipall into rest of pipeline RecoData rdmipall(rd); rdmipall.data(Rank<3>()).reference(float2real(mipall[idir])); rdmipall.coord().index[userdef]=2+idir; prot.study.set_Series(series+"_mip"+id,number); if(!execute_next_step(rdmipall,controller)) return false; } return true; } odin-1.8.5/odinreco/blackboard.h0000644000175000017500000000647311322062351013443 00000000000000/*************************************************************************** blackboard.h - description ------------------- begin : Mon Jan 24 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOBLACKBOARD_H #define RECOBLACKBOARD_H #include #include #include /** * @addtogroup odinreco * @{ */ /** * Manages data transfer between functors */ class RecoBlackBoard { public: /** * Constructs empty blackboard */ RecoBlackBoard() {} ~RecoBlackBoard(); /** * Announces that data with identifier 'label' will become available during pipeline execution. */ void announce(const STD_string& label) {ann[label]++;} /** * Posts 'data' with identifier 'label', it will be indexed according to the k-space coordinate in 'data'. */ void post(const STD_string& label, const RecoData& data); /** * Returns true only if data with identifier 'label' will become available during pipeline execution. */ bool announced(const STD_string& label) const {return ann.find(label)!=ann.end();} /** * Returns 'data' with identifier 'label' for k-space coordinate set in 'data'. * If 'blocking' is 'true', the function will return only if data becomes available. * Returns 'true' if data is available, otherwise returns 'false' if data not yet available. */ bool inquire(const STD_string& label, RecoData& data, bool blocking=false); private: bool get_data(const STD_string& label, RecoData& data); // The data on the blackboard typedef STD_map CoordDataMap; typedef STD_map LabelDataMap; LabelDataMap posted; // The events to signal the availability of new data typedef STD_map CoordEventMap; typedef STD_map LabelEventMap; LabelEventMap eventmap; Mutex mutex; // Mutex for both maps STD_map ann; }; /** @} */ /////////////////////////////////////////////////////////////////////////////////////////// class RecoPost : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "post";} STD_string description() const {return "Post data on blackboard";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::any();} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoPost;} void init(); JDXstring postlabel; }; #endif odin-1.8.5/odinreco/oversampling.h0000644000175000017500000000316411322062351014057 00000000000000/*************************************************************************** oversampling.h - description ------------------- begin : Thu Feb 22 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOOVERSAMPLING_H #define RECOOVERSAMPLING_H #include "step.h" class RecoOversampling : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "oversampling";} STD_string description() const {return "Remove oversampling in readout direction in image domain";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoOversampling;} void init() {} }; #endif odin-1.8.5/odinreco/expfit.cpp0000644000175000017500000000421511712547772013223 00000000000000#include "expfit.h" #include "data.h" #include "controller.h" #include /////////////////////////////////////////////////////////////////////////// void RecoExpFit::init() { invert=false; invert.set_description("Calculate inverse after exponential decay fit (for T2)"); append_arg(invert,"invert"); masklevel=0.5; masklevel.set_cmdline_option("el").set_description("Level relative to mean value of first echo for setting mask of exponential decay fit"); append_arg(masklevel,"masklevel"); } bool RecoExpFit::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); Data magn(cabs(indata)); TinyVector inshape=indata.shape(); TinyVector outshape(inshape(1), inshape(2), inshape(3)); dvector xvec=controller.dim_values(userdef); ODINLOG(odinlog,normalDebug) << "xvec=" << xvec.printbody() << STD_endl; int nx=xvec.size(); if(nx!=inshape(0)) { ODINLOG(odinlog,errorLog) << "size mismatch: nx(" << nx << ")!=" << inshape(0) << STD_endl; return false; } ComplexData<3>& outdata=rd.data(Rank<3>()); outdata.resize(outshape); outdata=STD_complex(0.0); float noiselevel=masklevel*mean(magn(0,all,all,all)); LinearFunction linf; Data echomagn(nx); Data echolog(nx); Data ysigma(nx); Data xvals(nx); for(int i=0; inoiselevel) { echomagn=magn(all,iphase3d,iphase,iread); echolog=log(echomagn); ysigma=pow(echomagn, -1); // weight fit by magnitude if(linf.fit(echolog,ysigma,xvals)) { if(invert) { outdata(iphase3d,iphase,iread)=secureDivision( 1.0, -linf.m.val ); } else { outdata(iphase3d,iphase,iread)=-linf.m.val; } } } } } } return execute_next_step(rd,controller); } odin-1.8.5/odinreco/store.h0000644000175000017500000000612711322062351012507 00000000000000/*************************************************************************** store.h - description ------------------- begin : Sat Dec 30 2006 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSTORE_H #define RECOSTORE_H #include "step.h" #include #include class RecoStore : public RecoStep { public: static STD_string default_format(); private: // implementing virtual functions of RecoStep STD_string label() const {return "store";} STD_string description() const {return "Store reconstructed images";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,repetition,slice,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoStore;} void init(); JDXstring extension; JDXstring prefix; JDXstring formats; JDXstring imageproc; JDXbool storephase; FileWriteOpts wopts; // for access to some autowrite opts bool store_images(const RecoController& controller); FileIO::ProtocolDataMap pdmap; // Will hold image data with protocol as key Mutex mutex; FilterChain filterchain; }; //////////////////////////////////////////////////////////////////////////// class RecoReal : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "real";} STD_string description() const {return "Throw away imaginary part of data and keep only real part";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::any();} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoReal;} void init() {} }; class RecoMagn : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "magn";} STD_string description() const {return "Only take magnitude and set phase to zero";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoMagn;} void init() {} }; #endif odin-1.8.5/odinreco/sum.cpp0000644000175000017500000000066111322062351012507 00000000000000#include "sum.h" #include "sum_code.h" // Instantiations used in step.cpp template class RecoSum<1, RecoDim<1, readout>, 1, RecoDim<1, average> >; template class RecoSum<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, cycle> >; template class RecoSum<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition> >; template class RecoSum<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition>, true >; odin-1.8.5/odinreco/odinreco.10000644000175000017500000001564611734623240013103 00000000000000.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. .TH ODINRECO "1" "March 2012" "odinreco 1.8.5" "User Commands" .SH NAME odinreco \- Automatic reconstruction for ODIN sequences .SH SYNOPSIS .B odinreco [ \fIoptions \fR] \fI-r \fR .SH DESCRIPTION odinreco: Automatic reconstruction for ODIN sequences .PP odinreco provides a generic reconstruction for imaging sequences (spin\-warp, EPI, RARE, ...). It retrieves the information about the acquired signal from the file 'recoInfo' which is stored on disk together with the raw data. The recoInfo file contains information about the k\-space position of each acquisition windows (ADC). As output, odinreco generates a bunch of files with different image formats (depending on the option \fB\-f\fR and third\-party libraries available to ODIN). The filename of each file starts with the given output prefix. .SH OPTIONS .HP \fB\-bcw\fR: Correlation weighting of all blades against the mean of all blades (in image space) .HP \fB\-bf\fR: Filter function for blade phase correction (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=NoFilter) .HP \fB\-bfw\fR: Width of the filter function used for blade phase correction.[0.0 (0%) ... 1.0 (100%) of blade width; \fB\-1\fR.0 (100%) ... 0.0 (0%) of center width] (default=1.0) .HP \fB\-bkf\fR: Blade\-keyhole filter function (and its arguments) (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=CosSq) .HP \fB\-bkt\fR: Blade\-keyhole transition width (fraction of oversampled k\-space center) (default=0.20) .HP \fB\-bwf\fR: Window/Filter function for kspace weighting of each blade (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=Triangle) .HP \fB\-bww\fR: Window/Filter width for kspace weighting of each blade (default=1.0) .HP \fB\-cp\fR: Use direct Fourier transform with conjugate\-phase correction instead of gridding .HP \fB\-dcr\fR: Load field drift from this file .HP \fB\-dcw\fR: Calculate and store field drift to file with this prefix .HP \fB\-df\fR: Output format (file extension) of dump files (default=nii) .HP \fB\-dg\fR: Disable GRAPPA interpolation .HP \fB\-dh\fR: Disable homodyne reconstruction .HP \fB\-dm\fR: Disable fieldmap\-based multi\-frequency reconstruction .HP \fB\-dp\fR: Prefix of dump files (default=./dump) .HP \fB\-ds\fR: Disable slice\-time correction .HP \fB\-el\fR: Level relative to mean value of first echo for setting mask of exponential decay fit (default=0.50) .HP \fB\-f\fR: Space sepapared list of output formats (file extensions), possible formats are '3db asc coi dat dcm double float gz hdr idx ima jdx mag mhd nii ph png pos pro reg s16bit s32bit s8bit smp u16bit u32bit u8bit vtk ' (default=nii) .HP \fB\-ff\fR: k\-space filter function (and its arguments) (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=NoFilter) .HP \fB\-fm\fR: Load fieldmap data from this file .HP \fB\-fp\fR: Filter plateau width (0=no plateau, 1=full plateau) (default=0.0) .HP \fB\-gd\fR: Fraction of k\-psace points to discard in auto\-calibration lines because of high residuals (default=0.010) .HP \fB\-gp\fR: Number of neigbouring measured k\-space lines used for GRAPPA interpolation (default=2) .HP \fB\-gr\fR: Number of neigbours in read direction used for GRAPPA interpolation (default=5) .HP \fB\-gs\fR: Scale Factor for the grid used for gridding (default=1.0) .HP \fB\-ip\fR: Command line args for extra processing of final images (default=none) .HP \fB\-j\fR: Number of concurrent jobs(threads) in reco (default=4) .HP \fB\-kg1d\fR: Kernel function for 1d k\-space gridding (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=Gauss(0.36169)) .HP \fB\-kg2d\fR: Kernel function for 2d k\-space gridding (options=Gauss NoFilter Triangle Hann Hamming CosSq Blackman BlackmanNuttall Exp , default=Gauss(0.36169)) .HP \fB\-kh\fR: Keyhole reconstruction, e.g. for PROPELLER .HP \fB\-ks\fR: Store k\-space data .HP \fB\-kw1d\fR: Kernel width for 1d k\-space gridding [Pixel] (default=4.24264Pixel) .HP \fB\-kw2d\fR: Kernel width for 2d k\-space gridding [Pixel] (default=3.0Pixel) .HP \fB\-mf\fR: Maximum number of frequencies for multi\-frequency reconstruction (default=256) .HP \fB\-mn\fR: In sliding\-window maximum\-intensity projection, use this number of neighbors in each direction (default=4) .HP \fB\-mr\fR: Maximum recursion of reconstruction when waiting for blackboard data, zero means no recursion (default=100) .HP \fB\-o\fR: Prefix of output files (default=./image) .HP \fB\-pc\fR: Combine phase of channels using a phase correction .HP \fB\-pe\fR: Exponent for magnitude weighting when calculating combined phase of all channels (default=0.0) .HP \fB\-pf\fR: File name of FIFO (named pipe) to obtain the raw data from .HP \fB\-pop\fR: Recipe for post processing of 3D volume after channel combining (default=null) .HP \fB\-prp\fR: Recipe for post processing of 3D volume before channel combining (default=null) .HP \fB\-pt\fR: Combine and store phase timecourse from all channels .HP \fB\-pz\fR: Pad missing raw data (of interrupted measurement) with zeroes .HP \fB\-qs\fR: Quality control: Check for spikes in data .HP \fB\-rd\fR: Dump signal data and its protocol to files with this prefix, do not reconstruct images .HP \fB\-rf\fR: Read reco recipe (pipeline layout) from this file .HP \fB\-rp\fR: Reco recipe (pipeline layout) .HP \fB\-s\fR: Select certain dimensions ranges (space separated list of 'dim=selection', e.g. slice=3) .HP \fB\-sc\fR: Store images from channels separately instead of combining them .HP \fB\-sp\fR: Store phase in addition to magnitude .HP \fB\-sw\fR: Sliding window reconstruction, e.g. for Spiral/PROPELLER .HP \fB\-t1f\fR: Use this type of T1 fit, can be one of 'simple', 'magnitude' (default=simple) .HP \fB\-t1l\fR: Level relative to mean value of first echo for setting mask of T1 fit (default=0.50) .HP \fB\-t1m\fR: Upper limit for T1 fit [ms] (default=3000.0ms) .HP \fB\-to\fR: Timeout for reco in seconds, 0=inifinite (default=0) .HP \fB\-type\fR: Image representation type (options=automatic float double s32bit u32bit s16bit u16bit s8bit u8bit , default=automatic) .HP \fB\-wdialect\fR: Write data using given dialect of the format. (default is no dialect) .HP \fB\-wp\fR: Store the protocol separately to this file. .HP \fB\-zp\fR: Minimum size of final image in phase direction obtained zero filling (default=0) .HP \fB\-zr\fR: Minimum size of final image in read direction obtained zero filling (default=0) .HP \fB\-zs\fR: Minimum size of final image in slice direction obtained zero filling (default=0) .HP \fB\-v\fR or for debugging/tracing all components or a single component, respectively. Possible values for loglevel are: 0(noLog), 1(errorLog), 2(warningLog), 3(infoLog). .HP \fB\-h\fR, \fB\-\-help\fR, \fB\-help\fR, \fB\-\-version\fR : Print help text or version information odin-1.8.5/odinreco/odinreco.h0000644000175000017500000001422211455553545013171 00000000000000/*************************************************************************** odinreco.h - description ------------------- begin : Sat Dec 30 2006 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef ODINRECO_H #define ODINRECO_H #include #include /** * \page odinreco_usage Automatic image reconstruction for ODIN sequences * * For image reconstruction, execute the program 'odinreco' within the directory of the file 'recoInfo' (the scan directory), * or use the option '-r' to specify the location of 'recoInfo'. For example, the commands * \verbatim odinreco -r /path/to/raw/data/recoInfo -o /path/to/raw/data/image \endverbatim * and * \verbatim cd /path/to/raw/data/recoInfo odinreco \endverbatim * will do the same, i.e. create an image using the raw data in '/path/to/raw/data/'. * * Full description: * \verbinclude odinreco/odinreco.usage * */ /** * \page odinreco_doc ODIN image reconstruction framework (odinreco) * * This page describes the usage and design guidelines of the module \ref odinreco. * For a description how to execute the reconstruction, please refer to \ref odinreco_usage. * * \section process The reconstruction process * Here, image reconstruction refers to converting MR raw data to an image. * It is achieved by the following processing strategy: * Each single acquisition (ADC) is fed separately into the reconstruction pipeline. * The pipeline consists of a chain of steps(functors) which are executed * subsequently in order to process the input data with the reconstructed image * as the final output. * ADCs are processed simultaneously in different threads allowing acceleration * of reconstruction on multi-processor systems. * It is the responsibility of the steps to synchronize properly * if they possess global (static) data. * * * \section pipeline Setting up a reconstruction pipeline * A reconstruction pipeline is described by a string. * This string consists of single tokens representing a step * which can be any of those described in * \ref odinreco_steps. * These steps are chained together using the pipe operator (|). * Only steps with a compatible input and output interface * may be chained together. * A step may accept additional arguments enclosed in parenthesis * after the step label. * In addition, a step may have command-line options to fine-tune * its behaviour. * Please refer to the manual at (\ref odinreco_steps) for the * input/output interface, arguments and options of each step. * * As an example, a simple 2D/3D reconstruction would look like this: * \verbatim kspace | filter(Gauss) | fft | offset | slicecoll | image | store(result) \endverbatim * This would collect k-space data (kspace), apply a Gaussian filter (filter), * perform an FFT if done (fft) and shift the image (offset). * Finally, after collecting slices and repetitions (slicecoll | image), * it would store the data in files starting with the prefix 'result'. * * * \section blackboard Blackboard * Some steps need data produced by another step in another branch * of the pipeline (e.g. phasemap, fieldmap). To pass this data around, * a thread-safe blackboard system is used to post data and retrieve it later. * In particular, the 'post' step (RecoPost) can used to post data and the function * RecoController::inquire_data() can be used to retrieve this data * in another step. * * \section options Reconstruction Options * Each step can have a number of options (i.e. parameters) to customize * its behavior. For instance, the step for zero filling accepts the * zero-padded sizes of the destination grid as its arguments. * For a list of available options of each step, please refer to * \ref odinreco_steps. * Options can be set in different ways. With ascending priority, * these are: * - Command line options as set in the sequence via recoInfo->set_CmdLineOpts(...); * - Command line options a set directly on the command line. * - By a comma-separated list in parenthesis following the step * string in the recipe, e.g. "... | zerofill(1,256,256) | ..." */ /** * @addtogroup odinreco * @{ */ //////////////////////////////////////////////////////////////// // helper class used for debugging the odinreco component class Reco { public: static const char* get_compName(); }; //////////////////////////////////////////////////////////////// /** * Unsigned integer which initializes to zero */ struct UInt { UInt(unsigned int v=0) : val(v) {} UInt& operator = (unsigned int v) {val=v; return *this;} operator unsigned int () const {return val;} unsigned int operator += (unsigned int rhsval) {val+=rhsval; return *this;} unsigned int operator -= (unsigned int rhsval) {val-=rhsval; return *this;} unsigned int operator *= (unsigned int rhsval) {val*=rhsval; return *this;} unsigned int operator /= (unsigned int rhsval) {val/=rhsval; return *this;} unsigned int operator ++ () {val=val+1; return val;} // prefix unsigned int operator ++ (int) {unsigned int tmp=val; val=val+1; return tmp;} // postfix unsigned int operator -- () {val=val-1; return val;} // prefix unsigned int operator -- (int) {unsigned int tmp=val; val=val-1; return tmp;} // postfix private: unsigned int val; }; /** @} */ #endif odin-1.8.5/odinreco/reader.cpp0000644000175000017500000000002411322062351013136 00000000000000#include "reader.h" odin-1.8.5/odinreco/data.h0000644000175000017500000000744211734622163012277 00000000000000/*************************************************************************** data.h - description ------------------- begin : Sat Dec 30 2006 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECODATA_H #define RECODATA_H #include #include /** * @addtogroup odinreco * @{ */ /////////////////////////////////////////////////////// /** * Helper class to resolve function overloading */ template struct Rank {}; /////////////////////////////////////////////////////// class Profiler; // forward declaration /** * Class to hold intermediate results (multidimensional complex data) of steps in the reconstruction pipeline. */ class RecoData { public: /** * Mode of complex data: * - complex_data : Regular complex data. * - real_data : Use only real part. * - weighted_real_data : weight real part by imaginray part. */ enum dataMode {complex_data=0, real_data, weighted_real_data}; /** * Creates object with initial k-space coordinate 'coord'. */ RecoData(const RecoCoord& coord=RecoCoord()) : override_protocol(0), mode(complex_data), interpolated(0), kcoord(coord), prof(0) {} /** * Copy constructor (deep copy) */ RecoData(const RecoData& rd) : prof(0) {RecoData::operator = (rd);} /** * Destructor */ ~RecoData(); /** * Assignment operator (deep copy) */ RecoData& operator = (const RecoData& rd); /** * Copy only the meta data from 'rd' */ RecoData& copy_meta(const RecoData& rd); /** * Returns reference to current N-dimensional complex data. * The dimension is determined according to the instantiation of template 'Rank'. */ ComplexData<1>& data(Rank<1>) const {return data1;} ComplexData<2>& data(Rank<2>) const {return data2;} ComplexData<3>& data(Rank<3>) const {return data3;} ComplexData<4>& data(Rank<4>) const {return data4;} ComplexData<5>& data(Rank<5>) const {return data5;} ComplexData<6>& data(Rank<6>) const {return data6;} /** * Returns reference to the k-space coordinate. */ RecoCoord& coord() {return kcoord;} /** * Free (deallocate) data with dimension 'dim'. */ RecoData& free(int dim); /** * Returns const reference to the k-space coordinate. */ const RecoCoord& coord() const {return kcoord;} /** * Override protocol in output files if non-zero */ const Protocol* override_protocol; /** * Type of data. */ dataMode mode; /** * Coordinates interpolated during pipeline execution. */ const CoordCountMap* interpolated; /** * Initializes new profiler object which is allocated/deallocted at the entry and exit of each step * to measure the performance of the pipeline. */ void new_profiler(const STD_string& steplabel); private: RecoCoord kcoord; const Profiler* prof; mutable ComplexData<1> data1; mutable ComplexData<2> data2; mutable ComplexData<3> data3; mutable ComplexData<4> data4; mutable ComplexData<5> data5; mutable ComplexData<6> data6; }; /** @} */ #endif odin-1.8.5/odinreco/swi.cpp0000644000175000017500000001065411363773557012536 00000000000000#include "swi.h" #include "data.h" #include "controller.h" #include #include STD_vector > neighb_indices(int radius_pixels) { STD_vector > result; int n=radius_pixels; for(int k=-n; k<=n; k++) { for(int