debian/0000755000000000000000000000000011421402553007163 5ustar debian/source/0000755000000000000000000000000011421372005010461 5ustar debian/source/format0000644000000000000000000000001411421372005011667 0ustar 3.0 (quilt) debian/libnifti2.lintian-overrides0000644000000000000000000000011611421375100014420 0ustar libnifti2: package-name-doesnt-match-sonames libnifticdf2 libniftiio2 libznz2 debian/compat0000644000000000000000000000000211421375100010356 0ustar 7 debian/libnifti-doc.docs0000644000000000000000000000001411421372005012371 0ustar docs/html debian/libnifti-doc.manpages0000644000000000000000000000002311421372005013234 0ustar debian/libnifti.1 debian/nifti-bin.docs0000644000000000000000000000000711421372005011707 0ustar README debian/copyright0000644000000000000000000000526511421372005011124 0ustar Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat Upstream-Name: nifticlib Upstream-Source: http://niftilib.sourceforge.net/ Files: * Copyright: none License: other nifticlib was written by the NIfTI Data Format Working Group (DFWG, http://nifti.nimh.nih.gov/). The NIFTI DFWG disclaims all copyright in nifticlib and places it in the public domain. Files: fsliolib/* Copyright: none License: other Upstream version 0.4 changed the copyright statements of all source files that were developed as part of FSL (http://www.fmrib.ox.ac.uk/fsl/) to make the package acceptable for Debian main. FSL itself is published under a non-free license. The