j=-n; j<=n; j++) { for(int i=-n; i<=n; i++) { float radius=sqrt(float(k*k+j*j+i*i)); if(radius<=radius_pixels && (k || j || i) ) { result.push_back(TinyVector( k, j, i)); } } } } return result; } /////////////////////////////////////////////////////////////////////// bool RecoSwi::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<3>& data=rd.data(Rank<3>()); TinyVector shape=data.shape(); Data pha(phase(data)); Data magn(cabs(data)); int pixelradius=3; // best // Create linear mask for valid pixels Data mask(magn.size()); mask=1; for(int i=0; i index=magn.create_index(i); for(int j=0; j<3; j++) { if(index(j)shape(j)-pixelradius-1) mask(i)=0; } } STD_vector > neighboffset=neighb_indices(pixelradius); int numof_neigb=neighboffset.size(); for(int j=0; j()).reference(float2real(phadiff)); prot.study.set_Series(series+"_phadiff",number); if(!execute_next_step(rdphadiff,controller)) return false; RecoData rdmed(rd); rdmed.coord().index[userdef]=3; rdmed.data(Rank<3>()).reference(float2real(med)); prot.study.set_Series(series+"_median",number); if(!execute_next_step(rdmed,controller)) return false; return true; } odin-1.8.5/odinreco/collector.h0000644000175000017500000000755111322062351013343 00000000000000/*************************************************************************** collector.h - description ------------------- begin : Sun Jan 14 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOCOLLECTOR_H #define RECOCOLLECTOR_H #include "step.h" /** * @addtogroup odinreco * @{ */ /** * Base class for all collector templates to hold code common to all collectors. */ class RecoCollectorBase : public RecoStep { protected: RecoCollectorBase() {} ~RecoCollectorBase(); /** * Removes 'coord' from the todo map, returns 'true' only if the * current set is fully collected, i.e. the todo map is emtpy. * Note: Do not lock any mutexes when calling this function. * If 'custom_count' is non-zero, it will be used instead * of the cached 'count'. */ bool completed(const RecoCoord& coord, unsigned int custom_count); /** * Calcuate the count, i.e. number inputs to be processed before executing the next step. * 'inmask' and 'outmask' are used to filter on particular indices when calculating the todo map. */ bool calculate_count(RecoQueryContext& context, const RecoCoord& inmask, const RecoCoord& outmask); private: CoordCountMap todo; // coordinate always refers to the output of functor, i.e. after applying 'modify_coord' Mutex todomutex; unsigned int count; // initialized in query/calculate_count, assumed to be the same for all coordinates STD_string label_cache; // label() might not be available in destructor }; ///////////////////////////////////////////////////////// /* * Template class to collect data in one or more dimensions. * The rank of the input data is given by 'Nin'. The particular input dimension are given * in 'In' by a specialization of 'RecoDim'. The numer of dimensions to collect data * for is given in 'Ncoll' and specified in 'Coll' by a specialization of 'RecoDim'. * The resulting data array will have the collected dimensions leftmost, i.e. * if In=i1,i2 and Coll=c1, the resulting array will have dimensions (c1,i1,i2) * If 'use_numof' is set to 'true', the numof of the collected indices will be used * for the count instead of using a count map. */ template class RecoCollector : public RecoCollectorBase, public Labeled { public: RecoCollector(const STD_string& coll_label) : Labeled(coll_label) {} private: // implementing virtual functions of RecoStep STD_string label() const {return get_label();} STD_string description() const {return "Collect data in one or more dimensions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return In::preset_coord(RecoIndex::collected);} void modify_coord(RecoCoord& coord) const {Coll::modify(RecoIndex::collected,coord);} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoCollector(get_label());} void init() {} typedef STD_map > DataMap; DataMap datamap; // the data collected Mutex mutex; }; /** @} */ #endif odin-1.8.5/odinreco/dump.h0000644000175000017500000000305311322062351012313 00000000000000/*************************************************************************** dump.h - description ------------------- begin : Mon Oct 13 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECODUMP_H #define RECODUMP_H #include "step.h" class RecoDump : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "dump";} STD_string description() const {return "Dump current data in reconstruction pipeline";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::any();} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoDump;} void init(); JDXstring prefix; JDXstring format; }; #endif odin-1.8.5/odinreco/fmri.h0000644000175000017500000000322411322062351012303 00000000000000/*************************************************************************** fmri.h - description ------------------- begin : Thu Apr 30 2009 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOFMRI_H #define RECOFMRI_H #include "step.h" class RecoFMRI : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "fmri";} STD_string description() const {return "Simple fMRI analysis for fMRI localizer";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected, repetition, line3d, line, readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single,repetition);} RecoStep* allocate() const {return new RecoFMRI;} void init(); JDXint stimsize; JDXint restsize; }; #endif odin-1.8.5/odinreco/Makefile.am0000644000175000017500000000675211725203123013243 00000000000000if ONLY_LIBS else INCLUDES = $(all_includes) bin_PROGRAMS = odinreco odinreco_SOURCES = \ odinreco.h odinreco.cpp \ adc.h adc.cpp \ b1fit.h b1fit.cpp \ blade.h blade.cpp \ bladegrid.h bladegrid.cpp \ blackboard.h blackboard.cpp \ channel.h channel.cpp \ circmask.h circmask.cpp \ collector.h collector_code.h collector.cpp \ conjphase.h conjphase.cpp \ controller.h controller.cpp \ data.h data.cpp \ dump.h dump.cpp \ driftcorr.h driftcorr.cpp \ dti.h dti.cpp \ epinavcorr.h epinavcorr.cpp \ expfit.h expfit.cpp \ fieldmap.h fieldmap.cpp \ filter.h filter.cpp \ fft.h fft.cpp \ fmri.h fmri.cpp \ grappa.h grappa_code.h grappa.cpp \ grid.h grid_code.h grid.cpp \ homodyne.h homodyne_code.h homodyne.cpp \ index.h index.cpp \ messer.h messer.cpp \ measindex.h measindex.cpp \ mip.h mip.cpp \ multifreq.h multifreq.cpp \ offset.h offset.cpp \ oversampling.h oversampling.cpp \ phasecorr.h phasecorr.cpp \ phasecourse.h phasecourse.cpp \ qualitycontrol.h qualitycontrol.cpp \ pilot.h pilot.cpp \ reader.h reader.cpp \ reader_odin.h reader_odin.cpp \ reader_custom.h reader_custom.cpp \ refgain.h refgain.cpp \ slicetime.h slicetime.cpp \ slidingwindow.h slidingwindow.cpp \ splitter.h splitter_code.h splitter.cpp \ step.h step.cpp \ store.h store.cpp \ swi.h swi.cpp \ sum.h sum_code.h sum.cpp \ switch.h switch.cpp \ t1fit.h t1fit.cpp \ zerofill.h zerofill.cpp \ main.cpp odinreco_LDADD = ../odindata/libodindata.la ../odinpara/libodinpara.la ../tjutils/libtjutils.la # Auto-generate manual pages, only if not in srcdir %.1: % if test ! -f $(srcdir)/$@ ; then $(HELP2MAN) --name="$$(./$< --help | grep $<: | sed s/'$<: '//)" ./$< > $@ ; fi # Manual pages for distribution dist_man_MANS = odinreco.1 testdata: rm -rf recotestdata if test ! -f recotestdata.tar.gz ; then wget http://downloads.sourceforge.net/od1n/recotestdata.tar.gz ; fi tar -xvzf recotestdata.tar.gz committest: testdata rm -rf recotestdata/*/test* for dir in recotestdata/*; do \ ./odinreco -f jdx -r $$dir/recoInfo -o $$dir/image; \ done rm -f recotestdata/*/image*.v rm -f recotestdata/*/image*.float rm -rf recotestdata/*/image_* rm -f recotestdata/*/diff* rm -f recotestdata/*/*.sum rm -f recotestdata/*/comp tar -cvzf recotestdata.tar.gz recotestdata # test ! # upload recotestdata.tar.gz to wodan@frs.sourceforge.net:uploads (via sftp) test ! # upload recotestdata.tar.gz via webinterface # Alternative with gdb: gdb -batch -return-child-result -eval-command=run -eval-command=bt -args .libs/odinreco -r $$dir/recoInfo -o $$dir/test test: testdata for dir in recotestdata/*; do \ .libs/odinreco -f jdx -r $$dir/recoInfo -o $$dir/test && \ ../cmdline-utils/micalc -if1 $$dir/test.jdx -op - -if2 $$dir/image.jdx -of $$dir/diff.jdx && \ ../cmdline-utils/micalc -if $$dir/diff.jdx -op abs -of $$dir/diffabs.jdx && \ ../cmdline-utils/micalc -if $$dir/diffabs.jdx -op + > $$dir/diff.sum && \ ../cmdline-utils/micalc -if $$dir/image.jdx -op + > $$dir/image.sum && \ echo "$$(cat $$dir/diff.sum) $$(cat $$dir/image.sum)" > $$dir/comp && \ export LC_ALL=C && \ cat $$dir/comp | awk '{if( 1e3*sqrt($$1*$$1)>sqrt($$2*$$2)) print "ERROR";}' >> $$dir/comp; \ if ! test -f $$dir/comp ; then echo "odinreco failed"; exit -1 ; fi; \ if grep -q ERROR $$dir/comp ; then echo "Difference detected in $$dir"; exit -1 ; fi \ done manual: $(bin_PROGRAMS) for prog in $(bin_PROGRAMS); do ./$$prog -h > ./`basename $$prog $(EXEEXT)`.usage ; done ./odinreco -manual > manual.h endif clean-local: -rm -rf recotestdata* *.usage manual.h odin-1.8.5/odinreco/Makefile.in0000644000175000017500000007506311734622602013264 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives 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detected in $$dir"; exit -1 ; fi \ @ONLY_LIBS_FALSE@ done @ONLY_LIBS_FALSE@manual: $(bin_PROGRAMS) @ONLY_LIBS_FALSE@ for prog in $(bin_PROGRAMS); do ./$$prog -h > ./`basename $$prog $(EXEEXT)`.usage ; done @ONLY_LIBS_FALSE@ ./odinreco -manual > manual.h clean-local: -rm -rf recotestdata* *.usage manual.h # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: odin-1.8.5/odinreco/grid.h0000644000175000017500000000664311455553545012324 00000000000000/*************************************************************************** grid.h - description ------------------- begin : Wed Feb 21 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOGRID_H #define RECOGRID_H #include "step.h" template class RecoGrid : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "grid"+postfix();} STD_string description() const {return "Grid signal data with arbitrary k-space trajectory in "+itos(NDim)+" dimensions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected, readout);} void modify_coord(RecoCoord& coord) const {if(NDim==2) coord.set_mode(RecoIndex::collected, line);} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoGrid;} void init(); JDXbool deapo_shift; JDXfilter kernel; JDXfloat kernelwidth; JDXfloat gridScale; static STD_string postfix() {return itos(NDim)+"d";} static TinyVector gridshape(const RecoCoord& coord, RecoController& controller); const Gridding& get_gridder(const RecoCoord& coord, RecoController& controller); // cache gridders typedef STD_map > GridderMap; GridderMap gridmap; Mutex gridmutex; }; ///////////////////////////////////////////////////////////////////////////////// template class RecoDeapodize : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "deapodize"+postfix();} STD_string description() const {return "De-apodize gridded data in "+itos(NDim)+" dimensions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected, line3d, line, readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoDeapodize;} void init() {} static STD_string postfix() {return itos(NDim)+"d";} }; class RecoGridCut : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "gridcut"; } STD_string description() const {return "Cut out central part of image to remove effects from gridding on a denser grid";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected, line3d, line, readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoGridCut;} void init() {} }; #endif odin-1.8.5/odinreco/slicetime.h0000644000175000017500000000316711322062351013332 00000000000000/*************************************************************************** slicetime.h - description ------------------- begin : Sun Jun 3 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSLICETIME_H #define RECOSLICETIME_H #include "step.h" class RecoSliceTime : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "slicetime";} STD_string description() const {return "Slice-time correction for data with multiple repetitions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected, repetition, slice, line3d, line, readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoSliceTime;} void init() {} }; #endif odin-1.8.5/odinreco/reader_custom.cpp0000644000175000017500000001204111322062351014532 00000000000000#include "reader_custom.h" #include // for loading sample file bool RecoReaderCustom::init(const STD_string& input_filename) { Log odinlog("RecoReaderCustom","init"); Range all=Range::all(); // Create synthetic raw data using a virtual sample // Load sample Sample smp; if(smp.load(input_filename)<0) { ODINLOG(odinlog,errorLog) << "Cannot read sample file " << input_filename << STD_endl; return false; } farray spinDensity=smp.get_spinDensity(); spinDensity.autosize(); ODINLOG(odinlog,infoLog) << "Read sample with extent " << STD_string(spinDensity.get_extent()) << STD_endl; ///////////////////////////////////////////////////////////////////////////////////// // Create the raw data // Create signal data for one image ComplexData<2> oneimage(float2real(Data(spinDensity))); oneimage.fft(); // Create 2-dim raw data array, these dims are: (repetition x slice x phase, read) int nrep=15; int nslice=7; int nphase=oneimage.extent(1); int nread=oneimage.extent(0); int nadcs=nrep*nslice*nphase; rawdata.resize(nadcs, nread); // Resize the vector of reco coordinates (indices) coord_vec_cache.resize(nadcs); // Iterate over dimensions and create raw data and reco indices count=0; for(int irep=0; irep(0.0,0.05,0.1); // shift image in phase and read direction by 0.05*FOV and 0.1*FOV, respectively ///////////////////////////////////////////////////////////////////////////////////// // Adjust protocol. We can keep the default settings, or fill in our own values. // Most of these settings are irrelevant for the reconstruction, but will // stored together with the raw data, e.g. in DICOM files // Study information, which is stored together with the raw data prot_cache.study.set_Patient("TESTID", "John Doe", "19730913", 'M', 80.0); prot_cache.study.set_Context("RecoReaderCustom","DrNo"); prot_cache.study.set_Series("Test",7); // Set some parameters that might be relevant to reco prot_cache.seqpars.set_RepetitionTime(1300.0).set_FlipAngle(66.0); // For correct T1 fit prot_cache.seqpars.set_ReductionFactor(1); // For correct GRAPPA interpolation // Geometry settings prot_cache.geometry.set_orientation(-66.7, 78.2, -124.7); prot_cache.geometry.set_offset(readDirection,22.7); prot_cache.geometry.set_offset(phaseDirection,-5.9); prot_cache.geometry.set_offset(sliceDirection,1.9); prot_cache.geometry.set_FOV(readDirection,192.6); prot_cache.geometry.set_FOV(phaseDirection,200.2); prot_cache.geometry.set_sliceDistance(6.1); prot_cache.geometry.set_sliceThickness(3.2); ///////////////////////////////////////////////////////////////////////////////////// count=0; // reset global counter because it is used in fetch return true; } bool RecoReaderCustom::fetch(RecoCoord& coord, ComplexData<1>& adc) { if(count>=coord_vec_cache.size()) return false; // This check is necessary for proper multi-threading // Return the next raw data ADC coord=coord_vec_cache[count]; adc.resize(rawdata.extent(1)); adc=rawdata(count, Range::all()); // Return deep copy bool contin=int(count) /////////////////////////////////////////////////////////////////////////// // function class to fit IR timecourse struct InversionRecoveryFunction : public ModelFunction { fitpar M0; fitpar lambda; float evaluate_f(float x) const {return M0.val * (1.0 - 2.0 * exp (lambda.val * x) );} fvector evaluate_df(float x) const { fvector result(numof_fitpars()); result[0]=1.0 - 2.0 * exp (lambda.val * x); result[1]=-x * 2.0 * M0.val * exp (lambda.val * x); return result; } unsigned int numof_fitpars() const {return 2;} fitpar& get_fitpar(unsigned int i) { if(i==0) return M0; if(i==1) return lambda; return dummy_fitpar; } }; /////////////////////////////////////////////////////////////////////////// // function class to fit magnitude IR timecourse struct InversionRecoveryAbsFunction : public ModelFunction { bool fitphi; fitpar M0; fitpar phi; fitpar Ri; float evaluate_f(float x) const { double winkel = atan(phi.val)/PII+0.5; double e = exp(-Ri.val*x); return fabs(M0.val*(1-2*winkel*e)); } fvector evaluate_df(float x) const { fvector result(numof_fitpars()); double winkel = atan(phi.val)/PII+0.5; double e = exp(-Ri.val*x); double Fun = (2*winkel*e-1); result[0]=fabs(M0.val)*fabs(Fun)/M0.val; result[1]=(-2.0*fabs(M0.val)*winkel*x*e*Fun)/(fabs(Fun)); if(fitphi) result[2]=(2.0*fabs(M0.val)*e*Fun)/(PII*(pow(phi.val,2)+1)*fabs(Fun)); return result; } unsigned int numof_fitpars() const {return 2+fitphi;} fitpar& get_fitpar(unsigned int i) { if(i==0) return M0; if(i==1) return Ri; if(i==2) return phi; return dummy_fitpar; } }; /////////////////////////////////////////////////////////////////////////// void RecoT1Fit::init() { fittype="simple"; fittype.set_cmdline_option("t1f").set_description("Use this type of T1 fit, can be one of 'simple', 'magnitude'"); append_arg(fittype,"fittype"); masklevel=0.5; masklevel.set_cmdline_option("t1l").set_description("Level relative to mean value of first echo for setting mask of T1 fit"); append_arg(masklevel,"masklevel"); maxt1=3000.0; maxt1.set_unit(ODIN_TIME_UNIT).set_cmdline_option("t1m").set_description("Upper limit for T1 fit"); append_arg(maxt1,"maxt1"); } #define START_T1 1000.0 bool RecoT1Fit::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); Data magn(cabs(indata)); TinyVector inshape=indata.shape(); TinyVector outshape(inshape(1), inshape(2), inshape(3)); // magn.autowrite("magn.jdx"); ODINLOG(odinlog,normalDebug) << "inshape=" << inshape << STD_endl; dvector tis=controller.dim_values(userdef); ODINLOG(odinlog,normalDebug) << "tis=" << tis.printbody() << STD_endl; int ntis=tis.size(); if(ntis!=inshape(0) || ntis<2) { ODINLOG(odinlog,errorLog) << "size mismatch or too small" << STD_endl; return false; } float noiselevel=masklevel*mean(magn(0,all,all,all)); float deltaEcho=tis[1]-tis[0]; Protocol prot(controller.protocol()); float pulse_term=log(cos(prot.seqpars.get_FlipAngle()/180.0*PII))/deltaEcho; ODINLOG(odinlog,normalDebug) << "pulse_term=" << pulse_term << STD_endl; InversionRecoveryFunction irfunc; InversionRecoveryAbsFunction irabsfunc; irabsfunc.fitphi=false; FunctionFit irfit(irfunc,ntis); FunctionFit irabsfit(irabsfunc,ntis); Data T1map(outshape); T1map=0.0; Data S0map(outshape); S0map=0.0; Data angmap(outshape); angmap=0.0; Data pixel4fit(ntis); Data ysigma(ntis); ysigma=1.0; Data xvals(ntis); for(int iti=0; itinoiselevel) { pixel4fit=magn(all,iphase3d,iphase,iread); int minindex=minIndex(pixel4fit)(0); float M0=0.0; float t1star=0.0; float angle=0.0; if(fittype=="magnitude") { irabsfunc.M0.val=max(pixel4fit); irabsfunc.phi.val=tan(PII*cos(PII*170/180-PII)-PII/2); irabsfunc.Ri.val=secureInv( 1.45*tis[minindex]); if(irabsfit.fit(pixel4fit, ysigma, xvals)) { M0=irabsfunc.M0.val; angle=acos(-atan(irabsfunc.phi.val)/PII-0.5)/PII*180.0; t1star=secureInv(irabsfunc.Ri.val); } } else { for(int i=0; i0.0) t1=secureDivision(1.0 , 1.0/t1star + pulse_term); // correction for Look Locker sequence check_range(t1, 0.0, maxt1); T1map(iphase3d,iphase,iread)=t1; S0map(iphase3d,iphase,iread)=M0; angmap(iphase3d,iphase,iread)=angle; } } } } // modify coordinate int numof_output=2; if(sum(angmap)>0.0) numof_output++; rd.coord().index[userdef].set_numof(numof_output); rd.override_protocol=&prot; STD_string series; int number; prot.study.get_Series(series, number); // feed T1 into rest of pipeline RecoData rdT1(rd); rdT1.data(Rank<3>()).resize(outshape); rdT1.data(Rank<3>())=float2real(T1map); rdT1.coord().index[userdef]=0; prot.study.set_Series(series+"_T1",number); if(!execute_next_step(rdT1,controller)) return false; // feed S0 into rest of pipeline RecoData rdS0(rd); rdS0.data(Rank<3>()).resize(outshape); rdS0.data(Rank<3>())=float2real(S0map); rdS0.coord().index[userdef]=1; prot.study.set_Series(series+"_S0",number); if(!execute_next_step(rdS0,controller)) return false; // feed angle into rest of pipeline if(sum(angmap)>0.0) { RecoData rdang(rd); rdang.data(Rank<3>()).resize(outshape); rdang.data(Rank<3>())=float2real(angmap); rdang.coord().index[userdef]=2; prot.study.set_Series(series+"_angle",number); if(!execute_next_step(rdang,controller)) return false; } return true; } odin-1.8.5/odinreco/zerofill.cpp0000644000175000017500000000444711455553545013560 00000000000000#include "zerofill.h" #include "data.h" #include "controller.h" void RecoZeroFill::init() { minread=0; minread.set_cmdline_option("zr").set_description("Minimum size of final image in read direction obtained zero filling"); append_arg(minread,"minread"); minphase=0; minphase.set_cmdline_option("zp").set_description("Minimum size of final image in phase direction obtained zero filling"); append_arg(minphase,"minphase"); minslice=0; minslice.set_cmdline_option("zs").set_description("Minimum size of final image in slice direction obtained zero filling"); append_arg(minslice,"minslice"); } bool RecoZeroFill::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); ComplexData<3>& data=rd.data(Rank<3>()); TinyVector oldshape=data.shape(); TinyVector newshape=controller.image_size(); ODINLOG(odinlog,normalDebug) << "controller.image_size()=" << newshape << STD_endl; newshape(0)=STD_max(newshape(0),int(minslice)); newshape(1)=STD_max(newshape(1),int(minphase)); newshape(2)=STD_max(newshape(2),int(float(minread)*rd.coord().overSamplingFactor+0.5)); // take oversampling into account if(oldshape!=newshape) { for(int idim=0; idim<3; idim++) { newshape(idim)=STD_max(newshape(idim),oldshape(idim)); // only size increase } ODINLOG(odinlog,normalDebug) << "newshape/oldshape=" << newshape << "/" << oldshape << STD_endl; TinyVector lowerBounds, upperBounds; for(int idim=0; idim<3; idim++) { int diff=newshape(idim)-oldshape(idim); if(diff>0) { lowerBounds(idim)=diff/2; // offset to center old data upperBounds(idim)=lowerBounds(idim)+oldshape(idim)-1; } else { lowerBounds(idim)=0; upperBounds(idim)=oldshape(idim)-1; } } ODINLOG(odinlog,normalDebug) << "lowerBounds/upperBounds=" << lowerBounds << "/" << upperBounds << STD_endl; ComplexData<3> datacopy(data); datacopy.makeUnique(); data.resize(newshape); data=STD_complex(0.0); data(RectDomain<3>(lowerBounds, upperBounds))=datacopy; // adjust numof rd.coord().index[line3d].set_numof(newshape(0)); rd.coord().index[line].set_numof(newshape(1)); rd.coord().index[readout].set_numof(newshape(2)); } return execute_next_step(rd,controller); } odin-1.8.5/odinreco/splitter.h0000644000175000017500000000454411322062351013222 00000000000000/*************************************************************************** splitter.h - description ------------------- begin : Fri Feb 2 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSPLITTER_H #define RECOSPLITTER_H #include "step.h" /* * Template class to split data in one or more dimensions and to feed it separately * into the remaining part of the pipeline. * The rank of the unmodified collected data dimensions is is given by 'Nunmod'. * The particular unmodified dimension are given in 'Unmod' by a specialization of 'RecoDim'. * The numer of dimensions to split is given in 'Nsplit' and specified in 'Split' by * a specialization of 'RecoDim'. * The dimensions to split are expected leftmost in the input data array. */ template class RecoSplitter : public RecoStep, public Labeled { public: RecoSplitter(const STD_string& split_label) : Labeled(split_label) {} private: // implementing virtual functions of RecoStep STD_string label() const {return get_label();} STD_string description() const {return "Split data in one or more dimensions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {RecoCoord result=Unmod::preset_coord(RecoIndex::collected); Split::modify(RecoIndex::collected,result); return result;} void modify_coord(RecoCoord& coord) const {Split::modify(RecoIndex::separate,coord);} RecoStep* allocate() const {return new RecoSplitter(get_label());} void init() {} }; #endif odin-1.8.5/odinreco/filter.cpp0000644000175000017500000000300711322062351013165 00000000000000#include "filter.h" #include "data.h" #include "controller.h" void RecoFilter::init() { filter.set_funcpars("NoFilter"); filter.set_cmdline_option("ff").set_description("k-space filter function (and its arguments)"); append_arg(filter,"filter"); plateau=0.0; plateau.set_cmdline_option("fp").set_description("Filter plateau width (0=no plateau, 1=full plateau)"); append_arg(plateau,"plateau"); } bool RecoFilter::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); ODINLOG(odinlog,normalDebug) << "filter/plateau=" << filter.get_function_name() << "/" << plateau << STD_endl; if(filter.get_function_name()!="NoFilter") { ComplexData<3>& data=rd.data(Rank<3>()); TinyVector shape=data.shape(); ODINLOG(odinlog,normalDebug) << "shape=" << shape << STD_endl; float plat=plateau; check_range(plat, 0.0, 1.0); float plateau_factor=secureInv( 1.0-plat); for(int i=0; i index=data.create_index(i); float factor=1.0; for(int idir=0; idir<3; idir++) { if(shape(idir)>1) { float relradius=2.0*secureDivision(abs(index(idir)-shape(idir)/2),shape(idir)); if(relradius>plat) { relradius=plateau_factor*(relradius-plateau); if(relradius<=1.0) factor*=filter.calculate(relradius); else factor=0.0; } } } data(index)*=STD_complex(factor); } } return execute_next_step(rd, controller); } odin-1.8.5/odinreco/index.cpp0000644000175000017500000000211711322062351013010 00000000000000#include "index.h" STD_string RecoIndex::print(recoDim dim, printMode printmode) const { bool do_print=false; if(printmode==brief && (numof>1 || mode==single)) do_print=true; if(printmode==all) do_print=true; if(printmode==filename && numof>1 && mode==separate) do_print=true; if(do_print) { STD_string result=kSpaceCoord::index2string(val, dim, numof); switch(mode) { case ignore: result+="i"; break; case single: result+="s"; break; case collected: result="all"; break; case any: result="any"; break; } return result; } return ""; } STD_string RecoCoord::print(RecoIndex::printMode printmode) const { STD_string result; const char* separator=","; const char* equals="="; if(printmode==RecoIndex::filename) { separator="_"; equals=""; } bool first=true; for(int i=0; i& data=rd.data(Rank<1>()); ComplexData<1> adc_reversed(data.copy()); adc_reversed.reverseSelf(firstDim); data(Range::all())=adc_reversed(Range::all()); } return execute_next_step(rd,controller); } /////////////////////////////////////////////////////////////////////////// bool RecoAdcGridPrep::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); if(rd.coord().readoutShape) { trajmutex.lock(); // also protect global readoutShape if(!traj.size()) { const Data& readoutShape=rd.coord().readoutShape->first; ComplexData<1>& indata=rd.data(Rank<1>()); int npts=indata.size(); ODINLOG(odinlog,normalDebug) << "npts=" << npts << STD_endl; if(readoutShape.size()!=npts) { trajmutex.unlock(); ODINLOG(odinlog,errorLog) << "Size mismatch: " << readoutShape.size() << "!=" << npts << STD_endl; return false; } // calc kspace by integration of readout shape fvector kspace(npts); kspace=0.0; if(npts) { kspace[0]=0.5*readoutShape(0); for(int i=1; i(0.0,0.0,kspace[i]); } } trajmutex.unlock(); rd.coord().kspaceTraj=&traj; } return execute_next_step(rd,controller); } /////////////////////////////////////////////////////////////////////////// bool RecoAdcWeight::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); const ComplexData<1>* weightVec=rd.coord().weightVec; if(weightVec) { MutexLock lock(weightMutex); // protect global weightVec int weightsize=weightVec->size(); ODINLOG(odinlog,normalDebug) << "weightsize=" << weightsize << STD_endl; ComplexData<1>& data=rd.data(Rank<1>()); if(weightsize!=data.extent(0)) { ODINLOG(odinlog,errorLog) << "Size mismatch weightsize(" << weightsize << ")!=adc(" << data.extent(0) << ")" << STD_endl; return false; } data=data*(*weightVec); } return execute_next_step(rd,controller); } /////////////////////////////////////////////////////////////////////////// bool RecoAdcBaseline::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); ComplexData<1>& adc=rd.data(Rank<1>()); float maxsig=max(cabs(adc)); // Calculate mean complex offset of samples with small magnitude int nsamples_bline=0; STD_complex sigsum(0.0); for(int isample=0; isample odinlog(c_label(),"process"); ComplexData<1>& adc=rd.data(Rank<1>()); float relcenter=rd.coord().relCenterPos; if(relcenter<0.0 || relcenter>1.0) { ODINLOG(odinlog,errorLog) << "relcenter=" << relcenter << STD_endl; return false; } bool end_omitted=false; if(relcenter>0.5) { relcenter=1.0-relcenter; } int oldsize=adc.size(); int newsize=int(2.0*(1.0-relcenter)*oldsize+0.5); ODINLOG(odinlog,normalDebug) << "oldsize/newsize=" << oldsize << "/" << newsize << STD_endl; ComplexData<1> newadc(newsize); newadc=STD_complex(0.0); int offset=newsize-oldsize; if(end_omitted) offset=0; newadc(Range(offset,offset+oldsize-1))=adc; adc.reference(newadc); // adjust numof and center position rd.coord().index[readout].set_numof(newsize); rd.coord().relCenterPos=0.5; // Adjust adcstart/end if(!end_omitted) { rd.coord().adcstart+=offset; rd.coord().adcend+=offset; } ODINLOG(odinlog,normalDebug) << "adcstart/adcend=" << rd.coord().adcstart << "/" << rd.coord().adcend << STD_endl; return execute_next_step(rd,controller); } odin-1.8.5/odinreco/epinavcorr.cpp0000644000175000017500000001033711734622163014066 00000000000000#include "epinavcorr.h" #include "data.h" #include "controller.h" #include static const char* posted_phasemap_label="epinav"; bool RecoEpiNavScan::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<2>& indata=rd.data(Rank<2>()); TinyVector inshape(indata.shape()); int nechoes=inshape(0); int nread=inshape(1); if(nechoes!=3) { ODINLOG(odinlog,errorLog) << "nechoes=" << nechoes << STD_endl; return false; } TinyVector navshape(2,nread); ComplexData<2> navdata(navshape); navdata(0,all)=STD_complex(0.5)*(indata(0,all)+indata(2,all)); // average both even echoes navdata(1,all)=indata(1,all); // FFT in read direction navdata.partial_fft(TinyVector(false,true)); ComplexData<2> phasemap(navshape); // The result // Calculate phase-difference Data phasediff(nread); Data sigma(nread); // Error for fit for(int iread=0; iread(expc(float2imag(phasediff))).phasemap(); // Linear fit to phasediff LinearFunction linf; linf.fit(phasediff, sigma); float slope=linf.m.val; float offset=linf.c.val; ODINLOG(odinlog,normalDebug) << "slope/offset=" << slope << "/" << offset << STD_endl; for(int iread=0; iread odinlog(c_label(),"process"); if(!controller.data_announced(posted_phasemap_label)) { ODINLOG(odinlog,errorLog) << posted_phasemap_label << " not available" << STD_endl; return false; } RecoData one_echo_phasemap; one_echo_phasemap.coord()=rd.coord(); RecoEpiNavScan::modify4blackboard(one_echo_phasemap.coord()); int itrain=rd.coord().echotrain; ODINLOG(odinlog,normalDebug) << "itrain=" << itrain << STD_endl; one_echo_phasemap.coord().index[epi]=itrain; int iecho=bool(rd.coord().flags&recoReflectBit); ODINLOG(odinlog,normalDebug) << "iecho=" << iecho << STD_endl; one_echo_phasemap.coord().index[echo]=iecho; if(!controller.inquire_data(posted_phasemap_label, one_echo_phasemap)) return false; ComplexData<1>& pmap=one_echo_phasemap.data(Rank<1>()); ComplexData<1>& adc=rd.data(Rank<1>()); if(pmap.size()!=adc.size()) { ODINLOG(odinlog,errorLog) << "Size mismatch: " << pmap.size() << " != " << adc.size() << STD_endl; return false; } // FFT forward adc.fft(true); // Phase correction Range all=Range::all(); adc(all)=adc(all)/pmap(all); // Blitz throws an error if arrays are used directly // FFT back adc.fft(false); return execute_next_step(rd,controller); } odin-1.8.5/odinreco/blackboard.cpp0000644000175000017500000000731111455553545014007 00000000000000#include "blackboard.h" #include "controller.h" RecoBlackBoard::~RecoBlackBoard() { // Free thread events for(LabelEventMap::iterator lit=eventmap.begin(); lit!=eventmap.end(); ++lit) { for(CoordEventMap::iterator cit=lit->second.begin(); cit!=lit->second.end(); ++cit) { delete cit->second; } } } void RecoBlackBoard::post(const STD_string& label, const RecoData& data) { Log odinlog("RecoBlackBoard","post"); mutex.lock(); CoordDataMap& cdmap=posted[label]; if(cdmap.find(data.coord())!=cdmap.end()) { ODINLOG(odinlog,warningLog) << label << "(" << data.coord().print() << ") posted already, will overwrite it" << STD_endl; } cdmap[data.coord()]=data; // deep copy ODINLOG(odinlog,normalDebug) << "Posted " << label << "(" << data.coord().print() << ")" << STD_endl; // Notify other waiting threads via event STD_list eventlist; LabelEventMap::iterator lit=eventmap.find(label); if(lit!=eventmap.end()) { CoordEventMap& ccm=lit->second; for(CoordEventMap::const_iterator cit=ccm.begin(); cit!=ccm.end(); ++cit) { if(cit->first==data.coord()) eventlist.push_back(cit->second); // Find ALL coords whicht match the data } } mutex.unlock(); if(eventlist.size()) { ODINLOG(odinlog,normalDebug) << "Signaling " << eventlist.size() << " threads waiting for " << label << "(" << data.coord().print() << ")" << STD_endl; for(STD_list::const_iterator it=eventlist.begin(); it!=eventlist.end(); ++it) { (*it)->signal(); } } } bool RecoBlackBoard::get_data(const STD_string& label, RecoData& data) { Log odinlog("RecoBlackBoard","get_data"); LabelDataMap::const_iterator lit=posted.find(label); if(lit==posted.end()) return false; const CoordDataMap& cdmap=lit->second; CoordDataMap::const_iterator cit=cdmap.find(data.coord()); if(cit==cdmap.end()) return false; data=cit->second; // deep copy return true; } bool RecoBlackBoard::inquire(const STD_string& label, RecoData& data, bool blocking) { Log odinlog("RecoBlackBoard","inquire"); ODINLOG(odinlog,normalDebug) << "Requested " << label << "(" << data.coord().print() << ")" << STD_endl; mutex.lock(); if(get_data(label,data)) {mutex.unlock(); return true;} // We're done here if(!blocking) {mutex.unlock(); return false;} // We're done here Event* event=0; CoordEventMap& ccm=eventmap[label]; CoordEventMap::iterator cit=ccm.find(data.coord()); if(cit==ccm.end()) { ODINLOG(odinlog,normalDebug) << "New event for " << label << "(" << data.coord().print() << ")" << STD_endl; event=new Event; ccm[data.coord()]=event; } else { event=cit->second; // Already there } mutex.unlock(); if(event) event->wait(); ODINLOG(odinlog,normalDebug) << "received signal for " << label << "(" << data.coord().print() << ")" << STD_endl; mutex.lock(); bool result=get_data(label,data); // Try again mutex.unlock(); if(!result) { ODINLOG(odinlog,warningLog) << "Data not available after wait: " << label << "(" << data.coord().print() << ")" << STD_endl; } return result; } /////////////////////////////////////////////////////////////////////////////////////////// void RecoPost::init() { postlabel.set_description("Post data on blackboard with this label"); append_arg(postlabel,"postlabel"); } bool RecoPost::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); controller.post_data(postlabel, rd); return execute_next_step(rd,controller); } bool RecoPost::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { context.controller.announce_data(postlabel); } return RecoStep::query(context); } odin-1.8.5/odinreco/epinavcorr.h0000644000175000017500000000476411322062351013530 00000000000000/*************************************************************************** epinavcorr.h - description ------------------- begin : Fr Sep 19 2008 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOEPINAVCORR_H #define RECOEPINAVCORR_H #include "step.h" class RecoEpiNavScan : public RecoStep { public: static void modify4blackboard(RecoCoord& coord) { // index for blackboard coord.set_uniform_mode(RecoIndex::ignore); coord.set_mode(RecoIndex::separate, echo, channel, epi); // the three coordinates relevant to navigators, 'epi' will be used for the echo-train index } private: // implementing virtual functions of RecoStep STD_string label() const {return "epinavscan";} STD_string description() const {return "Calculate and post data for Siemens EPI phase correction";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,echo,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoEpiNavScan;} void init() {} }; ////////////////////////////////////////////////////////////// class RecoEpiNavCorr : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "epinavcorr";} STD_string description() const {return "Apply Siemens EPI phase correction";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoEpiNavCorr;} void init() {} }; #endif odin-1.8.5/odinreco/collector.cpp0000644000175000017500000001125011734622163013677 00000000000000#include "collector.h" #include "controller.h" #include "phasecorr.h" // for phasemapcoll #include "epinavcorr.h" // for epinavcoll #include "collector_code.h" RecoCollectorBase::~RecoCollectorBase() { Log odinlog(label_cache.c_str(),"~RecoCollectorBase"); if(todo.size()) { ODINLOG(odinlog,errorLog) << "TODO list not empty:" << STD_endl; for(CoordCountMap::const_iterator it=todo.begin(); it!=todo.end(); ++it) { ODINLOG(odinlog,errorLog) << "(" << it->first.print(RecoIndex::all) << "): " << it->second << STD_endl; } } } bool RecoCollectorBase::completed(const RecoCoord& coord, unsigned int custom_count) { Log odinlog(c_label(),"completed"); unsigned int numof_todo=count; if(custom_count) numof_todo=custom_count; if(numof_todo<2) return true; // dataset is always complete in this case RecoCoord coord_copy=coord; modify_coord(coord_copy); // just make sure we check against the output side of the functor ODINLOG(odinlog,normalDebug) << "coord_copy=" << coord_copy.print() << STD_endl; MutexLock lock(todomutex); CoordCountMap::iterator it=todo.find(coord_copy); if(it==todo.end()) { // add new entry in todo todo[coord_copy]=(numof_todo-1); } else { it->second--; // reduce todo count by one if(!it->second) { // is count zero ? todo.erase(it); return true; } } return false; } bool RecoCollectorBase::calculate_count(RecoQueryContext& context, const RecoCoord& inmask, const RecoCoord& outmask) { Log odinlog(c_label(),"calculate_count"); label_cache=label(); ODINLOG(odinlog,normalDebug) << "context.coord=" << context.coord.print() << STD_endl; // modify_input_coord(context.coord); const CoordCountMap* inmap=context.controller.create_count_map(inmask); ODINLOG(odinlog,normalDebug) << "inmask=" << inmask.print() << STD_endl; if(!inmap) return false; const CoordCountMap* outmap=context.controller.create_count_map(outmask); ODINLOG(odinlog,normalDebug) << "outmask=" << outmask.print() << STD_endl; if(!outmap) return false; unsigned int incount=inmap->size(); unsigned int outcount=outmap->size(); ODINLOG(odinlog,normalDebug) << "incount/outcount=" << incount << "/" << outcount << STD_endl; if(!incount) { ODINLOG(odinlog,errorLog) << "No input data" << STD_endl; return false; } if(!outcount) { ODINLOG(odinlog,errorLog) << "No output data" << STD_endl; return false; } if(incount%outcount) { ODINLOG(odinlog,errorLog) << "incount(" << incount << ") not a multiple of outcount(" << outcount << ")" << STD_endl; ODINLOG(odinlog,errorLog) << "inmask=" << inmask.print() << STD_endl; ODINLOG(odinlog,errorLog) << "outmask=" << outmask.print() << STD_endl; return false; } count=incount/outcount; // simply take the quotient ODINLOG(odinlog,normalDebug) << "count=" << count << STD_endl; return true; } ////////////////////////////////////////////////////////////////////////////////////////////////////// // Instantiations used in step.cpp template class RecoCollector<1, RecoDim<1, readout>, 2, RecoDim<2, line3d, line> >; template class RecoCollector<2, RecoDim<2, line, readout>, 1, RecoDim<1, line3d> >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, slice>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, channel>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, cycle>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, te>, true >; //template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, epi>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, userdef>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, freq>, true >; template class RecoCollector<4, RecoDim<4, slice, line3d, line, readout>, 1, RecoDim<1, repetition>, true >; template class RecoCollector<1, RecoDim<1, readout>, 1, RecoDim<1, average>, true >; template class RecoCollector<1, RecoDim<1, readout>, 1, RecoDim<1, echo>, true >; template class RecoCollector<1, RecoDim<1, readout>, 1, RecoDim<1, channel>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 2, RecoDim<2, channel, repetition>, true >; template class RecoCollector<3, RecoDim<3, line3d, line, readout>, 3, RecoDim<3, channel, repetition, slice>, true >; odin-1.8.5/odinreco/step.h0000644000175000017500000001150111322062351012316 00000000000000/*************************************************************************** step.h - description ------------------- begin : Sat Dec 30 2006 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOSTEP_H #define RECOSTEP_H #include #include #include /** * @addtogroup odinreco * @{ */ class RecoData; // forward declaration class RecoController; // forward declaration /////////////////////////////////////////////////////////////////////////////////// /** * Context when querying reconstruction pipeline. */ struct RecoQueryContext { /** * Mode for querying pipeline. * - prep: Will be set when querying once before starting the pipeline * - finalize: Will be set when querying once after the pipeline was used * - print: print pipeline layout */ enum queryMode {prep=0, finalize, print}; queryMode mode; /** * The reconstruction controller. */ RecoController& controller; /** * Prefix when printing functors. */ STD_string printprefix; /** * Postfix when printing functors. */ STD_string printpostfix; /** * State/index in each dimension during current step of the pipeline. */ RecoCoord coord; RecoQueryContext(queryMode m, RecoController& contr, unsigned short numof[n_recoDims]) : mode(m), controller(contr) { for(int idim=0; idim { public: virtual ~RecoStep() {} /** * Overload this function to perform the reconstruction step. * Input data should be taken from 'rd' and the result stored back into 'rd' * before executing the next step with 'execute_next_step()'. * Read-only access to the current reconstruction controller is possible * via 'controller'. * Return 'true' on sucess, and 'false' if functor fails. */ virtual bool process(RecoData& rd, RecoController& controller) = 0; /** * Overload this function to specify the input dimensions state/index of the functor. */ virtual RecoCoord input_coord() const = 0; /** * Overload this function to specify the modification of the input dimensions state/index after applying the functor. */ virtual void modify_coord(RecoCoord& coord) const = 0; /** * Overload this function to initialize the step for usage in the pieline. * Read-only access to the current reconstruction controller is possible via 'controller'. * The input interface of the step is passed in 'input_coord'. */ virtual bool pipeline_init(const RecoController& controller, const RecoCoord& input_coord) {return true;} /** * Queries the reconstruction pipeline. * Overload this function for particular actions depending on 'context'. * Returns 'true' only if sucessful. */ virtual bool query(RecoQueryContext& context); /** * Sets the functor to be executed after this. */ void set_next_step(RecoStep* step) {next_step=step;} // To be used by factory via duck typing static void create_templates(STD_list& result); static STD_string manual_group() {return "odinreco_steps";} static void interface_description(const RecoStep* step, STD_string& in, STD_string& out); protected: friend class RecoController; /** * Default constructor */ RecoStep() : next_step(0) {} /** * Execute next functor in reconstruction pipeline, * returns 'true' on sucess, and 'false' if functor fails. * Note: Do not lock any mutexes when calling this function. */ bool execute_next_step(RecoData& rd, RecoController& controller); private: void interface_dims(int& in, int& out) const; RecoStep* next_step; }; /////////////////////////////////////////////////////////////////////////////////// typedef StepFactory RecoStepFactory; // The factory for reco steps /** @} */ #endif odin-1.8.5/odinreco/t1fit.h0000644000175000017500000000330311322062351012373 00000000000000/*************************************************************************** t1fit.h - description ------------------- begin : Thu Mar 15 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOT1FIT_H #define RECOT1FIT_H #include "step.h" class RecoT1Fit : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "t1fit";} STD_string description() const {return "Calculate T1 relaxation time using data from Look-Locker sequence";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,userdef,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::separate,userdef);} RecoStep* allocate() const {return new RecoT1Fit;} void init(); JDXstring fittype; JDXfloat masklevel; JDXfloat maxt1; }; #endif odin-1.8.5/odinreco/refgain.h0000644000175000017500000000323211322062351012760 00000000000000/*************************************************************************** refgain.h - description ------------------- begin : Thu Feb 22 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOREFGAIN_H #define RECOREFGAIN_H #include "step.h" class RecoRefGain : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "refgain";} STD_string description() const {return "Calculate reference gain (Bruker)";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,userdef,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single,userdef);} RecoStep* allocate() const {return new RecoRefGain;} void init(); JDXfloat pulsedur; JDXfloat pulsegain; }; #endif odin-1.8.5/odinreco/splitter.cpp0000644000175000017500000000041711322062351013550 00000000000000#include "splitter.h" #include "splitter_code.h" // Instantiations used in step.cpp template class RecoSplitter<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, channel> >; template class RecoSplitter<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition> >;odin-1.8.5/odinreco/circmask.cpp0000644000175000017500000000136511322062351013501 00000000000000#include "circmask.h" #include "data.h" bool RecoCircMask::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<3>& data=rd.data(Rank<3>()); TinyVector shape=data.shape(); if(shape(1)!=shape(2)) { ODINLOG(odinlog,errorLog) << "non-quadratic image shape=" << shape << STD_endl; return false; } float radius=0.5*float(shape(1)-1); for(int iphase3d=0; iphase3dradius) data(iphase3d,iphase,iread)=STD_complex(0.0); } } } return execute_next_step(rd,controller); } odin-1.8.5/odinreco/step.cpp0000644000175000017500000002146311734622163012673 00000000000000#include "step.h" #include "b1fit.h" #include "blade.h" #include "blackboard.h" #include "channel.h" #include "circmask.h" #include "collector.h" #include "conjphase.h" #include "controller.h" #include "adc.h" #include "dump.h" #include "dti.h" #include "driftcorr.h" #include "epinavcorr.h" #include "expfit.h" #include "fieldmap.h" #include "filter.h" #include "fft.h" #include "fmri.h" #include "grappa.h" #include "grid.h" #include "homodyne.h" #include "messer.h" #include "mip.h" #include "multifreq.h" #include "offset.h" #include "oversampling.h" #include "phasecorr.h" #include "phasecourse.h" #include "pilot.h" #include "qualitycontrol.h" #include "refgain.h" #include "slicetime.h" #include "slidingwindow.h" #include "splitter.h" #include "store.h" #include "sum.h" #include "swi.h" #include "switch.h" #include "t1fit.h" #include "zerofill.h" // Instantiate template classes #include template class Step; template class StepFactory; bool RecoStep::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); ODINLOG(odinlog,normalDebug) << "mode=" << context.mode << STD_endl; if(context.mode==RecoQueryContext::print) { int padlength=STD_max(1,16-int(label().size())); int in, out; interface_dims(in, out); STD_string ifacestr; if(in || out) { if(in==out) ifacestr="(dim: "+itos(in)+")"; else ifacestr="(dim: "+itos(in)+"->"+itos(out)+")"; } ODINLOG(odinlog,infoLog) << STD_string(padlength,' ') << context.printprefix << " " << context.printpostfix << ifacestr << STD_endl; } modify_coord(context.coord); // apply changes to coordinate before querying next step if(next_step) return next_step->query(context); return true; } bool RecoStep::execute_next_step(RecoData& rd, RecoController& controller) { if(next_step) { rd.new_profiler(next_step->label()); modify_coord(rd.coord()); // apply changes to coordinate // delete old data int in, out; interface_dims(in, out); if(in != out) rd.free(in); return next_step->process(rd,controller); } return true; } void RecoStep::create_templates(STD_list& result) { result.push_back(new RecoAdcBaseline()); result.push_back(new RecoAdcGridPrep()); result.push_back(new RecoAdcPad()); result.push_back(new RecoAdcReflect()); result.push_back(new RecoAdcWeight()); result.push_back(new RecoB1Fit()); result.push_back(new RecoBladeComb()); result.push_back(new RecoBladeCorr()); result.push_back(new RecoBladeGrid()); result.push_back(new RecoChannelSum()); result.push_back(new RecoCircMask()); result.push_back(new RecoCollector<1, RecoDim<1, readout>, 2, RecoDim<2, line3d, line> > ("kspace")); result.push_back(new RecoCollector<2, RecoDim<2, line, readout>, 1, RecoDim<1, line3d> > ("line3dcoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, slice>, true > ("slicecoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, channel>, true > ("chancoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, cycle>, true > ("cyclecoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, te>, true > ("tecoll")); // result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, epi>, true > ("epicoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, userdef>, true > ("usercoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition>, true > ("repcoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, freq>, true > ("freqcoll")); result.push_back(new RecoCollector<4, RecoDim<4, slice, line3d, line, readout>, 1, RecoDim<1, repetition>, true > ("image")); result.push_back(new RecoCollector<1, RecoDim<1, readout>, 1, RecoDim<1, average>, true > ("averagecoll")); result.push_back(new RecoCollector<1, RecoDim<1, readout>, 1, RecoDim<1, echo>, true > ("echocoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 2, RecoDim<2, channel, repetition>, true > ("chanrepcoll")); result.push_back(new RecoCollector<3, RecoDim<3, line3d, line, readout>, 3, RecoDim<3, channel, repetition, slice>, true > ("chanrepslicecoll")); result.push_back(new RecoConjPhaseFT()); result.push_back(new RecoCycleRot()); result.push_back(new RecoDeapodize<1>()); result.push_back(new RecoDeapodize<2>()); result.push_back(new RecoDump()); result.push_back(new RecoDTI()); result.push_back(new RecoDriftCalc()); result.push_back(new RecoDriftCorr()); result.push_back(new RecoEpiNavScan()); result.push_back(new RecoEpiNavCorr()); result.push_back(new RecoExpFit()); result.push_back(new RecoFieldMap()); result.push_back(new RecoFilter()); result.push_back(new RecoFFT()); result.push_back(new RecoFMRI()); result.push_back(new RecoFreqComb()); result.push_back(new RecoGrappaWeights()); // result.push_back(new RecoGrappaWeights >()); // Assume only one GRAPPA template for all userdef indices result.push_back(new RecoGrappaWeights >()); result.push_back(new RecoGrappaWeights()); // result.push_back(new RecoGrappaWeights >()); // Assume only one GRAPPA template for all userdef indices result.push_back(new RecoGrappaWeights >()); result.push_back(new RecoGrappa()); result.push_back(new RecoGrappa()); result.push_back(new RecoGrid<1>()); result.push_back(new RecoGrid<2>()); result.push_back(new RecoGridCut()); result.push_back(new RecoHomodyne()); result.push_back(new RecoHomodyne()); result.push_back(new RecoHomodyne()); result.push_back(new RecoStore()); // result.push_back(new RecoInterpolate()); result.push_back(new RecoMesser()); result.push_back(new RecoMip()); result.push_back(new RecoMultiFreq()); result.push_back(new RecoOffset()); result.push_back(new RecoOversampling()); result.push_back(new RecoPhaseMap()); result.push_back(new RecoPhaseCorr()); result.push_back(new RecoPhaseCourse()); result.push_back(new RecoPilot()); result.push_back(new RecoPost()); result.push_back(new RecoQualityControlSpike()); result.push_back(new RecoReal()); result.push_back(new RecoMagn()); result.push_back(new RecoRefGain()); result.push_back(new RecoSliceTime()); result.push_back(new RecoSlidingWindow()); result.push_back(new RecoSplitter<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, channel> > ("chansplit")); result.push_back(new RecoSplitter<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition> > ("repsplit")); result.push_back(new RecoSum<1, RecoDim<1, readout>, 1, RecoDim<1, average> > ("averagesum")); result.push_back(new RecoSum<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, cycle> > ("cyclesum")); result.push_back(new RecoSum<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition> > ("repsum")); result.push_back(new RecoSum<3, RecoDim<3, line3d, line, readout>, 1, RecoDim<1, repetition>, true > ("repmagnsum")); result.push_back(new RecoSwi()); result.push_back(new RecoSwitch()); result.push_back(new RecoT1Fit()); result.push_back(new RecoZeroFill()); } STD_string interface_str(const RecoCoord& coord) { STD_list colldims; for(int i=0; i::const_iterator it=colldims.begin(); it!=colldims.end(); ++it) { if(collstr!="") collstr+=","; collstr+=*it; } return itos(ncoll)+"-dimensional, these dimensions are: \\verbatim ("+collstr+") \\endverbatim"; } void RecoStep::interface_description(const RecoStep* step, STD_string& in, STD_string& out) { RecoCoord coord=step->input_coord(); in=interface_str(coord); step->modify_coord(coord); out=interface_str(coord); } void RecoStep::interface_dims(int& in, int& out) const { RecoCoord coord=input_coord(); in=0; for(int i=0; i odinlog("RecoReaderOdin","concat_data"); // Find and sort file names svector fnames=browse_dir(scandir); STD_list sorted_names; for(unsigned int i=0; i0) fileunmap(fd, dataptr, fsize, 0); rmfile(fname.c_str()); } if(file_ptr!=NULL) fclose(file_ptr); return true; } bool RecoReaderOdin::init(const STD_string& input_filename) { Log odinlog("RecoReaderOdin","init"); ODINLOG(odinlog,infoLog) << "Loading recoInfo ..." << STD_endl; if(recoInfo.load(input_filename)<0) return false; const JDXkSpaceCoords& coords=recoInfo.get_kSpaceCoords(); if(!coords.size()) { ODINLOG(odinlog,errorLog) << "JDXkSpaceCoords empty" << STD_endl; return false; } // get weighting factors for different channels nChannels_cache=coords[0].channels; // assume the same for all ADCs channelFactors=recoInfo.get_ChannelScales(); if(channelFactors.extent(firstDim)0) { ODINLOG(odinlog,infoLog) << "Using CoordinateScaling=" << CoordinateScaling.printbody() << STD_endl; if(CoordinateScaling[1]<0.0) { image_proc_cache="-pflip"; } } else { image_proc_cache=recoInfo.get_ImageProc(); } // Get offset, thereby reverse dimension order from (read,phase,slice) to (slice,phase,read) for(int idir=0; idir<3; idir++) { reloffset_cache(2-idir)=recoInfo.get_RelativeOffset()[idir]; } STD_string scandir=JDXfileName(input_filename).get_dirname(); // Concat data and create filename if(fifoFile=="") { if(!concat_data(rawdata_filename, scandir, recoInfo.get_RawFile())) return false; } else { rawdata_filename=fifoFile; } // get format and endianess of raw data dataformat=recoInfo.get_DataFormat(); if(dataformat=="long") dataformat="s32bit"; // for backwards compatability rawtypesize=TypeTraits::typesize(dataformat); if(!rawtypesize) { ODINLOG(odinlog,errorLog) << "Unrecognized dataformat >" << dataformat << "<" << STD_endl; return false; } bool little_endian=recoInfo.is_LittleEndian(); ODINLOG(odinlog,infoLog) << "Raw data is in file " << rawdata_filename << ", dataformat=" << dataformat << ", typesize=" << rawtypesize << ", little endian=" << little_endian << STD_endl; // swap raw data if neccessary if(little_endian!=little_endian_byte_order()) { ODINLOG(odinlog,infoLog) << "Swabbing raw data ..." << STD_endl; STD_string newrawfile(rawdata_filename+"."+SWAB_SUFFIX); STD_string swabcmd("swab "+itos(rawtypesize)+" "+rawdata_filename+" "+newrawfile+" 20"); system(swabcmd.c_str()); rawdata_filename=newrawfile; } // precalculations to remove zero padding from fid nadc=recoInfo.numof_adcs(); zeroesPerChunk=0; ODINLOG(odinlog,infoLog) << "nadc=" << nadc << STD_endl; if(fifoFile=="") { LONGEST_INT nAdcChunks=recoInfo.get_NumOfAdcChunks(); LONGEST_INT rawheadersize=recoInfo.get_RawHeaderSize(); LONGEST_INT fsize_bytes=filesize(rawdata_filename.c_str()); if(fsize_bytes<=rawheadersize) { ODINLOG(odinlog,errorLog) << "File size of " << rawdata_filename << " too small (fsize_bytes=" << fsize_bytes << ", rawheadersize=" << rawheadersize << " )" << STD_endl; return false; } LONGEST_INT rawfilesize=(fsize_bytes-rawheadersize)/(2*rawtypesize); LONGEST_INT sizePaddedChunk=rawfilesize/nAdcChunks; LONGEST_INT samplesTotal=recoInfo.get_TotalNumOfSamples(); if(samplesTotal>rawfilesize) { if(padZero) { LONGEST_INT padbytes=(samplesTotal-rawfilesize)*2*rawtypesize; ODINLOG(odinlog,infoLog) << "Padding raw data with " << padbytes << " bytes" << STD_endl; if(create_empty_file(rawdata_filename, padbytes, appendMode)) { ODINLOG(odinlog,errorLog) << "Cannot zero pad file : " << lasterr() << STD_endl; return false; } rawfilesize=samplesTotal; } else { ODINLOG(odinlog,errorLog) << "Total number of expected sampling points ( " <0) { prot_cache.load(protfile); // Backwards compatability ODINLOG(odinlog,infoLog) << "Loading protocol from " << protfile << STD_endl; } else { prot_cache=recoInfo.get_protocol(); // The new way: Assume protocol is contained in recoInfo ODINLOG(odinlog,infoLog) << "Using protocol from recoInfo" << STD_endl; } size_cache(0)=1; if(prot_cache.geometry.get_Mode()==voxel_3d) size_cache(0)=prot_cache.seqpars.get_MatrixSize(sliceDirection); size_cache(1)=prot_cache.seqpars.get_MatrixSize(phaseDirection); size_cache(2)=prot_cache.seqpars.get_MatrixSize(readDirection); ODINLOG(odinlog,normalDebug) << "size_cache=" << size_cache << STD_endl; // If series number is zero, set series number according to current scandir number STD_string seriesdescr; int seriesno; prot_cache.study.get_Series(seriesdescr,seriesno); if(seriesno<=0) { seriesno=atoi(JDXfileName(scandir).get_basename().c_str()); // Try passed in scandir number first } if(seriesno<=0) { seriesno=atoi(JDXfileName(getpwd()).get_basename().c_str()); // Try PWD next } prot_cache.study.set_Series(seriesdescr,seriesno); ODINLOG(odinlog,infoLog) << "Using seriesno=" << seriesno << " for file conversion" << STD_endl; // get read-out shape arrays (for ramp-sampling EPI) for(int j=0; j(shape)); readoutShape_cache[j].second=dstsize; ODINLOG(odinlog,normalDebug) << "shape/dstsize(" << j << ")=" << readoutShape_cache[j].first.size() << "/" << readoutShape_cache[j].second << STD_endl; } } // get k-space trajectories for(int itraj=0; itraj(ktraj(iseg,ipt,2), ktraj(iseg,ipt,1), ktraj(iseg,ipt,0)); // reverse order of x,y,z kspaceTraj_cache[itraj](iseg,ipt).weight=1.0; } } } } // get weighting vectors for(int iweight=0; iweight(recoInfo.get_AdcWeightVector(iweight))); } index=0; ri_index=0; chancount=0; return true; } template bool RecoReaderOdin::read_block(T2 dummy, ComplexData<2>& block) { Log odinlog("RecoReaderOdin","read_block"); bool result=true; // Delay opening opening raw data file until neccessary for reading of FIFO if(rawdata_fileptr==NULL) { rawdata_fileptr=FOPEN(rawdata_filename.c_str(),modestring(readMode)); if(rawdata_fileptr==NULL) { ODINLOG(odinlog,errorLog) << "fopen(" << rawdata_filename << "): " << lasterr() << STD_endl; return false; } int offset_bytes=recoInfo.get_RawHeaderSize(); if(offset_bytes>0) { // Only if neccessary, to allow reading from a named pipe if(FSEEK(rawdata_fileptr, offset_bytes, SEEK_SET)) { ODINLOG(odinlog,errorLog) << "fseek: " << lasterr() << STD_endl; return false; } } } int nitems=2*block.size(); T2* ptr=new T2[nitems]; int toberead=nitems; int currpos=0; while(toberead) { // While loop for FIFO int freadresult=fread(ptr+currpos, sizeof(T2), toberead, rawdata_fileptr); if(!freadresult) { // signals an error, even for a FIFO ODINLOG(odinlog,errorLog) << "fread() failed: " << lasterr() << STD_endl; result=false; break; } currpos+=freadresult; toberead=nitems-currpos; } if(result) convert_from_ptr(block, ptr, block.shape()); delete[] ptr; return result; } bool RecoReaderOdin::fetch(RecoCoord& coord, ComplexData<1>& adc) { Log odinlog("RecoReaderOdin","fetch"); if(index>=get_coords().size()) return false; coord=get_coords()[index]; // Load next block of raw data if(!chancount) { kcoord_cache=recoInfo.get_kSpaceCoord(ri_index); rawdata.resize(kcoord_cache.channels,kcoord_cache.adcSize); bool readresult=false; if(dataformat==TypeTraits::type2label((s16bit)0)) readresult=read_block((s16bit)0, rawdata); if(dataformat==TypeTraits::type2label((s32bit)0)) readresult=read_block((s32bit)0, rawdata); if(dataformat==TypeTraits::type2label((float)0)) readresult=read_block((float)0, rawdata); if(!readresult) { ODINLOG(odinlog,errorLog) << "Failed to read coord[" << ri_index << "]" << STD_endl; return false; } // skip padding at end of chunk if(kcoord_cache.flags&recoLastInChunkBit) { int skip_bytes=zeroesPerChunk*kcoord_cache.channels*rawtypesize*2; if(skip_bytes>0) { // Only if neccessary, to allow reading from a named pipe if(FSEEK(rawdata_fileptr, skip_bytes, SEEK_CUR)) { ODINLOG(odinlog,errorLog) << "fseek: " << lasterr() << STD_endl; return false; } } } // reorder data in case of conctatenated acquisitions if(kcoord_cache.concat>1) { if(kcoord_cache.adcSize%kcoord_cache.concat) { ODINLOG(odinlog,errorLog) << "adcSize(" << kcoord_cache.adcSize << ") not a multiple of concat(" << kcoord_cache.concat << ")" << STD_endl; return false; } int onesize=kcoord_cache.adcSize/kcoord_cache.concat; TinyVector shape_concat(kcoord_cache.concat, kcoord_cache.channels, onesize); ODINLOG(odinlog,normalDebug) << "shape_concat=" << shape_concat << STD_endl; ComplexData<3> data_concat(Array(rawdata.c_array(), shape_concat, neverDeleteData).copy()); Range all=Range::all(); for(int icat=0; icat=0) coord.readoutShape=&(readoutShape_cache[kcoord.readoutIndex]); if(kcoord.trajIndex>=0) coord.kspaceTraj=&(kspaceTraj_cache[kcoord.trajIndex]); if(kcoord.weightIndex>=0) coord.weightVec=&(weightVec_cache[kcoord.weightIndex]); coord.dwellTime=recoInfo.get_DwellTime(kcoord.dtIndex); coord.overSamplingFactor=kcoord.oversampling; coord.relCenterPos=kcoord.relcenter; coord.echopos=coord.index[echo]; // Move echo index to echopos to avoid it to interfere with other indices coord.echotrain=coord.index[epi]; // Move EPI index to echotrain to avoid it to interfere with other indices if(coord.index[templtype]==phasecorr_template) { // PE indices can and should be ignored coord.index[line]=0; coord.index[line3d]=0; } else { coord.index[echo]=0; // ignore, echopos will be used instead coord.index[epi]=0; // ignore, echotrain will be used instead } } const STD_vector& RecoReaderOdin::get_coords() const { Log odinlog("RecoReaderOdin","get_coords"); if(!coord_vec_cache.size()) { coord_vec_cache.resize(nadc*nChannels_cache); STD_map repcounter_cache; // to adjust repetition index RecoCoord coord; unsigned int index=0; for(unsigned int iadc=0; iadc odinlog(c_label(),"init"); extension.set_description("Extra file name extension"); append_arg(extension,"extension"); // make this come 1st so it can be easily used when creating recipe prefix=STD_string(".")+SEPARATOR_STR+"image"; prefix.set_cmdline_option("o").set_description("Prefix of output files"); append_arg(prefix,"prefix"); formats=default_format(); formats.set_cmdline_option("f").set_description("Space sepapared list of output formats (file extensions), possible formats are '"+FileIO::autoformats().printbody()+"'"); append_arg(formats,"formats"); imageproc="none"; imageproc.set_cmdline_option("ip").set_description("Command line args for extra processing of final images"); append_arg(imageproc,"imageproc"); storephase=false; storephase.set_cmdline_option("sp").set_description("Store phase in addition to magnitude"); append_arg(storephase,"storephase"); // Add useful options of FileWriteOpts append_arg(wopts.dialect,"wopts.dialect"); append_arg(wopts.wprot,"wopts.wprot"); append_arg(wopts.datatype,"wopts.datatype"); ODINLOG(odinlog,normalDebug) << "storephase=" << bool(storephase) << STD_endl; } bool RecoStore::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<5>& indata=rd.data(Rank<5>()); TinyVector inshape=indata.shape(); int nrep=inshape(0); int nslice=inshape(1); int nphase3d=inshape(2); int nphase=inshape(3); int nread=inshape(4); if(nslice>1 && nphase3d>1) { ODINLOG(odinlog,errorLog) << "Implement me: multi-slice 3D data" << STD_endl; return false; } Data fdata(inshape); if(rd.mode==RecoData::real_data || rd.mode==RecoData::weighted_real_data) fdata=creal(indata); else fdata=cabs(indata); ODINLOG(odinlog,normalDebug) << "storephase=" << bool(storephase) << STD_endl; Data pdata; if(storephase) { pdata.resize(inshape); pdata=phase(indata); } TinyVector storeshape(nrep, nslice*nphase3d, nphase, nread); // collapse slices and phase3d to one dimension Data storefdata(storeshape); Data storepdata; if(storephase) storepdata.resize(storeshape); if(nslice>1) { storefdata(all,all,all,all)=fdata(all,all,0,all,all); if(storephase) storepdata(all,all,all,all)=pdata(all,all,0,all,all); } else { storefdata(all,all,all,all)=fdata(all,0,all,all,all); if(storephase) storepdata(all,all,all,all)=pdata(all,0,all,all,all); } // create protocol Protocol prot(controller.protocol()); if(rd.override_protocol) prot=(*(rd.override_protocol)); // make sure protocol dimension are set correctly prot.seqpars.set_NumOfRepetitions(inshape(0)); prot.seqpars.set_MatrixSize(phaseDirection, inshape(3)); prot.seqpars.set_MatrixSize(readDirection, inshape(4)); // Store float data whenever possible prot.system.set_data_type(TypeTraits::type2label(float(0))); Protocol protphase(prot); // Add fileid to series description to distinguish separate protocols STD_string idstr=rd.coord().print(RecoIndex::filename); STD_string seriesdescr; int seriesno; prot.study.get_Series(seriesdescr,seriesno); if(idstr!="") seriesdescr=idstr+"_"+seriesdescr; // make idstr become first for better lexicographical comparison of filenames prot.study.set_Series(seriesdescr,seriesno); protphase.study.set_Series(seriesdescr+"_phase",seriesno); mutex.lock(); pdmap[prot].reference(storefdata); if(storephase) pdmap[protphase].reference(storepdata); mutex.unlock(); return execute_next_step(rd,controller); } bool RecoStore::store_images(const RecoController& controller) { Log odinlog(c_label(),"store_images"); svector format=tokens(formats); ODINLOG(odinlog,normalDebug) << "formats/format=" << formats << "/" << format.printbody() << STD_endl; if(!filterchain.apply(pdmap)) return false; // Store all data in one file/directory, if possible for(unsigned int i=0; i odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { STD_string procstr; if(imageproc!="none") procstr=imageproc; else procstr=context.controller.image_proc(); ODINLOG(odinlog,normalDebug) << "procstr=" << procstr << STD_endl; if(!filterchain.init(procstr)) return false; } ODINLOG(odinlog,normalDebug) << "storephase=" << bool(storephase) << STD_endl; if(context.mode==RecoQueryContext::finalize) { if(!store_images(context.controller)) return false; } return RecoStep::query(context); } //////////////////////////////////////////////////////////////////////////// bool RecoReal::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); rd.mode=RecoData::real_data; return execute_next_step(rd,controller); } //////////////////////////////////////////////////////////////////////////// bool RecoMagn::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); ComplexData<3>& indata=rd.data(Rank<3>()); indata = float2real(cabs(indata)); return execute_next_step(rd,controller); } odin-1.8.5/odinreco/odinreco.cpp0000644000175000017500000000017611322062351013506 00000000000000#include "odinreco.h" #include const char* Reco::get_compName() {return "Reco";} LOGGROUNDWORK(Reco) odin-1.8.5/odinreco/collector_code.h0000644000175000017500000000623111322062351014327 00000000000000#include "collector.h" template bool RecoCollector::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); TinyVector index; Coll::create_index(rd.coord(), index); TinyVector shape; Coll::create_shape(rd.coord(), shape); // create shape of collected data TinyVector collshape; for(int i=0; i()).extent(i); ODINLOG(odinlog,normalDebug) << "index/shape/collshape=" << index << "/" << shape << "/" << collshape << STD_endl; if(!product(collshape)) { ODINLOG(odinlog,errorLog) << "Zero-size shape " << collshape << STD_endl; return false; } // adjust coordinate to output dims for correct indexing of todo map modify_coord(rd.coord()); // create new view of input data ComplexData indata; rd.data(Rank()).convert_to(indata); // bring to same rank // create domains for copying input data to the correct position TinyVector lowin=0; TinyVector uppin=0; TinyVector lowdst=0; TinyVector uppdst=0; for(int i=0; i()).extent(i)-1; ODINLOG(odinlog,normalDebug) << "lowin/uppin=" << lowin << "/" << uppin << STD_endl; ODINLOG(odinlog,normalDebug) << "lowdst/uppdst=" << lowdst << "/" << uppdst << STD_endl; RectDomain indomain(lowin,uppin); RectDomain dstdomain(lowdst,uppdst); // fill data mutex.lock(); ComplexData& dataref=datamap[rd.coord()]; if(dataref.shape()!=collshape) { dataref.resize(collshape); dataref=STD_complex(0.0); // Initialize to zero for partial k-space acquisition } dataref(dstdomain)=dataref(dstdomain)+indata(indomain); mutex.unlock(); unsigned int numof_count=0; if(use_numof) numof_count=product(shape); if( completed(rd.coord(),numof_count) ) { ODINLOG(odinlog,normalDebug) << " data " << collshape << " complete" << STD_endl; // fill rd with collected data mutex.lock(); typename DataMap::iterator it=datamap.find(rd.coord()); // typename is necessary here for GCC4 rd.data(Rank()).free(); // deallocate input data rd.data(Rank()).reference(it->second); datamap.erase(it); // delete entry from map to save memory and to trigger initialization if data is needed again mutex.unlock(); if(!execute_next_step(rd,controller)) return false; } return true; } template bool RecoCollector::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { if(!use_numof) { RecoCoord outmask=context.coord; modify_coord(outmask); if(!calculate_count(context, context.coord, outmask)) return false; } } return RecoStep::query(context); } odin-1.8.5/odinreco/controller.cpp0000644000175000017500000010232411734622163014077 00000000000000#include "controller.h" #include "data.h" #include "step.h" #include "reader.h" #include "measindex.h" #include "fieldmap.h" // for posted_fmap_str #include "driftcorr.h" // for posted_drift_str RecoController::RecoController(JcampDxBlock& parblock) : input(0), pipeline(0), factory(0), pmeter(display) { jobs=numof_cores(); jobs.set_cmdline_option("j").set_description("Number of concurrent jobs(threads) in reco"); parblock.append(jobs); recipe.set_cmdline_option("rp").set_description("Reco recipe (pipeline layout)"); parblock.append(recipe); recipeFile.set_cmdline_option("rf").set_description("Read reco recipe (pipeline layout) from this file"); parblock.append(recipeFile); select.set_cmdline_option("s").set_description("Select certain dimensions ranges (space separated list of 'dim=selection', e.g. slice=3)"); parblock.append(select); timeout=0; timeout.set_cmdline_option("to").set_description("Timeout for reco in seconds, 0=inifinite"); parblock.append(timeout); maxrecursion=100; maxrecursion.set_cmdline_option("mr").set_description("Maximum recursion of reconstruction when waiting for blackboard data, zero means no recursion"); parblock.append(maxrecursion); conjPhaseFT=false; conjPhaseFT.set_cmdline_option("cp").set_description("Use direct Fourier transform with conjugate-phase correction instead of gridding"); parblock.append(conjPhaseFT); slidingWindow=false; slidingWindow.set_cmdline_option("sw").set_description("Sliding window reconstruction, e.g. for Spiral/PROPELLER"); parblock.append(slidingWindow); keyhole=false; keyhole.set_cmdline_option("kh").set_description("Keyhole reconstruction, e.g. for PROPELLER"); parblock.append(keyhole); sepChannels=false; sepChannels.set_cmdline_option("sc").set_description("Store images from channels separately instead of combining them"); parblock.append(sepChannels); dumpKspace=false; dumpKspace.set_cmdline_option("ks").set_description("Store k-space data"); parblock.append(dumpKspace); disableHomodyne=false; disableHomodyne.set_cmdline_option("dh").set_description("Disable homodyne reconstruction"); parblock.append(disableHomodyne); disableMultiFreq=false; disableMultiFreq.set_cmdline_option("dm").set_description("Disable fieldmap-based multi-frequency reconstruction"); parblock.append(disableMultiFreq); disableSliceTime=false; disableSliceTime.set_cmdline_option("ds").set_description("Disable slice-time correction"); parblock.append(disableSliceTime); disableGrappa=false; disableGrappa.set_cmdline_option("dg").set_description("Disable GRAPPA interpolation"); parblock.append(disableGrappa); phaseCourse=false; phaseCourse.set_cmdline_option("pt").set_description("Combine and store phase timecourse from all channels"); parblock.append(phaseCourse); qcspike=false; qcspike.set_cmdline_option("qs").set_description("Quality control: Check for spikes in data"); parblock.append(qcspike); preproc3d="null"; preproc3d.set_cmdline_option("prp").set_description("Recipe for post processing of 3D volume before channel combining"); parblock.append(preproc3d); postproc3d="null"; postproc3d.set_cmdline_option("pop").set_description("Recipe for post processing of 3D volume after channel combining"); parblock.append(postproc3d); dumpRawPrefix=""; dumpRawPrefix.set_cmdline_option("rd").set_description("Dump signal data and its protocol to files with this prefix, do not reconstruct images"); parblock.append(dumpRawPrefix); fieldmapFile=""; fieldmapFile.set_cmdline_option("fm").set_description("Load fieldmap data from this file"); parblock.append(fieldmapFile); driftcalcFile=""; driftcalcFile.set_cmdline_option("dcw").set_description("Calculate and store field drift to file with this prefix"); parblock.append(driftcalcFile); driftcorrFile=""; driftcorrFile.set_cmdline_option("dcr").set_description("Load field drift from this file"); parblock.append(driftcorrFile); factory=new RecoStepFactory(&parblock); } RecoController::~RecoController() { delete_countmap_cache(); delete factory; } TinyVector RecoController::reloffset() const { TinyVector result; result=0.0; MutexLock lock(inputmutex); if(input) result=input->reloffset(); return result; } dvector RecoController::dim_values(recoDim dim) const { dvector result; MutexLock lock(inputmutex); if(input) result=input->dim_values(dim); return result; } STD_string RecoController::image_proc() const { STD_string result; MutexLock lock(inputmutex); if(input) result=input->image_proc(); return result; } TinyVector RecoController::image_size() const { TinyVector result; result=0; MutexLock lock(inputmutex); if(input) result=input->image_size(); return result; } TinyVector RecoController::kspace_extent() const { TinyVector result; result=0; TinyVector imgshape=image_size(); for(int i=0; i odinlog("RecoController","inquire_data"); if(!status) return false; // Return immediately if an error occured, i.e. do not wait for any data in this case ODINLOG(odinlog,normalDebug) << "Requested " << label << "(" << data.coord().print() << ")" << STD_endl; if(blackboard.inquire(label,data)) return true; // 1st shot without feeding pipeline or signalling waiting state ODINLOG(odinlog,normalDebug) << label << "(" << data.coord().print() << ") not ready" << STD_endl; int depth=thread_depth[Thread::self()]; if(depthfirst)+": "+it->second+"\n"; } return false; } // ODINLOG(odinlog,normalDebug) << "sleeping while waiting for " << label << STD_endl; // sleep_ms(10); // Avoid tight inifinite loop, give other threads CPU time to process their input } ODINLOG(odinlog,normalDebug) << "blocked inquire successful" << STD_endl; decr_waiting_threads(); return true; } void RecoController::delete_countmap_cache() { for(STD_map::const_iterator it=countmap_cache.begin(); it!=countmap_cache.end(); ++it) { delete it->second; } countmap_cache.clear(); } const CoordCountMap* RecoController::create_count_map(const RecoCoord& mask) const { Log odinlog("RecoController","create_count_map"); if(!input) { ODINLOG(odinlog,errorLog) << "Input reader not initialized yet" << STD_endl; return 0; } STD_string maskstring=mask.print(RecoIndex::all); // Using full printout as unique key for masks STD_map::const_iterator it=countmap_cache.find(maskstring); if(it!=countmap_cache.end()) { ODINLOG(odinlog,normalDebug) << "Using cached countmap for " << mask.print() << STD_endl; return it->second; } const STD_vector& coords=input->get_coords(); ODINLOG(odinlog,normalDebug) << "sizeof(RecoCoord)/coords.size()=" << sizeof(RecoCoord) << "/" << coords.size() << STD_endl; CoordCountMap* countmap=new CoordCountMap; ODINLOG(odinlog,normalDebug) << "coords.size()=" << coords.size() << STD_endl; for(unsigned int iadc=0; iadcbegin(); it!=countmap->end(); ++it) { const RecoCoord& coord=it->first; ODINLOG(odinlog,normalDebug) << "coord(" << it->second << ")=" << coord.print() << STD_endl; for(unsigned int idim=0; idim1.0) has_oversampling_cache=true; if(coord.relCenterPos!=0.5) has_relcenter_cache=true; } } for(int idim=0; idim1) printed+="#"+STD_string(recoDimLabel[idim])+"="+itos(numof[idim])+" "; } ODINLOG(odinlog,normalDebug) << "numof: " << printed << STD_endl; return true; } static bool in_tracefunction=false; // to avoid recursion void RecoController::tracefunction(const LogMessage& msg) { if(in_tracefunction) return; in_tracefunction=true; int selfid=Thread::self(); if(selfid!=controlthread) STD_cerr << "job" << selfid << "-"; // Do not prefix messages of control thread STD_cerr << msg.str(); in_tracefunction=false; } RecoStep* RecoController::create_pipeline(const STD_string& rec, const RecoCoord* initial_coord, int argc, char* argv[]) const { Log odinlog("RecoController","create_pipeline"); RecoStep* result=0; svector toks(tokens(rec,'|','(',')')); RecoCoord coord; // coordinate interfaces during pipeline if(initial_coord) coord=(*initial_coord); RecoStep* laststep=0; for(unsigned int itok=0; itok" << toks[itok] << "/" << functorstr << "/" << args << "<" << STD_endl; RecoStep* step=factory->create(functorstr); if(!step) { ODINLOG(odinlog,errorLog) << "Could not create functor with label >" << functorstr << "<" << STD_endl; return 0; // Return immediately if functor could not be created } if(args!="") step->set_args(args); if(!step->pipeline_init(*this,coord)) { ODINLOG(odinlog,errorLog) << "Could not initialize pipeline of functor >" << functorstr << "< with arguments >" << args << "<" << STD_endl; return 0; } // check interface between steps RecoCoord coordin=step->input_coord(); if(!coord.compatible(coordin)) { STD_string lastlabel; if(laststep) lastlabel=laststep->label(); ODINLOG(odinlog,errorLog) << "Interface mismatch: output(" << lastlabel << ")=" << coord.print(RecoIndex::all) << " does not match input(" << step->label() << ")=" << coordin.print(RecoIndex::all) << STD_endl; return 0; } step->modify_coord(coord); // update interface if(!itok) result=step; if(laststep) { laststep->set_next_step(step); } laststep=step; } return result; } STD_string RecoController::stepmanual() const { return factory->manual(); } ////////////////////////////////////////////////////////////////////////////////////// class TimeOutThread : public Thread { public: TimeOutThread(unsigned int seconds) : secs(seconds) {} bool init(unsigned int seconds) { return true; } private: void run() { Log odinlog("TimeOutThread","run"); sleep_ms(1000*secs); ODINLOG(odinlog,warningLog) << "Reco timed out after " << secs << " seconds, exiting" << STD_endl; exit(1); } unsigned int secs; }; ////////////////////////////////////////////////////////////////////////////////////// template bool RecoController::get_kspace_sampling_pattern(const RecoCoord& mask, unsigned int& reduction_factor, bool& partial_fourier) const { Log odinlog("RecoController","get_kspace_sampling_pattern"); reduction_factor=1; partial_fourier=false; if(numof_cache[Dim]<2) return true; RecoMeasIndex > measlines; // exclude unimportant dimensions for effiency measlines.init(mask, *this); for(unsigned int iorth=0; iorth=int(reduction_factor)) partial_fourier=true; } return true; } ////////////////////////////////////////////////////////////////////////////////////// bool RecoController::autorecipe(const RecoCoord& mask, STD_string& result) const { Log odinlog("RecoController","autorecipe"); result=""; ODINLOG(odinlog,infoLog) << "Creating default recipe ..." << STD_endl; unsigned int reduction_factor=0; bool partial_fourier=false; if(!get_kspace_sampling_pattern(mask,reduction_factor, partial_fourier)) return false; ODINLOG(odinlog,normalDebug) << "reduction_factor/partial_fourier=" << reduction_factor << "/" << partial_fourier << STD_endl; unsigned int reduction_factor3d=0; bool partial_fourier3d=false; if(!get_kspace_sampling_pattern(mask,reduction_factor3d, partial_fourier3d)) return false; ODINLOG(odinlog,normalDebug) << "reduction_factor3d/partial_fourier3d=" << reduction_factor3d << "/" << partial_fourier3d << STD_endl; unsigned int max_reduction_factor=STD_max(reduction_factor,reduction_factor3d); unsigned int reduction_factor_prot=protocol().seqpars.get_ReductionFactor(); if(max_reduction_factor!=reduction_factor_prot) { ODINLOG(odinlog,warningLog) << "Mismatch: max_reduction_factor(" << max_reduction_factor << ")=!reduction_factor_prot(" << reduction_factor_prot << ")" << STD_endl; } bool max_partial_fourier=partial_fourier || partial_fourier3d; bool partial_fourier_prot=(protocol().seqpars.get_PartialFourier()>0.0); if(max_partial_fourier!=partial_fourier_prot) { ODINLOG(odinlog,warningLog) << "Mismatch: max_partial_fourier(" << max_partial_fourier << ")=!partial_fourier_prot(" << partial_fourier_prot << ")" << STD_endl; } STD_string driftcorrstr; if(driftcorrFile!="") driftcorrstr="driftcorr | "; STD_string averagestr; if(numof_cache[average]>1) averagestr="averagecoll | averagesum | "; bool has_blade=(numof_cache[cycle]>1 && !has_traj); // Assume PROPELLER STD_string adcprep; if(!has_traj && has_relcenter_cache) adcprep+="adc_pad | "; STD_string adcdeapodize; STD_string adcdeapodize_blade; if(has_readoutshape) { STD_string gridarg; if(has_blade) gridarg="(false)"; // no deapo shift adcprep+="adc_gridprep | grid1d"+gridarg+" | "; // regrid first to correct for antisymmetric gradient distortions before reflecting / adc_regrid does not work well for blades yet if(!dumpKspace) { if(has_blade) adcdeapodize_blade="deapodize1d | "; else adcdeapodize ="deapodize1d | "; } } if(has_flag_cache&recoReflectBit) adcprep+="adc_reflect | "; STD_string chanstr; if(numof_cache[channel]>1 && !sepChannels && !dumpKspace) chanstr="chancoll | chansum | "; STD_string corrstr; STD_string navstr; STD_string phasecorrstr; if(has_templcorr_cache[phasecorr_template]) { phasecorrstr="phasecorr | "; corrstr+="templtype=P { "+averagestr+adcprep+"echocoll | phasemap}"; } STD_string oversamplingstr; if(has_oversampling_cache && !dumpKspace) oversamplingstr="oversampling | "; STD_string mfreqbegin; STD_string mfreqend; STD_string chansumopt; bool ext_fieldmap=fieldmapFile!=""; if(!disableMultiFreq && (has_templcorr_cache[fieldmap_template] || ext_fieldmap) ) { if(!conjPhaseFT && !dumpKspace) { mfreqbegin="multifreq | "; mfreqend="freqcoll | freqcomb | "; } if(!ext_fieldmap) { if(corrstr!="") corrstr+="; "; STD_string fmap_offsetstr="offset | "; if(has_blade && mfreqend!="") fmap_offsetstr=""; // disable offset for multi-frequency reco of blades //STD_string cyclerotstr; //if(has_blade) cyclerotstr="cyclerot | "; //corrstr+="templtype=F { adc_reflect | kspace | offset | filter(Hann) | fft | tecoll | fieldmap | "+chanstr+"interpolate | "+cyclerotstr+"post(fieldmap) | "+oversamplingstr+"slicecoll | image | store(fieldmap)}"; corrstr+="templtype=F { adc_reflect | kspace |"+fmap_offsetstr+"filter(Hann) | fft | tecoll | fieldmap | "+chanstr+oversamplingstr+" post(fieldmap) | "+"slicecoll | image | store(fieldmap)}"; } } if(has_navigator_cache[epi_navigator]) { phasecorrstr="epinavcorr | "; if(navstr!="") navstr+="; "; navstr+="navigator=e { "+adcprep+"echocoll | epinavscan }"; } STD_string interpolstr; if(!disableGrappa) { bool has_grappa_template=has_templcorr_cache[grappa_template]; if(has_grappa_template || reduction_factor>1 || reduction_factor3d>1) { STD_string redfactstr=itos(reduction_factor); STD_string redfactstr3d=itos(reduction_factor3d); if(has_grappa_template) { if(corrstr!="") corrstr+="; "; corrstr+="templtype=G {"+averagestr+adcprep+phasecorrstr+"kspace | chancoll | "; if(reduction_factor>1) corrstr+="grappaweightstempl(" +redfactstr+ ")"; if(reduction_factor3d>1) corrstr+="grappaweightstempl3d("+redfactstr3d+")"; corrstr+="}"; } STD_string weightsstr; if(!has_grappa_template) { if(reduction_factor>1) weightsstr+="grappaweights("+ redfactstr+ ") | "; if(reduction_factor3d>1) weightsstr+="grappaweights3d("+redfactstr3d+") | "; } interpolstr+="chancoll | "+weightsstr; STD_string keephshapestr; if(has_blade) keephshapestr=",true"; // do not expand k-space to image matrix size if(reduction_factor>1) interpolstr+="grappa(" +redfactstr+keephshapestr+ ") | "; if(reduction_factor3d>1) interpolstr+="grappa3d("+redfactstr3d+keephshapestr+") | "; interpolstr+="chansplit | "; } } STD_string fftstr="fft | "; if(!has_traj && !disableHomodyne) { unsigned int homodyne_dims=0; if(has_relcenter_cache) {fftstr="homodyneread | "; homodyne_dims++;} if (partial_fourier && !has_blade) {fftstr="homodyne | "; homodyne_dims++;} if(partial_fourier3d) {fftstr="homodyne3d | "; homodyne_dims++;} if(homodyne_dims>1) { ODINLOG(odinlog,errorLog) << "Not yet implemented: partial Fourier reconstruction in more than one direction" << STD_endl; return false; } } STD_string offsetstr="offset | "; if(dumpKspace) { fftstr=""; offsetstr=""; } STD_string swstr; if(slidingWindow || (keyhole && has_blade) ) swstr="slidingwindow | "; STD_string spikestr=""; if(qcspike) spikestr="qcspike | "; // insert after k-space has been collected but before interpolation STD_string kspacestr=adcprep + phasecorrstr + "kspace | " + spikestr + interpolstr; STD_string adcbaselinestr; STD_string deapodizestr; STD_string gridstr; if(has_traj) { adcbaselinestr="adc_baseline | "; if(conjPhaseFT) { kspacestr="adc_weight | conjphase | " + spikestr + swstr + "cyclecoll | cyclesum | "; offsetstr=""; fftstr=""; } else { kspacestr="grid2d | line3dcoll | " + spikestr + swstr + "cyclecoll | cyclesum | "; if(!dumpKspace) deapodizestr="deapodize2d | "; gridstr="gridcut | "; } oversamplingstr=""; } STD_string bladestr; if(has_blade) { STD_string keyholeopt; if(keyhole) keyholeopt="(true)"; // partial fourier reconstruction has to be applied before combining the blades! STD_string bladefftstr = ""; if (mfreqend!="") bladefftstr = "fft | "; if (!disableHomodyne && partial_fourier) { if (mfreqend!="") bladefftstr = "homodyne | "; else bladefftstr = "homodyne | fft(false) | "; } STD_string bladecorrstr="bladecorr | "; if(mfreqend!="") bladecorrstr=mfreqend+"magn | "+adcdeapodize_blade+"fft(false) | "; mfreqend=""; // do not use in rest of pipeline bladestr=bladefftstr+bladecorrstr+swstr+"cyclecoll | bladecomb"+keyholeopt+" | grid2d | line3dcoll | "; if(!dumpKspace) deapodizestr="deapodize2d | "; gridstr="gridcut | "; } STD_string maskstr; if(has_traj || has_blade) maskstr="circmask | "; STD_string slicetimestr; if(!disableSliceTime && numof_cache[repetition]>1 && numof_cache[slice]>1 && !dumpKspace) { slicetimestr="slicetime | "; } STD_string pp3dpre; STD_string pp3dpost; if(!dumpKspace) { if(preproc3d!="null") pp3dpre=preproc3d; else pp3dpre=shrink(input->preProc3D()); if(postproc3d!="null") pp3dpost=postproc3d; else pp3dpost=shrink(input->postProc3D()); if(pp3dpre.size() && (pp3dpre[pp3dpre.size()-1]!='|') ) pp3dpre+="|"; if(pp3dpost.size() && (pp3dpost[pp3dpost.size()-1]!='|') ) pp3dpost+="|"; } STD_string freqcomb_and_oversampling=mfreqend+oversamplingstr; if(ext_fieldmap) freqcomb_and_oversampling=oversamplingstr+mfreqend; // remove oversampling 1st before combining with external fieldmap STD_string phasecoursestr; if(phaseCourse) { phasecoursestr="switch( { chanrepcoll | phasecourse | repsplit | "+ freqcomb_and_oversampling + "slicecoll | image | " + slicetimestr + "store(phasecourse) } ) | "; } STD_string kspaceprep="zerofill | filter | "; if(dumpKspace) kspaceprep=""; if(numof_cache[dti]>1) pp3dpost+="dti | "; result = driftcorrstr + averagestr + adcbaselinestr + mfreqbegin + kspacestr + bladestr + offsetstr + kspaceprep + fftstr + adcdeapodize + deapodizestr + gridstr + phasecoursestr + pp3dpre + chanstr + freqcomb_and_oversampling + pp3dpost + maskstr + "slicecoll | image | " + slicetimestr + "store"; if(driftcalcFile!="") { result= averagestr + adcbaselinestr + kspacestr + bladestr + offsetstr + kspaceprep + fftstr + adcdeapodize + deapodizestr + gridstr + oversamplingstr + " chanrepslicecoll | driftcalc | dump("+driftcalcFile+",asc)"; } if(disableGrappa || corrstr!="") { result="switch(templtype=N { "+result+"} ; "+corrstr+")"; } if(navstr!="") { result="switch(navigator=n { "+result+"} ; "+navstr+")"; } ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return true; } ////////////////////////////////////////////////////////////////////////////////////// bool RecoController::init(RecoReaderInterface* reader, JcampDxBlock& opts, int argc, char* argv[]) { Log odinlog("RecoController","init"); input=reader; if(!input) { ODINLOG(odinlog,errorLog) << "no reader provided" << STD_endl; return false; } // Initialize default protocol by reader, do this as afirst step prot_cache=input->protocol(); bool modify_args=false; // Do not modify command-line args since the same option may be used in different template instantiations // Parse recoInfo args svector riargs(tokens(input->cmdline_opts(),' ','\"','\"')); int riargc=riargs.size()+1; // 1st string is neglected ODINLOG(odinlog,normalDebug) << "riargc=" << riargc << STD_endl; char* riargv[riargc+1]; for(int i=0; i<(riargc+1); i++) riargv[i]=0; for(unsigned int i=0; i0) { (new TimeOutThread(timeout))->start(); } #endif // Parse selected dimensions RecoCoord initcoord; STD_map selmap; svector seltoks(tokens(select)); for(unsigned int isel=0; isel reloffset() const; /** * Extra command-line arguments for processing of final images. */ STD_string image_proc() const; /** * Returns the image size, will be used if it cannot be determined from the k-space * coordinates (i.e. when gridding). */ TinyVector image_size() const; /** * Returns the extent of the k-space in each direction (in rad/mm) */ TinyVector kspace_extent() const; /** * Returns the scan protocol. */ const Protocol& protocol() const {return prot_cache;} /** * Announces to blackboard that data with identifier 'label' will become available during pipeline execution. */ void announce_data(const STD_string& label) {blackboard.announce(label);} /** * Posts 'data' with identifier 'label' on blackboard, it will be indexed according to the k-space coordinate in 'data'. */ void post_data(const STD_string& label, const RecoData& data) {blackboard.post(label,data);} /** * Returns whether data with 'label' will become available during pipeline execution. */ bool data_announced(const STD_string& label) {return blackboard.announced(label);} /** * Returns 'data' with identifier 'label' for k-space coordinate set in 'data' from blackboard. * Waits until data becomes available. Returns 'true' if data is available, otherwise returns 'false' if all data was processed * and the requested data was not available. */ bool inquire_data(const STD_string& label, RecoData& data); /** * Returns a map where the key are k-space coordinates * (except those not in 'mask') and the value of the map is a count * of ADC indices with this particular k-space coordinate. */ const CoordCountMap* create_count_map(const RecoCoord& mask) const; /** * Creates the maximum extent of reco dimension in 'numof' * using all coordinates except those not in 'mask'. * In addition, returns a printed version of the result in 'printed'. */ bool create_numof(const RecoCoord& mask, unsigned short numof[n_recoDims], STD_string& printed) const; /** * Creates a pipeline and returns its 1st functor according to the recipe (pieline layout) given in 'rec'. * Checking of input/output dimension match starts with 'initial_coord', if non-zero. * Returns zero if the pipeline could not be created because of input/output dimension mismatches. */ RecoStep* create_pipeline(const STD_string& rec, const RecoCoord* initial_coord=0, int argc=0, char* argv[]=0) const; /** * Returns documention 'code' of steps for doxygen. */ STD_string stepmanual() const; private: friend class RecoThread; // Options JDXint jobs; JDXstring recipe; JDXstring recipeFile; JDXstring select; JDXint timeout; JDXint maxrecursion; JDXbool conjPhaseFT; JDXbool slidingWindow; JDXbool keyhole; JDXbool sepChannels; JDXbool dumpKspace; JDXbool disableHomodyne; JDXbool disableMultiFreq; JDXbool disableSliceTime; JDXbool disableGrappa; JDXbool phaseCourse; JDXbool qcspike; JDXstring preproc3d; JDXstring postproc3d; JDXstring dumpRawPrefix; JDXstring fieldmapFile; JDXstring driftcalcFile; JDXstring driftcorrFile; bool execute_pipeline(); bool prepare_pipeline(); bool finalize_pipeline(); bool feed_pipeline(); bool dump_raw() const; static void tracefunction(const LogMessage& msg); static int controlthread; template bool get_kspace_sampling_pattern(const RecoCoord& mask, unsigned int& reduction_factor, bool& partial_fourier) const; bool autorecipe(const RecoCoord& mask, STD_string& result) const; typedef STD_map WaitingMap; WaitingMap waiting; STD_string waiting_error; Mutex waiting_mutex; void incr_waiting_threads(const STD_string& condition) {MutexLock lock(waiting_mutex); waiting[Thread::self()]=condition;} void decr_waiting_threads() {MutexLock lock(waiting_mutex); waiting.erase(waiting.find(Thread::self()));} unsigned int numof_waiting_threads() {MutexLock lock(waiting_mutex); return waiting.size();} STD_map thread_depth; // trace the depth (recursion level) of each thread RecoReaderInterface* input; mutable Mutex inputmutex; RecoStep* pipeline; RecoStepFactory* factory; RecoBlackBoard blackboard; ProgressDisplayConsole display; // Create display before pmeter ProgressMeter pmeter; // ProgressMeter is thread-safe unsigned short numof_cache[n_recoDims]; mutable bool has_readoutshape; mutable unsigned char has_flag_cache; mutable bool has_templcorr_cache[n_templateTypes]; mutable bool has_navigator_cache[n_navigatorTypes]; mutable bool has_traj; mutable bool has_oversampling_cache; mutable bool has_relcenter_cache; Protocol prot_cache; volatile bool status; // Although it is used in different threads, we will assume that reads/writes to bool are atomic mutable STD_map countmap_cache; // cache countmap since the same countmap is calculated several times in create_count_map() void delete_countmap_cache(); }; /** @} */ #endif odin-1.8.5/odinreco/grid_code.h0000644000175000017500000002064411455553545013313 00000000000000#include "grid.h" #include "data.h" #include "controller.h" static const char* deapodize_post_str="deapodize"; template void RecoGrid::init() { deapo_shift=true; deapo_shift.set_description("Shift deapodization function for correct offset"); append_arg(deapo_shift,"deapo_shift"); kernel.set_funcpars("Gauss"); kernel.set_cmdline_option("kg"+postfix()).set_description("Kernel function for "+postfix()+" k-space gridding"); append_arg(kernel,"kernel"); kernelwidth=sqrt(float(3-NDim))*3.0; // found empirically kernelwidth.set_cmdline_option("kw"+postfix()).set_unit("Pixel").set_description("Kernel width for "+postfix()+" k-space gridding"); append_arg(kernelwidth,"kernelwidth"); gridScale = 1.0; gridScale.set_cmdline_option("gs").set_description("Scale Factor for the grid used for gridding"); append_arg(gridScale,"gridScale"); } template TinyVector RecoGrid::gridshape(const RecoCoord& coord, RecoController& controller) { Log odinlog("RecoGrid","gridshape"); TinyVector imagesize=controller.image_size(); TinyVector result; for(int i=0; isecond)>0) result(0)=coord.readoutShape->second; // already includes oversampling else result(0)=int(result(0)*coord.overSamplingFactor+0.5); // only for ADC regridding, oversampling will be removed later in image domain } ODINLOG(odinlog,normalDebug) << "result=" << result << STD_endl; return result; } template const Gridding& RecoGrid::get_gridder(const RecoCoord& coord, RecoController& controller) { Log odinlog(c_label(),"get_gridder"); MutexLock lock(gridmutex); const KspaceTraj* traj=coord.kspaceTraj; // access is protected by mutex typename GridderMap::const_iterator it=gridmap.find(traj); if(it==gridmap.end()) { Gridding& gridder=gridmap[traj]; float appGridScale = gridScale; if (NDim == 1) appGridScale = 1.0; // don't use grid scaling for 1D Gridding TinyVector dstshape=gridshape(coord, controller); int nseg=traj->extent(0); // e.g. spiral segments int npts=traj->extent(1); STD_vector > srccoords(nseg*npts); // all segments in one gridder for correct weighting of src values for(int iseg=0; iseg& kpoint=(*traj)(iseg,ipt).coord; TinyVector& srcpoint=srccoords[iseg*npts+ipt].coord; for(int i=0; i kmax=controller.kspace_extent(); TinyVector dstextent; for(int i=0; i sampldens(dstshape); sampldens=gridder.init(dstshape, dstextent, srccoords, kernel, kwidth); // sampldens.autowrite("sampldens.jdx"); // Create magnitude correction for regridded data according to the gridding kernel used int deapo_os_factor=4; // oversampling to account for small kernels TinyVector shape_os(deapo_os_factor*dstshape); ComplexData kspace_kernel_os(shape_os); kspace_kernel_os=STD_complex(0.0); // fill k-space with gridding kernel for(int i=0; i index=kspace_kernel_os.create_index(i); TinyVector dist=index-shape_os/2; float radius=secureDivision( sqrt(double(sum(dist*dist))), 0.5*deapo_os_factor*kernelwidth*appGridScale); if(radius<=1.0) kspace_kernel_os(index)=STD_complex(kernel.calculate(radius)); } ODINLOG(odinlog,normalDebug) << "deapo_shift=" << deapo_shift << STD_endl; if(deapo_shift) { // Take spatial offset into account TinyVector reloffset=controller.reloffset(); TinyVector reloffset_os; for(int i=0; i0.0) kspace_kernel_os.modulate_offset(reloffset_os); } // FFT and cutting out central part with de-apodize function kspace_kernel_os.fft(); Data apodize(dstshape); apodize=cabs(kspace_kernel_os(RectDomain((shape_os-dstshape)/2, (shape_os-dstshape)/2+dstshape-1))); // apodize.autowrite("apodize"+ptos(traj)+".jdx"); if(min(apodize)>0.0) { RecoData rdposted; // post separately for templates rdposted.coord().index[templtype]=coord.index[templtype]; rdposted.coord().index[templtype].set_mode(RecoIndex::separate); rdposted.data(Rank()).reference(float2real(mean(apodize)/apodize)); controller.post_data(deapodize_post_str+postfix(), rdposted); } else { ODINLOG(odinlog,warningLog) << "FT of gridding kernel contains zero, not applying de-apodize correction" << STD_endl; } return gridder; } return it->second; } template bool RecoGrid::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); if(!rd.coord().kspaceTraj) { ODINLOG(odinlog,errorLog) << "No kspaceTraj available for coord=" << rd.coord().print() << STD_endl; return false; } rd.coord().gridScaleFactor = gridScale; const Gridding& gridder=get_gridder(rd.coord(), controller); TinyVector outshape=gridshape(rd.coord(), controller); if (NDim > 1) { for (int i=0; i outdata(outshape); ComplexData<1>& adc=rd.data(Rank<1>()); int adcSize=adc.extent(0); ODINLOG(odinlog,normalDebug) << "adcSize=" << adcSize << STD_endl; unsigned int offset=0; if(rd.coord().kspaceTraj->extent(0)>1) offset=rd.coord().index[cycle]*adcSize; // only for segmented 2D spirals, ignore cycle otherwise outdata=gridder(adc, offset); rd.data(Rank()).reference(outdata); return execute_next_step(rd,controller); } template bool RecoGrid::query(RecoQueryContext& context) { if(context.mode==RecoQueryContext::prep) { context.controller.announce_data(deapodize_post_str+postfix()); } return RecoStep::query(context); } ///////////////////////////////////////////////////////////////////////////////// template bool RecoDeapodize::process(RecoData& rd, RecoController& controller) { RecoData rddeapo; if(!controller.inquire_data(deapodize_post_str+postfix(), rddeapo)) return false; ComplexData<3>& data=rd.data(Rank<3>()); ComplexData& deapo=rddeapo.data(Rank()); for(int i=0; i index=data.create_index(i); TinyVector deapoindex; for(int i=0; i& indata=rd.data(Rank<3>()); TinyVector inshape(indata.shape()); TinyVector outshape(inshape(0), inshape(1) / scaleFactor, inshape(2) / scaleFactor); TinyVector phasebounds((inshape(1) - outshape(1)) / 2, (inshape(1) + outshape(1)) / 2); TinyVector readbounds((inshape(1) - outshape(1)) / 2, (inshape(1) + outshape(1)) / 2); ComplexData<3> outdata(outshape); outdata = indata(all,Range(phasebounds(0),phasebounds(1)),Range(readbounds(0),readbounds(1))); rd.data(Rank<3>()).reference(outdata); rd.coord().gridScaleFactor = 1.0; // reset to 1.0 since the scaling has been removed from the data } return execute_next_step(rd,controller); } odin-1.8.5/odinreco/index.h0000644000175000017500000002705111734622163012473 00000000000000/*************************************************************************** index.h - description ------------------- begin : Mon Jan 27 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOINDEX_H #define RECOINDEX_H #include #include /** * @addtogroup odinreco * @{ */ /** * Manages information of data in one dimension. */ class RecoIndex { public: /** * Mode the index is used for: * - separate : Dimensions are processed separately. * - ignore : Same as 'separate', but the index is ignored when comparing indices. * - single : In a previous processing step, a single index was selected (or reduction to a single index), as an effect, this index is always zero. (Since only one value is possible, it is ignored when sorting indices (operator <)) * - collected : Data from all inidices is combined and transfered simultaneously. * - any : Any of the above (for checking functor interfaces). */ enum indexMode {separate=0, ignore, single, collected, any}; /** * Constructs default index object. */ RecoIndex(unsigned short v=0) : mode(separate), val(v), numof(1) {} /** * Assignment operator from integer. */ RecoIndex& operator = (unsigned short v) {val=v; return *this;} /** * Comparison operator for indexing */ bool operator < (const RecoIndex& ri) const { // comparison makes sense only in 'separate' mode. if( mode==separate && ri.mode==separate ) { return val < ri.val; } return false; // equal or ignored when comparing } /** * Conversion operator */ operator unsigned short () const {if(mode==single) return 0; return val;} // return zero index in single mode for numof=1 /** * Sets the mode */ RecoIndex& set_mode(indexMode m) {mode=m; return *this;} /** * Returns the mode */ indexMode get_mode() const {return indexMode(mode);} /** * Returns true if two indices are compatible when chaining functors */ bool compatible(const RecoIndex& ri) const { if(mode==any || ri.mode==any) return true; if(mode==collected && ri.mode!=collected) return false; if(mode!=collected && ri.mode==collected) return false; if(mode==single && ri.mode==single && val!=ri.val) return false; return true; } /** * Returns true if this is in the range of 'mask'. Prepares index for count map. */ bool prep_count(const RecoIndex& mask) { if(mask.mode==single) { if(val!=mask.val) return false; } mode=mask.mode; return true; } /** * Sets the number of indices */ RecoIndex& set_numof(unsigned short n) {numof=n; return *this;} /** * Returns the number of indices */ unsigned short get_numof() const {if(mode==single) return 1; return numof;} /** * Mode for printing the index: * - brief : Brief version for debugging * - all : Include all information, i.e. all indices will be printed with their current value, regardless of their mode or numof * - filename : Suitable for generating filenames */ enum printMode {brief=0, all, filename}; /** * Converts the index to a string for reco dimension 'dim' according to 'printmode' */ STD_string print(recoDim dim, printMode printmode=brief) const; private: unsigned char mode; unsigned short val; unsigned short numof; }; ////////////////////////////////////////////////////////////////// typedef Data ,2> KspaceTraj; // dimension is (nsegments, npoints) typedef STD_pair, int> ReadoutShape; // shape and target grid size /** * Holds reconstruction coordinate of one acquisition frame, i.e. position of reconstruction data in multiple dimensions. */ struct RecoCoord { /** * Construct default coordinate */ RecoCoord() {common_init();} /** * Comparison operator for indexing */ bool operator < (const RecoCoord& rc) const { for(int i=0; i* weightVec; /** * Dwell time of the signal data */ double dwellTime; /** * Oversampling factor in readout direction */ float overSamplingFactor; /** * Relative position of k-space center in readout direction */ float relCenterPos; /** * First index in readout direction actually measured */ unsigned short adcstart; /** * Last index in readout direction actually measured */ unsigned short adcend; /** * Scale factor for gridding reconstruction */ float gridScaleFactor; /** * Echo-train index in a multi-echo readout, e.g. an CPMG or EPI echo train. * Use this for non-phasecorr template scans and set echo index to zero. */ unsigned short echopos; /** * EPI echo-train index for 3D multi-EPI readout and EPI navigator correction. */ unsigned short echotrain; private: void common_init() { flags=0; readoutShape=0; kspaceTraj=0; weightVec=0; dwellTime=0.0; overSamplingFactor=1.0; relCenterPos=0.5; adcstart=0; adcend=0; gridScaleFactor=1.0; echopos=0; echotrain=0; index[readout].set_mode(RecoIndex::collected); // readout is already collected for ADCs } }; //////////////////////////////////////////////////////////////////////////// /** * Map to count the number of times a coordinate was measured/interpolated */ typedef STD_map CoordCountMap; //////////////////////////////////////////////////////////////////////////// /** * Helper template to define a set of 'Ndim' dimensions using default arguments for unused dimensions. */ template struct RecoDim { /** * Returns the number of dimensions to set/modify. */ static unsigned int dim() {return Ndim;} /** * Returns coordinate with specified dimensions set to mode 'm'. */ static RecoCoord preset_coord(RecoIndex::indexMode m) {return RecoCoord::coord_with_mode(m, d1, d2, d3, d4, d5, d6);} /** * Sets specified dimensions in coordinate 'coord' to mode 'm'. */ static void modify(RecoIndex::indexMode m, RecoCoord& coord) {coord.set_mode(m, d1, d2, d3, d4, d5, d6);} /** * Creates 'Ndim' dimensional index vector in specified dimensions using coordinate 'coord'. */ static void create_index(const RecoCoord& coord, TinyVector& index) { unsigned int idim=0; if(d1!=n_recoDims) {index(idim)=coord.index[d1]; idim++;} if(d2!=n_recoDims) {index(idim)=coord.index[d2]; idim++;} if(d3!=n_recoDims) {index(idim)=coord.index[d3]; idim++;} if(d4!=n_recoDims) {index(idim)=coord.index[d4]; idim++;} if(d5!=n_recoDims) {index(idim)=coord.index[d5]; idim++;} if(d6!=n_recoDims) {index(idim)=coord.index[d6]; idim++;} } /** * Creates 'Ndim' dimensional shape vector in specified dimensions using coordinate 'coord'. */ static void create_shape(const RecoCoord& coord, TinyVector& shape) { unsigned int idim=0; if(d1!=n_recoDims) {shape(idim)=coord.numof(d1); idim++;} if(d2!=n_recoDims) {shape(idim)=coord.numof(d2); idim++;} if(d3!=n_recoDims) {shape(idim)=coord.numof(d3); idim++;} if(d4!=n_recoDims) {shape(idim)=coord.numof(d4); idim++;} if(d5!=n_recoDims) {shape(idim)=coord.numof(d5); idim++;} if(d6!=n_recoDims) {shape(idim)=coord.numof(d6); idim++;} } /** * Copies values of 'Ndim' dimensional index vector to specified dimensions in 'coord'. */ static void set_index(const TinyVector& index, RecoCoord& coord) { unsigned int idim=0; if(d1!=n_recoDims) {coord.index[d1]=index(idim); idim++;} if(d2!=n_recoDims) {coord.index[d2]=index(idim); idim++;} if(d3!=n_recoDims) {coord.index[d3]=index(idim); idim++;} if(d4!=n_recoDims) {coord.index[d4]=index(idim); idim++;} if(d5!=n_recoDims) {coord.index[d5]=index(idim); idim++;} if(d6!=n_recoDims) {coord.index[d6]=index(idim); idim++;} } }; /** @} */ #endif odin-1.8.5/odinreco/driftcorr.cpp0000644000175000017500000000613711734622163013717 00000000000000#include "driftcorr.h" #include "data.h" #include "controller.h" bool RecoDriftCalc::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<6>& indata=rd.data(Rank<6>()); ComplexData<1>& outdata=rd.data(Rank<1>()); TinyVector inshape=indata.shape(); ODINLOG(odinlog,normalDebug) << "inshape=" << inshape << STD_endl; int nchan=inshape(0); int nrep=inshape(1); int nslice=inshape(2); ComplexData<1> cplxtcourse(nrep); Data phasecourse(nrep); Data phasecoursesum(nrep); phasecoursesum=0.0; float magnsum=0.0; for(int ichan=0; ichan0.0 && te>0.0) { rd.mode=RecoData::real_data; outdata.resize(nrep); outdata=float2real(phasecoursesum/(magnsum*te)); } else { ODINLOG(odinlog,errorLog) << "Cannot calculate field drift" << STD_endl; return false; } indata.free(); return execute_next_step(rd,controller); } ///////////////////////////////////////////////////////////////////////// bool RecoDriftCorr::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); double freq=0.0; mutex.lock(); int cachesize=driftcache.size(); mutex.unlock(); ODINLOG(odinlog,normalDebug) << "cachesize=" << cachesize << STD_endl; if(!cachesize) { RecoData rdfdrift; if(!controller.inquire_data(posted_drift_str, rdfdrift)) return false; mutex.lock(); driftcache.reference(creal(rdfdrift.data(Rank<1>()))); ODINLOG(odinlog,normalDebug) << "driftcache" << driftcache << STD_endl; mutex.unlock(); } int irep=rd.coord().index[repetition]; mutex.lock(); int nrep=driftcache.size(); if(irep& data=rd.data(Rank<1>()); unsigned int adcSize=data.extent(0); double dt=rd.coord().dwellTime; ODINLOG(odinlog,normalDebug) << "freq/adcSize/dt=" << freq << "/" << adcSize << "/" << dt << STD_endl; double reftime=0.0; dvector echostart=controller.dim_values(echo); unsigned int iecho=rd.coord().echopos; if(echostart.size()) reftime=echostart[iecho]; ODINLOG(odinlog,normalDebug) << "echostart/reftime=" << echostart << "/" << reftime << STD_endl; for(unsigned int isample=0; isample #include /** * @addtogroup odinreco * @{ */ /** * Interface class for all raw-data readers. */ class RecoReaderInterface { public: virtual ~RecoReaderInterface() {} /** * Initializes reader. * 'input_filename' contains meta and/or references raw data. */ virtual bool init(const STD_string& input_filename) = 0; /** * Returns the next available ADC (each channel has its own ADC) in 'adc' with k-space coordinates 'coord', * returns 'false' only if none left. */ virtual bool fetch(RecoCoord& coord, ComplexData<1>& adc) = 0; /** * Gets the k-space coordinates of all ADCs (each channel has its own ADC) in a single vector. */ virtual const STD_vector& get_coords() const = 0; /** * Returns vector of values associated with a certain dimension. */ virtual dvector dim_values(recoDim dim) const = 0; /** * Returns the relative spatial offset the image should be shifted after reconstruction. * The result contains the offsets in (phase3d,phase,read) direction. */ virtual const TinyVector& reloffset() const = 0; /** * Extra command-line arguments for processing of final images. */ virtual STD_string image_proc() const = 0; /** * Returns the image size, will be used if it cannot be determined from the k-space * coordinates (i.e. when gridding). */ virtual const TinyVector& image_size() const = 0; /** * Returns the scan protocol. */ virtual const Protocol& protocol() const = 0; /** * Returns the reco recipe (pipeline layout) as specified by the sequence. * If result is left blank, the recipe will be generated automatically. */ virtual STD_string seqrecipe() const = 0; /** * Returns the extra chain of reconstruction steps (functors) which will be * performed after 3D reconstruction (including channel combination) but before * data is stored on disk. Leave blank if no extra steps are necessary. */ virtual STD_string postProc3D() const = 0; /** * Returns the extra chain of reconstruction steps (functors) described by 'recipe' * wil be performed after 3D FFT but before channel combination. * Leave blank if no extra steps are necessary. */ virtual STD_string preProc3D() const = 0; /** * Returns extra command-line options for the reco. */ virtual STD_string cmdline_opts() const = 0; }; /** @} */ #endif odin-1.8.5/odinreco/homodyne_code.h0000644000175000017500000001315311455553545014205 00000000000000#include "homodyne.h" #include "data.h" #include "controller.h" #include template bool RecoHomodyne::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<3>& data=rd.data(Rank<3>()); TinyVector shape=data.shape(); int nipol=shape(interpolIndex); int startindex=0; if(interpolDim==readout) { if(rd.coord().adcend<(nipol-1)) { ODINLOG(odinlog,errorLog) << "Not implemented: Interpolation at end of readout" << STD_endl; return false; } startindex=rd.coord().adcstart; } else { if(rd.interpolated) measlines.update(*(rd.interpolated)); // take previously interpolated coords into account ivector indexvec=measlines.get_indices(rd.coord()); startindex=indexvec.minvalue(); } float center=0.5*float(nipol-1); int endindex=nipol-1-startindex; ODINLOG(odinlog,normalDebug) << "startindex/endindex/center=" << startindex << "/" << endindex << "/" << center << STD_endl; if(float(startindex) symmetric(shape); symmetric=STD_complex(0.0); if(startindex>0) { // Don't do this for fully-sampled k-space // symmetric part Range symrange(startindex,endindex); if(interpolIndex==0) symmetric(symrange,all,all)=data(symrange,all,all); if(interpolIndex==1) symmetric(all,symrange,all)=data(all,symrange,all); if(interpolIndex==2) symmetric(all,all,symrange)=data(all,all,symrange); symmetric.fft(); // pre weighting fvector transition(endindex-startindex+1); transition.fill_linear(0.0,1.0); ComplexData<1> weight(shape(interpolIndex)); weight=STD_complex(1.0); TinyVector index; for(int i=0; i0) { // Don't do this for fully-sampled k-space // phase correction data*=expc(float2imag(-phase(symmetric))); // take real part ComplexData<3> realpart(shape); realpart=float2real(creal(data)); data.reference(realpart); } } else if(fabs(float(startindex)-center)<=1.0) { // Just mirror k-space ODINLOG(odinlog,significantDebug) << "Conjugate-mirror reco with startindex=" << startindex << STD_endl; if(interpolDim!=line) { ODINLOG(odinlog,errorLog) << "Not implemented: Conjugate-mirror reco in dimension " << recoDimLabel[interpolDim] << STD_endl; return false; } int nread=shape(2); // Apply phase correction using the central line data.partial_fft(TinyVector(false,false,true)); // FFT in read ComplexData<1> centline(data(shape(0)/2,startindex,all)); Data centphase(centline.phasemap()); Data centmagn(cabs(centline)); Data centerr(nread); for(int iread=0; iread(false,false,true),false); // inv FFT in read ComplexData<1> oneline(nread); int nmeas=nipol-startindex; for(int iphase3d=0; iphase3d=0) { oneline=conjc(data(iphase3d,isrc,all).reverse(0)); if(!(nread%2)) oneline.shift(0,1); // for even nread, the center frequency is at nread/2 data(iphase3d,idst,all)=oneline; } } } if(!(nread%2)) data(all,0,all)=STD_complex(0.0); // zero-fill garbage from cyclic shift // do the FFT data.fft(); /* Data(creal(data)).autowrite("creal_"+rd.coord().print(RecoIndex::filename)+".jdx"); Data(cimag(data)).autowrite("cimag_"+rd.coord().print(RecoIndex::filename)+".jdx"); Data(cabs(data)).autowrite("cabs_"+rd.coord().print(RecoIndex::filename)+".jdx"); Data(phase(data)).autowrite("phase_"+rd.coord().print(RecoIndex::filename)+".jdx"); */ } else { ODINLOG(odinlog,errorLog) << "startindex=" << startindex << " larger than center=" << center << STD_endl; return false; } return execute_next_step(rd,controller); } /////////////////////////////////////////////////////// template bool RecoHomodyne::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { if(interpolDim!=readout) { if(!measlines.init(context.coord, context.controller)) return false; } } return RecoStep::query(context); } odin-1.8.5/odinreco/qualitycontrol.cpp0000644000175000017500000000616511725203123015002 00000000000000#include "qualitycontrol.h" #include "data.h" bool RecoQualityControlSpike::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); ComplexData<3>& data=rd.data(Rank<3>()); TinyVector shape=data.shape(); float kspace_center_frac=0.5; float kspace_magn_excess=4.0; float spike_excess=3.0; TinyVector lowerBounds, upperBounds; for(int idim=0; idim<3; idim++) { int low=int(0.5*shape(idim) * (1.0-kspace_center_frac) + 0.5); if(low<0) low=0; lowerBounds(idim) = low; int upp=int(0.5*shape(idim) * (1.0+kspace_center_frac) + 0.5); if(upp>(shape(idim)-1)) upp=shape(idim)-1; upperBounds(idim) = upp; } ODINLOG(odinlog,normalDebug) << "lowerBounds/upperBounds=" << lowerBounds << "/" << upperBounds << STD_endl; RectDomain<3> kspace_center(lowerBounds, upperBounds); int npts_kspace=data.size(); int npts_kspace_center=product(TinyVector(upperBounds-lowerBounds+1)); int npts_kspace_periphery=npts_kspace-npts_kspace_center; ODINLOG(odinlog,normalDebug) << "npts_kspace/npts_kspace_center=" << npts_kspace << "/" << npts_kspace_center << STD_endl; totalmutex.lock(); total_acqpts+=npts_kspace_periphery; totalmutex.unlock(); Data magn(cabs(data)); magn(kspace_center)=0.0; float meanmagn_periphery=secureDivision(sum(magn),npts_kspace_periphery); ODINLOG(odinlog,normalDebug) << "meanmagn_periphery=" << meanmagn_periphery << STD_endl; float kpsace_thresh=kspace_magn_excess*meanmagn_periphery; for(int iphase3d=0; iphase3dkpsace_thresh) { if(magnval>(spike_excess*magn(iphase3d,iphase,iread-2)) && magnval>(spike_excess*magn(iphase3d,iphase,iread+2))) { MutexLock lock(spikemutex); spikecount[ rd.coord().index[channel]]++; // data(iphase3d,iphase,iread)=STD_complex(1.0); ODINLOG(odinlog,normalDebug) << "Spike detected at iphase3d/iphase/iread=" << iphase3d << "/" << iphase << "/" << iread << " in k-space of " << rd.coord().print() << STD_endl; } } } } } return execute_next_step(rd,controller); } ////////////////////////////////////////////////////////////////////// bool RecoQualityControlSpike::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { total_acqpts=0; spikecount.clear(); } unsigned int total=0; STD_string spikestr; if(context.mode==RecoQueryContext::finalize) { for(STD_map::const_iterator it=spikecount.begin(); it!=spikecount.end(); ++ it) { spikestr+=itos(it->second)+"("+itos(it->first)+") "; total+=it->second; } ODINLOG(odinlog,infoLog) << "spikecount=" << spikestr << " total / ratio = " << total << " / " << secureDivision(total,total_acqpts) << STD_endl; if(spikecount.size()) ODINLOG(odinlog,warningLog) << "Spikes detected" << STD_endl; } return RecoStep::query(context); } odin-1.8.5/odinreco/multifreq.h0000644000175000017500000000531011322062351013354 00000000000000/*************************************************************************** multifreq.h - description ------------------- begin : Wed Jun 6 2007 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECOMULTIFREQ_H #define RECOMULTIFREQ_H #include "fieldmap.h" class RecoMultiFreq : public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "multifreq";} STD_string description() const {return "Generate multi-frequency ADCs based on fieldmap";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} bool query(RecoQueryContext& context); RecoStep* allocate() const {return new RecoMultiFreq;} void init(); JDXint max_numof_freq; bool get_freqs(Data& result, const RecoCoord& fmapcoord, double adcdur, RecoController& controller); // cache frequency values typedef STD_map > FreqMap; FreqMap freqmap; Mutex freqmutex; darray echoTimeStamps; // epis x echoes Mutex stampmutex; }; ///////////////////////////////////////////////////////////////////////////////////////////////////////// class RecoFreqComb : public RecoFieldMapUser { // implementing virtual functions of RecoStep STD_string label() const {return "freqcomb";} STD_string description() const {return "Combine multi-frequency images using fieldmap";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,freq,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single,freq);} RecoStep* allocate() const {return new RecoFreqComb;} void init() {} bool get_freqs(Data& result, const RecoCoord& fmapcoord, RecoController& controller); }; #endif odin-1.8.5/odinreco/driftcorr.h0000644000175000017500000000451111734622163013356 00000000000000/*************************************************************************** driftcorr.h - description ------------------- begin : Thu Mar 1 2012 copyright : (C) 2001 by Thies Jochimsen email : jochimse@cns.mpg.de ***************************************************************************/ /*************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * ***************************************************************************/ #ifndef RECODRIFTCORR_H #define RECODRIFTCORR_H #include "step.h" static const char* posted_drift_str="fielddrift"; class RecoDriftCalc: public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "driftcalc";} STD_string description() const {return "Calculate field drift over repetitions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,channel,repetition,slice,line3d,line,readout);} void modify_coord(RecoCoord& coord) const {coord.set_mode(RecoIndex::single, channel,slice,line3d,line,readout);} RecoStep* allocate() const {return new RecoDriftCalc;} void init() {} }; //////////////////////////////////////////////////////// class RecoDriftCorr: public RecoStep { // implementing virtual functions of RecoStep STD_string label() const {return "driftcorr";} STD_string description() const {return "Correct for linear field drift over repetitions";} bool process(RecoData& rd, RecoController& controller); RecoCoord input_coord() const {return RecoCoord::coord_with_mode(RecoIndex::collected,readout);} void modify_coord(RecoCoord& coord) const {} RecoStep* allocate() const {return new RecoDriftCorr;} void init() {} Data driftcache; Mutex mutex; }; #endif odin-1.8.5/odinreco/blade.cpp0000644000175000017500000004672111363773557013007 00000000000000#include "blade.h" #include "data.h" #include "controller.h" #include "bladegrid.h" #include #include #include void RecoBladeGrid::init() { fft = false; fft.set_description("Perform partial FFT into image space before feeding data into rest of the pipeline"); append_arg(fft,"fft"); filtermask.set_funcpars("Triangle"); filtermask.set_description("Filter function for k-space center. NoFilter = whole blade (not only center)"); append_arg(filtermask,"filtermask"); } bool RecoBladeGrid::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& data=rd.data(Rank<4>()); TinyVector inshape=data.shape(); TinyVector inshape3d(inshape(1), inshape(2), inshape(3)); ODINLOG(odinlog,normalDebug) << "inshape3d=" << inshape3d << STD_endl; float os_factor=rd.coord().overSamplingFactor; ODINLOG(odinlog,normalDebug) << "os_factor=" << os_factor << STD_endl; if(os_factor<1.0) { ODINLOG(odinlog,errorLog) << "os_factor(" << os_factor << ") < 1.0" << STD_endl; return false; } dvector angles=controller.dim_values(cycle); ODINLOG(odinlog,normalDebug) << "angles=" << angles.printbody() << STD_endl; TinyVector fov; fov=1; // fov(0)=controller.protocol().geometry.get_FOV(sliceDirection); fov(1)=controller.protocol().geometry.get_FOV(phaseDirection); fov(2)=controller.protocol().geometry.get_FOV(readDirection); ODINLOG(odinlog,normalDebug) << "fov=" << fov << STD_endl; // Prepare Input Data if(rd.interpolated) measlines.update(*(rd.interpolated)); // take previously interpolated coords into account ivector indexvec3d=measlines.get_indices(rd.coord()); // Use only planes actually measured ComplexData<4> infixed(inshape(0),indexvec3d.size(),inshape(2),inshape(3)); for(int i = 0; i < indexvec3d.size(); i++) { int iphase3d = indexvec3d[i]; infixed(all,i,all,all) = data(all,iphase3d,all,all); } // Grid blades BladeGrid bg; bg.init(inshape3d,fov,controller.image_size(),os_factor,filtermask); ComplexData<4> bladesgrid_kspace = bg(infixed,angles); // perform FFT if parameter is set if (fft) { TinyVector fftdims(false,false,true,true); bladesgrid_kspace.partial_fft(fftdims,true); } data.resize(bladesgrid_kspace.shape()); data = bladesgrid_kspace; return execute_next_step(rd,controller); } /////////////////////////////////////////////////////////////////////////// bool RecoBladeGrid::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { if(!measlines.init(context.coord, context.controller)) return false; } return RecoStep::query(context); } //////////////////////////////////////////////////////////////////////////////////// bool RecoCycleRot::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); dvector angles=controller.dim_values(cycle); if(!angles.size()) { ODINLOG(odinlog,errorLog) << "No angles available for cycle" << STD_endl; return false; } // feed each rotated dataset into rest of pipeline for(int i=0; i& data=rdcopy.data(Rank<3>()); RotMatrix rotmat; rotmat.set_inplane_rotation(-angles[i]); TinyVector offset=0.0; TinyMatrix rotation; for(int irow=0; irow<2; irow++) { for(int icol=0; icol<2; icol++) { rotation(1-irow,1-icol)=rotmat[irow][icol]; } } CoordTransformation transform(TinyVector(data.extent(1),data.extent(2)), rotation, offset, 2.0); for(int iphase3d=0; iphase3d odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<3>& indata=rd.data(Rank<3>()); float os_factor=rd.coord().overSamplingFactor; ODINLOG(odinlog,normalDebug) << "os_factor=" << os_factor << STD_endl; if(os_factor<1.0) { ODINLOG(odinlog,errorLog) << "os_factor(" << os_factor << ") < 1.0" << STD_endl; return false; } TinyVector inshape3d(indata.shape()); TinyVector inshape3d_no(inshape3d(0), inshape3d(1), int(inshape3d(2)/os_factor+0.5)); // without oversampling ODINLOG(odinlog,normalDebug) << "inshape3d=" << inshape3d << STD_endl; ODINLOG(odinlog,normalDebug) << "inshape3d_no=" << inshape3d_no << STD_endl; int center_diameter=STD_min(inshape3d_no(1),inshape3d_no(2)); // Size of the fully oversampled center of k-space int kspace_diameter=STD_max(inshape3d_no(1),inshape3d_no(2)); // The size of the overall k-space ODINLOG(odinlog,normalDebug) << "center_diameter/kspace_diameter=" << center_diameter << "/" << kspace_diameter << STD_endl; TinyVector diashape(inshape3d(0), kspace_diameter, int(kspace_diameter*os_factor+0.5)); if(inshape3d(1)%2 != diashape(1)%2) diashape(1)++; // for correct placing at center if(inshape3d(2)%2 != diashape(2)%2) diashape(2)++; // for correct placing at center ODINLOG(odinlog,normalDebug) << "diashape=" << diashape << STD_endl; TinyVector centshape(inshape3d(0), center_diameter, int(center_diameter*os_factor+0.5)); if(inshape3d(1)%2 != centshape(1)%2) centshape(1)++; // for correct placing at center if(inshape3d(2)%2 != centshape(2)%2) centshape(2)++; // for correct placing at center ODINLOG(odinlog,normalDebug) << "centshape=" << centshape << STD_endl; TinyVector lowsrc(0, (inshape3d(1)-centshape(1))/2, (inshape3d(2)-centshape(2))/2); TinyVector uppsrc(inshape3d(0)-1,(inshape3d(1)+centshape(1))/2-1,(inshape3d(2)+centshape(2))/2-1); ODINLOG(odinlog,normalDebug) << "lowsrc=" << lowsrc << STD_endl; ODINLOG(odinlog,normalDebug) << "uppsrc=" << uppsrc << STD_endl; TinyVector lowdst(0, (diashape(1)-centshape(1))/2, (diashape(2)-centshape(2))/2); TinyVector uppdst(inshape3d(0)-1,(diashape(1)+centshape(1))/2-1,(diashape(2)+centshape(2))/2-1); ODINLOG(odinlog,normalDebug) << "lowdst=" << lowdst << STD_endl; ODINLOG(odinlog,normalDebug) << "uppdst=" << uppdst << STD_endl; // The domains when copying data from central part of blades to central part of square k-space RectDomain<3> srcdomain(lowsrc,uppsrc); RectDomain<3> dstdomain(lowdst,uppdst); // Consistency check TinyVector srcrange=srcdomain.ubound()-srcdomain.lbound(); TinyVector dstrange=dstdomain.ubound()-dstdomain.lbound(); if(srcrange!=dstrange) { ODINLOG(odinlog,errorLog) << "range error:" << STD_endl; ODINLOG(odinlog,errorLog) << "srcrange=" << srcrange << STD_endl; ODINLOG(odinlog,errorLog) << "dstrange=" << dstrange << STD_endl; return false; } TinyVector lowpad(0, (diashape(1)-inshape3d(1))/2, (diashape(2)-inshape3d(2))/2); TinyVector upppad(inshape3d(0)-1,(diashape(1)+inshape3d(1))/2-1,(diashape(2)+inshape3d(2))/2-1); RectDomain<3> paddomain(lowpad,upppad); ODINLOG(odinlog,normalDebug) << "lowpad=" << lowpad << STD_endl; ODINLOG(odinlog,normalDebug) << "upppad=" << upppad << STD_endl; // Remove apodization from ramp regridding STD_string deapo_postlabel="deapodize1d"; bool has_deapo=false; ComplexData<3> deapo; if(controller.data_announced(deapo_postlabel)) { RecoData rddeapo; if(!controller.inquire_data(deapo_postlabel, rddeapo)) return false; const ComplexData<1>& deapoline=rddeapo.data(Rank<1>()); if(deapoline.size()!=inshape3d(2)) { ODINLOG(odinlog,errorLog) << "Size mistmatch" << STD_endl; return false; } deapo.resize(inshape3d); for(int iphase3d=0; iphase3d(cabs(deapo)).autowrite("deapo.jdx"); } bool isNoFilter = (phasecorr_filter.get_function_name() == "NoFilter"); ComplexData<3> blade_pad(diashape); blade_pad=STD_complex(0.0); // 2D Phase correction // Phase correction by windowed fourier transformation and phase removing if (isNoFilter) { // simply remove all phase in image space blade_pad(paddomain) = indata; // Put blade at center of padded kspace blade_pad.fft(true); // FFT into image space blade_pad = float2real(cabs(blade_pad)); // remove phase } else { // Low pass filter for k-space center Data filtermask(inshape3d); filtermask=0.0; TinyVector bounds(inshape3d); if (phasecorr_width < 0.0) bounds(2) = centshape(2) * (-1) * phasecorr_width; else bounds(2) *= phasecorr_width; for(int j=0; j lowpass_kspace(diashape); // 2D Phase correction // Phase correction by windowed fourier transformation and phase removing Data phasemap(diashape); lowpass_kspace=STD_complex(0.0); blade_pad=STD_complex(0.0); lowpass_kspace(paddomain) = indata * float2real(filtermask); // Smooth transition at edges blade_pad(paddomain) = indata; // Put blade at center of padded kspace lowpass_kspace.fft(true); blade_pad.fft(true); phasemap = phase(lowpass_kspace); blade_pad=blade_pad*expc(float2imag(-phasemap)); // Phase correction } if(has_deapo) blade_pad=blade_pad*deapo; // deapodization in image space blade_pad.fft(false); // inverse FFT indata=blade_pad(paddomain); return execute_next_step(rd,controller); } /////////////////////////////////////////////////////////////////////////// void RecoBladeComb::init() { keyhole=false; keyhole.set_description("Keyhole combination of blades"); append_arg(keyhole,"keyhole"); corrweight=false; corrweight.set_cmdline_option("bcw").set_description("Correlation weighting of all blades against the mean of all blades (in image space)"); append_arg(corrweight,"corrweight"); keyhole_filter.set_funcpars("CosSq"); keyhole_filter.set_cmdline_option("bkf").set_description("Blade-keyhole filter function (and its arguments)"); append_arg(keyhole_filter,"keyhole_filter"); kspaceweight_filter.set_funcpars("Triangle"); kspaceweight_filter.set_cmdline_option("bwf").set_description("Window/Filter function for kspace weighting of each blade"); append_arg(kspaceweight_filter,"kspaceweight_filter"); kspaceweight_width = 1; kspaceweight_width.set_cmdline_option("bww").set_description("Window/Filter width for kspace weighting of each blade"); append_arg(kspaceweight_width,"kspaceweight_width"); transition=0.2; transition.set_cmdline_option("bkt").set_description("Blade-keyhole transition width (fraction of oversampled k-space center)"); append_arg(transition,"transition"); } /////////////////////////////////////////////////////////////////////////// bool RecoBladeComb::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); TinyVector inshape=indata.shape(); TinyVector inshape3d(inshape(1), inshape(2), inshape(3)); int nblades=inshape(0); dvector angles=controller.dim_values(cycle); ODINLOG(odinlog,normalDebug) << "angles=" << angles.printbody() << STD_endl; TinyVector fov; fov=1; // fov(0)=controller.protocol().geometry.get_FOV(sliceDirection); // No regridding in line3d direction fov(1)=controller.protocol().geometry.get_FOV(phaseDirection); fov(2)=controller.protocol().geometry.get_FOV(readDirection); ODINLOG(odinlog,normalDebug) << "fov=" << fov << STD_endl; Data corrweights(nblades); // correlation weighting if (corrweight) { float os_factor=rd.coord().overSamplingFactor; ODINLOG(odinlog,normalDebug) << "os_factor=" << os_factor << STD_endl; if(os_factor<1.0) { ODINLOG(odinlog,errorLog) << "os_factor(" << os_factor << ") < 1.0" << STD_endl; return false; } // Filter for k-space center JDXfilter kernel_center; kernel_center.set_funcpars("Triangle"); // Prepare Input Data if(rd.interpolated) measlines.update(*(rd.interpolated)); // take previously interpolated coords into account ivector indexvec3d=measlines.get_indices(rd.coord()); // Use only planes actually measured ComplexData<4> infixed(inshape(0),indexvec3d.size(),inshape(2),inshape(3)); for(int i = 0; i < indexvec3d.size(); i++) { int iphase3d = indexvec3d[i]; infixed(all,i,all,all) = indata(all,iphase3d,all,all); } // Grid blades BladeGrid bg; bg.init(inshape3d,fov,controller.image_size(),os_factor,kernel_center); ComplexData<4> bladesgrid_kspace = bg(infixed,angles); // FFT TinyVector gridshape(bladesgrid_kspace.shape()); Data bladesgrid(gridshape(0),gridshape(1),gridshape(2),gridshape(3)); TinyVector fftdims(false,false,true,true); bladesgrid_kspace.partial_fft(fftdims,true); bladesgrid = cabs(bladesgrid_kspace); //bladesgrid.autowrite("grid-blades.nii"); // Calculate correlation coefficient for all blades and planes corrweights = 0.0; for (int iphase3d = 0; iphase3d < gridshape(1); iphase3d++) { // Merge all blades Data bladesmean(gridshape(2),gridshape(3)); bladesmean = 0.0; for (int iblade = 0; iblade < nblades; iblade++) { bladesmean += bladesgrid(iblade,iphase3d,all,all); } bladesmean /= nblades; //bladesmean.autowrite("grid-blades-mean.nii"); // Calculate correlation coefficient for all blades for (int iblade = 0; iblade < nblades; iblade++) { correlationResult cr = correlation(bladesmean,bladesgrid(iblade,iphase3d,all,all)); corrweights(iblade) += cr.r; } } corrweights /= gridshape(1); ODINLOG(odinlog,normalDebug) << "corrweights=" << corrweights << STD_endl; } else corrweights = 1.0; int ikey=0; // the index for the blade filling the center of k-space in keyhole mode if(keyhole) { int irep=rd.coord().index[repetition]; ikey=(irep+nblades/2)%nblades; ODINLOG(odinlog,normalDebug) << "ikey(" << irep << ")=" << ikey << STD_endl; } KspaceTraj* trajptr=0; trajmutex.lock(); if(trajmap.find(ikey)==trajmap.end()) { trajptr=new KspaceTraj; trajmap[ikey]=trajptr; int npts=inshape(0)*inshape(2)*inshape(3); // cycles x 2D plane trajptr->resize(1,npts); TinyVector kspace_center=inshape3d/2; // correct index of center: odd N -> N/2 / even N -> (N-1)/2 ODINLOG(odinlog,normalDebug) << "kspace_center=" << kspace_center << STD_endl; TinyVector kmax=inshape3d*2.0*PII/fov; kmax(2)/=rd.coord().overSamplingFactor; float kcent_radius=0.5*STD_min(kmax(1),kmax(2)); TinyVector findex; TinyVector kcoord; TinyVector kcoord_shift; TinyVector kcoord_rot; int itraj=0; for(int iblade=0; iblade inplaneindex(0, iphase, iread); double angle_rad=-angles[iblade]; // Reverse blade rotation findex=(inplaneindex-kspace_center)/inshape3d; kcoord=findex*kmax; kcoord_shift=kcoord; float si=sin(angle_rad); float co=cos(angle_rad); /*if (shiftPhaseCorr) { kcoord_shift(1) += koffset(iblade,0) / inshape3d(1) * kmax(1); kcoord_shift(2) += koffset(iblade,1) / inshape3d(2) * kmax(2); }*/ kcoord_rot(0)=0.0; kcoord_rot(1)=co*kcoord_shift(1)-si*kcoord_shift(2); kcoord_rot(2)=si*kcoord_shift(1)+co*kcoord_shift(2); (*trajptr)(0,itraj).coord=kcoord_rot; float weight = corrweights(iblade); float kcoord_temp; if (kmax(1) > kmax(2)) kcoord_temp = kcoord(2); // select the smaller(=y) coordinate else kcoord_temp = kcoord(1); float y = secureDivision(abs(kcoord_temp),kcent_radius); if (y > 1) // ouside of the blade weight = 0.0; else weight *= kspaceweight_filter.calculate(kspaceweight_width * y); if(keyhole && iblade!=ikey) { float relradius=secureDivision(norm(kcoord_rot(1),kcoord_rot(2)),kcent_radius); float plateau=1.0-transition; float r=1.0-secureDivision(relradius-plateau,transition); if(r>=0.0 && r<=1.0) weight*=keyhole_filter.calculate(r); if(r>1.0) weight=0.0; } (*trajptr)(0,itraj).weight=weight; itraj++; } } } } else { trajptr=trajmap[ikey]; } trajmutex.unlock(); if(rd.interpolated) measlines.update(*(rd.interpolated)); // take previously interpolated coords into account ivector indexvec3d=measlines.get_indices(rd.coord()); // Use only planes actually measured // feed each 3d-phase encoded k-space plane separately into rest of pipeline for(int i=0; i& outdata=rdcopy.data(Rank<1>()); ComplexData<3> indata2d; indata2d.reference(indata(all,iphase3d,all,all)); indata2d.convert_to(outdata); if(!execute_next_step(rdcopy,controller)) return false; } return true; } /////////////////////////////////////////////////////////////////////////// bool RecoBladeComb::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { if(!measlines.init(context.coord, context.controller)) return false; } return RecoStep::query(context); } /////////////////////////////////////////////////////////////////////////// RecoBladeComb::~RecoBladeComb() { Log odinlog("","~RecoBladeComb"); for(STD_map::iterator it=trajmap.begin(); it!=trajmap.end(); ++it) { delete it->second; } } odin-1.8.5/odinreco/dump.cpp0000644000175000017500000000315711322062351012653 00000000000000#include "dump.h" #include "store.h" #include "data.h" template bool dump_recodata(const ComplexData& indata, const STD_string& filename, RecoData::dataMode mode) { if(indata.size()) { Data magn(indata.shape()); if (mode==RecoData::real_data || mode==RecoData::weighted_real_data) magn = creal(indata); else magn = cabs(indata); magn.autowrite(filename); return true; } return false; } void RecoDump::init() { Log odinlog(c_label(),"init"); prefix=STD_string(".")+SEPARATOR_STR+"dump"; prefix.set_cmdline_option("dp").set_description("Prefix of dump files"); append_arg(prefix,"prefix"); format=RecoStore::default_format(); format.set_cmdline_option("df").set_description("Output format (file extension) of dump files"); append_arg(format,"format"); } bool RecoDump::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); STD_string filename=prefix; STD_string coordstr=rd.coord().print(RecoIndex::filename); if(coordstr!="") filename+="_"+coordstr; filename+="."+format; ODINLOG(odinlog,normalDebug) << "filename=" << filename << STD_endl; bool dumped= // stop if data with highest dim written dump_recodata(rd.data(Rank<5>()),filename,rd.mode) || dump_recodata(rd.data(Rank<4>()),filename,rd.mode) || dump_recodata(rd.data(Rank<3>()),filename,rd.mode) || dump_recodata(rd.data(Rank<2>()),filename,rd.mode) || dump_recodata(rd.data(Rank<1>()),filename,rd.mode); ODINLOG(odinlog,normalDebug) << "dumped=" << dumped << STD_endl; return execute_next_step(rd,controller); } odin-1.8.5/odinreco/bladegrid.cpp0000644000175000017500000001043611363773557013647 00000000000000#include "bladegrid.h" #include bool BladeGrid::init(const TinyVector& inshape, const TinyVector fov, const TinyVector image_size, const float os_factor, const JDXfilter& filterkernel) { Log odinlog("BladeGrid","init"); Range all=Range::all(); // Initialize important dimensions TinyVector inshape_no(inshape(0), inshape(1), int(inshape(2)/os_factor+0.5)); // without oversampling ODINLOG(odinlog,normalDebug) << "inshape_no=" << inshape_no << STD_endl; int center_diameter=STD_min(inshape_no(1),inshape_no(2)); // Size of the fully oversampled center of k-space int kspace_diameter=STD_max(inshape_no(1),inshape_no(2)); // The size of the overall k-space ODINLOG(odinlog,normalDebug) << "center_diameter/kspace_diameter=" << center_diameter << "/" << kspace_diameter << STD_endl; TinyVector centshape(inshape(0), center_diameter, int(center_diameter*os_factor+0.5)); if(inshape(1)%2 != centshape(1)%2) centshape(1)++; // for correct placing at center if(inshape(2)%2 != centshape(2)%2) centshape(2)++; // for correct placing at center ODINLOG(odinlog,normalDebug) << "centshape=" << centshape << STD_endl; // prepare filtermask TinyVector inshape2d(inshape(1),inshape(2)); filtermask_center.resize(inshape2d); filtermask_center = 0.0; if (filterkernel.get_function_name() == "NoFilter") { // NoFilter means entire blade filtermask_center = 1.0; } else { TinyVector bounds(inshape2d); bounds(0) = centshape(1); bounds(1) = centshape(2); for(int j=0; j BladeGrid::operator () (const ComplexData<4>& src, const dvector& angles) const { Log odinlog("BladeGrid","()"); Range all=Range::all(); JDXfilter gridkernel; gridkernel.set_function("Gauss"); TinyVector inshape4d(src.shape()); TinyVector inshape3d(inshape4d(1),inshape4d(2),inshape4d(3)); TinyVector inshape2d(inshape4d(2),inshape4d(3)); int nBlades = inshape4d(0); int npts3d = product(inshape3d); TinyVector kspace_center = inshape2d/2; // correct index of center: odd N -> N/2 / even N -> (N-1)/2 float dk = max(dstextent/dstshape); float kwidth = 3*dk; ComplexData<4> images(nBlades,inshape3d(0),dstshape(0),dstshape(1)); ODINLOG(odinlog,normalDebug) << "dstshape/dstextent/dk/kwidth=" << dstshape << "/" << dstextent << "/" << dk << "/" << kwidth << STD_endl; for (int iblade = 0; iblade < nBlades; iblade++) { // Prepare Gridder TinyVector findex; TinyVector kcoord; TinyVector kcoord_rot; STD_vector > src_coords(npts3d); int n = 0; for (int iphase = 0; iphase < inshape3d(1); iphase++) { for (int iread = 0; iread < inshape3d(2); iread++) { TinyVector inplaneindex(iphase, iread); findex = (inplaneindex - kspace_center) / inshape2d; kcoord = findex*kmax; float si = sin(-angles[iblade]); float co = cos(-angles[iblade]); kcoord_rot(0)=co*kcoord(0)-si*kcoord(1); kcoord_rot(1)=si*kcoord(0)+co*kcoord(1); src_coords[n].coord(0) = kcoord_rot(0); src_coords[n].coord(1) = kcoord_rot(1); src_coords[n].weight = 1.0; n++; } } Gridding gridder; gridder.init(dstshape, dstextent, src_coords, gridkernel, kwidth); for (int islice = 0; islice < inshape3d(0); islice++) { ComplexData<2> image(dstshape); ComplexData<2> blade(inshape2d); blade = src(iblade,islice,all,all) * filtermask_center; image = gridder(blade); images(iblade,islice,all,all) = image; } } return images; }odin-1.8.5/odinreco/pilot.cpp0000644000175000017500000000617411322062351013037 00000000000000#include "pilot.h" #include "data.h" #include "controller.h" /////////////////////////////////////////////////////////////////////////// void RecoPilot::init() { slicedist=0.0; slicedist.set_description("Inter-slice distance"); append_arg(slicedist,"slicedist"); } /////////////////////////////////////////////////////////////////////////// void RecoPilot::transpose_inplane(ComplexData<5>& data, Geometry& geo, bool reverse_read, bool reverse_phase) { geo.transpose_inplane(reverse_read,reverse_phase); if(reverse_read) data.reverseSelf(4); if(reverse_phase) data.reverseSelf(3); data.transposeSelf(0,1,2,4,3); data.reference(data.copy()); } /////////////////////////////////////////////////////////////////////////// bool RecoPilot::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); ComplexData<4>& indata=rd.data(Rank<4>()); TinyVector inshape=indata.shape(); TinyVector outshape(1, 1, inshape(1), inshape(2), inshape(3)); // slice size will be adjusted later ODINLOG(odinlog,normalDebug) << "inshape/outshape=" << inshape << "/" << outshape << STD_endl; dvector orientations=controller.dim_values(userdef); int nimages=orientations.size(); if(nimages!=inshape(0)) { ODINLOG(odinlog,errorLog) << "size mismatch" << STD_endl; return false; } STD_map slicecount; for(int i=0; i& dataref=data[ior].data(Rank<5>()); outshape(1)=slicecount[sliceOrientation(ior)]; dataref.resize(outshape); // Modify protocol prot[ior]=controller.protocol(); Geometry& geo=prot[ior].geometry; geo.set_orientation(sliceOrientation(ior)); geo.set_nSlices(outshape(1)); geo.set_sliceDistance(slicedist); data[ior].override_protocol=&(prot[ior]); // modify coordinate data[ior].coord().index[userdef].set_numof(n_orientations); data[ior].coord().index[userdef]=ior; } // fill data UInt index[n_orientations]; for(int i=0; i& outdata=data[ior].data(Rank<5>()); outdata(0,int(index[ior]),all,all,all)=indata(i,all,all,all); index[ior]++; } STD_string series; int number; controller.protocol().study.get_Series(series, number); // transpose and feed rest of pipeline for(unsigned int ior=0; ior()), prot[ior].geometry, true,false);} if(ior==coronal) {seriesname=series+"_Coronal"; transpose_inplane(data[ior].data(Rank<5>()), prot[ior].geometry, true,true);} if(ior==axial) {seriesname=series+"_Axial";} prot[ior].study.set_Series(seriesname,number); if(!execute_next_step(data[ior],controller)) return false; } return true; } odin-1.8.5/odinreco/multifreq.cpp0000644000175000017500000002057411725203122013720 00000000000000#include "multifreq.h" #include "data.h" #include "controller.h" static const char* posted_freqs_str="multifreqs"; ///////////////////////////////////////////////////////////////////////////////////////////////////////// void RecoMultiFreq::init() { max_numof_freq=256; max_numof_freq.set_cmdline_option("mf").set_description("Maximum number of frequencies for multi-frequency reconstruction"); append_arg(max_numof_freq,"max_numof_freq"); } bool RecoMultiFreq::get_freqs(Data& result, const RecoCoord& fmapcoord, double adcdur, RecoController& controller) { Log odinlog(c_label(),"get_freqs"); bool calc_freqs=true; freqmutex.lock(); FreqMap::const_iterator it=freqmap.find(fmapcoord); if(it!=freqmap.end()) { result.reference(it->second.copy()); // deep copy for thread-safe access when using freqs calc_freqs=false; } freqmutex.unlock(); if(calc_freqs) { if(!controller.data_announced(posted_fmap_str)) { ODINLOG(odinlog,errorLog) << "fieldmap not available" << STD_endl; return false; } RecoData rdfieldmap(fmapcoord); if(!controller.inquire_data(posted_fmap_str, rdfieldmap)) return false; Data fieldmap(creal(rdfieldmap.data(Rank<3>()))); float minfreq=min(fieldmap); float maxfreq=max(fieldmap); float deltafreq=fabs(maxfreq-minfreq); stampmutex.lock(); double echoTrainDur=echoTimeStamps.maxvalue()-echoTimeStamps.minvalue(); stampmutex.unlock(); echoTrainDur+=adcdur; ODINLOG(odinlog,normalDebug) << "deltafreq/adcdur/echoTrainDur=" << deltafreq << "/" << adcdur << "/" << echoTrainDur << STD_endl; int nFreq=int(4.0*deltafreq*echoTrainDur/PII+0.5); // According to Man et al., MRM 37:785(1997) nFreq*=2; // slightly more to avoid Moire-type artifacts if(nFreq>max_numof_freq) nFreq=max_numof_freq; if(nFreq<=0) nFreq=1; fvector fv(nFreq); if(nFreq>1) fv.fill_linear(minfreq,maxfreq); else fv=0.0; // use zero frequency if multi-frequency interpolation is disabled result=fv; ODINLOG(odinlog,normalDebug) << "nFreq/result=" << nFreq << "/" << fv.printbody() << STD_endl; MutexLock lock(freqmutex); if(freqmap.find(fmapcoord)==freqmap.end()) { // Do this only once, otherwise post_data() will throw an error freqmap[fmapcoord].reference(result); // Cache result // post freqs to blackboard for later use by freqcomb RecoData rdposted(fmapcoord); rdposted.data(Rank<1>()).resize(nFreq); rdposted.data(Rank<1>())=float2real(result); controller.post_data(posted_freqs_str, rdposted); } } return true; } bool RecoMultiFreq::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); ComplexData<1>& indata=rd.data(Rank<1>()); unsigned int adcSize=indata.extent(0); double dt=rd.coord().dwellTime; // coord for indexing field maps RecoCoord fmapcoord=rd.coord(); RecoFieldMapUser::modify4fieldmap(fmapcoord); Data freqs; if(!get_freqs(freqs,fmapcoord,double(adcSize)*dt,controller)) return false; double reftime=0.0; // The absolute time within an echo train unsigned int iecho=rd.coord().echopos; unsigned int iepi=rd.coord().echotrain; stampmutex.lock(); if(echoTimeStamps.size(0)<2) iepi=0; // do not throw error if EPI start times are not provided (e.g. TWIX data), use zero instead if(iepi& modulated=rdcopy.data(Rank<1>()); modulated.resize(adcSize); rdcopy.coord().index[freq].set_numof(nfreq); rdcopy.coord().index[freq]=ifreq; for(unsigned int isample=0; isample odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { dvector echostart=context.controller.dim_values(echo); if(!echostart.size()) { echostart.resize(1); echostart=0.0; } ODINLOG(odinlog,normalDebug) << "echostart=" << echostart << STD_endl; dvector epistart=context.controller.dim_values(epi); if(!epistart.size()) { epistart.resize(1); epistart=0.0; } ODINLOG(odinlog,normalDebug) << "epistart=" << epistart << STD_endl; echoTimeStamps.redim(epistart.size(), echostart.size()); for(unsigned int iepi=0; iepi& cfreqs=rdfreqs.data(Rank<1>()); result.resize(cfreqs.shape()); result=creal(cfreqs); return true; } bool RecoFreqComb::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); const ComplexData<4>& allfreq=rd.data(Rank<4>()); int nfreq=allfreq.extent(0); TinyVector outshape(allfreq.extent(1), allfreq.extent(2), allfreq.extent(3)); ComplexData<3>& outdata=rd.data(Rank<3>()); outdata.resize(outshape); RecoCoord fmapcoord=rd.coord(); RecoFieldMapUser::modify4fieldmap(fmapcoord); Data freqs; if(!get_freqs(freqs, fmapcoord, controller)) return false; if(nfreq!=freqs.size()) { ODINLOG(odinlog,errorLog) << "nfreq=" << nfreq << "!=" << freqs.size() << STD_endl; return false; } Data fieldmap; if(rd.coord().index[cycle].get_mode()==RecoIndex::separate) { // for separate PROPELLER blades fmapcoord.index[cycle].set_mode(RecoIndex::separate); fmapcoord.index[cycle]=rd.coord().index[cycle]; } if(!get_fmap(fieldmap, outshape, fmapcoord, controller)) return false; // fieldmap.autowrite("fieldmap_"+fmapcoord.print(RecoIndex::filename)+".nii"); // Combine frequency values if(nfreq>1) { outdata=STD_complex(0.0); double deltafreq=fabs(freqs(1)-freqs(0)); for(int iphase3d=0; iphase3d Pixel is zero in reconstructed image float norm=0.0; STD_complex pixsum(0.0); for(int ifreq=0; ifreq odinlog(c_label(),"process"); int oldnrep=rd.coord().numof(repetition); int ncycle=rd.coord().numof(cycle); int newnrep=(oldnrep-1)*ncycle+1; ODINLOG(odinlog,normalDebug) << "oldnrep/ncycle/newnrep=" << oldnrep << "/" << ncycle << "/" << newnrep << STD_endl; rd.coord().index[repetition].set_numof(newnrep); int icycle=rd.coord().index[cycle]; int ioldrep=rd.coord().index[repetition]; int index=ioldrep*ncycle+icycle; ODINLOG(odinlog,normalDebug) << "index=" << index << STD_endl; ivector inewreplist; for(int i=0; i=0 && inewrep static const char* posted_phasemap_label="phasemap"; bool RecoPhaseMap::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); modify4blackboard(rd.coord()); ComplexData<2>& data=rd.data(Rank<2>()); TinyVector shape(data.shape()); int nechoes=shape(0); int nread=shape(1); ODINLOG(odinlog,normalDebug) << "PhaseMap" << "(" << rd.coord().print() << ")/" << shape << " complete" << STD_endl; // FFT in read direction data.partial_fft(TinyVector(false,true)); ComplexData<2> phasemap(shape); if(odd_even_echoes) { // phase correction for EPI // Calculate phase-difference for each odd and even pair of echoes Data phasediff(nechoes/2, nread); Data sigma(nechoes/2, nread); // Error for fit for(int iecho=0; iecho(expc(float2imag(phasediff))).phasemap(); // Linear fit to phase, weighted by signal magnitude for each odd-even-echo pair LinearFunction linf; Data slope(nechoes/2); Data fiterr(nechoes/2); Data offset(nechoes/2); Data phasediff_oneline(nread); for(int iecho=0; iecho slope_fit(nechoes/2); Data offset_fit(nechoes/2); for(int iecho=0; iecho oneline(nread); for(int iecho=0; iecho(cabs(oneline)), 1, 3.0))); } } // Post data for each echo separately on blackboard RecoData one_echo_phasemap; one_echo_phasemap.data(Rank<1>()).resize(nread); one_echo_phasemap.coord()=rd.coord(); for(int i=0; i())=phasemap(i,all); one_echo_phasemap.coord().index[echo]=i; controller.post_data(posted_phasemap_label, one_echo_phasemap); } // For debugging, apply phase correction to template data // and apss it to next functor data=data/phasemap; data.partial_fft(TinyVector(false,true),false); return execute_next_step(rd,controller); } ////////////////////////////////////////////////////////////// bool RecoPhaseMap::query(RecoQueryContext& context) { Log odinlog(c_label(),"query"); if(context.mode==RecoQueryContext::prep) { context.controller.announce_data(posted_phasemap_label); ODINLOG(odinlog,normalDebug) << "announced " << posted_phasemap_label << STD_endl; RecoCoord coord4count=context.coord; modify(coord4count); const CoordCountMap* countmap=context.controller.create_count_map(coord4count); if(!countmap) return false; odd_even_echoes=false; for(CoordCountMap::const_iterator it=countmap->begin(); it!=countmap->end(); ++it) { if(it->first.flags&recoReflectBit) { odd_even_echoes=true; break; } } ODINLOG(odinlog,normalDebug) << "odd_even_echoes=" << odd_even_echoes << STD_endl; } return RecoStep::query(context); } ////////////////////////////////////////////////////////////// bool RecoPhaseCorr::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); if(!controller.data_announced(posted_phasemap_label)) { ODINLOG(odinlog,errorLog) << posted_phasemap_label << " not available" << STD_endl; return false; } RecoData one_echo_phasemap; one_echo_phasemap.coord()=rd.coord(); RecoPhaseMap::modify4blackboard(one_echo_phasemap.coord()); // override (zero) echo/epi index for phasemap retrieval one_echo_phasemap.coord().index[echo]=rd.coord().echopos; one_echo_phasemap.coord().index[epi]=rd.coord().echotrain; if(!controller.inquire_data(posted_phasemap_label, one_echo_phasemap)) return false; ComplexData<1>& pmap=one_echo_phasemap.data(Rank<1>()); ComplexData<1>& adc=rd.data(Rank<1>()); if(pmap.size()!=adc.size()) { ODINLOG(odinlog,errorLog) << "Size mismatch: " << pmap.size() << " != " << adc.size() << STD_endl; return false; } // FFT forward adc.fft(true); // Phase correction Range all=Range::all(); adc(all)=adc(all)/pmap(all); // Blitz throws an error if arrays are used directly // FFT back adc.fft(false); return execute_next_step(rd,controller); } odin-1.8.5/odinreco/channel.cpp0000644000175000017500000000616111665172216013330 00000000000000#include "channel.h" #include "data.h" void RecoChannelSum::init() { Log odinlog(c_label(),"init"); phasecomb=false; phasecomb.set_cmdline_option("pc").set_description("Combine phase of channels using a phase correction"); append_arg(phasecomb,"phasecomb"); magnexp=0.0; magnexp.set_cmdline_option("pe").set_description("Exponent for magnitude weighting when calculating combined phase of all channels"); append_arg(magnexp,"magnexp"); } bool RecoChannelSum::process(RecoData& rd, RecoController& controller) { Log odinlog(c_label(),"process"); Range all=Range::all(); TinyVector inshape(rd.data(Rank<4>()).shape()); TinyVector outshape(inshape(1), inshape(2), inshape(3)); ODINLOG(odinlog,normalDebug) << "inshape/outshape=" << inshape << "/" << outshape << STD_endl; ComplexData<4>& indata=rd.data(Rank<4>()); int nchan=indata.extent(0); ODINLOG(odinlog,normalDebug) << "nchan=" << nchan << STD_endl; ComplexData<3>& outdata=rd.data(Rank<3>()); outdata.resize(outshape); if(rd.mode==RecoData::real_data || rd.mode==RecoData::weighted_real_data) { outdata=STD_complex(0.0); for(int i=0; i index=outdata.create_index(i); float valsum=0.0; float relsum=0.0; for(int i=0; i mag(outshape); mag=0.0; Data magall(cabs(indata)); for(int i=0; i; template class RecoGrappaWeights >; template class RecoGrappaWeights; template class RecoGrappaWeights >; template class RecoGrappa; template class RecoGrappa;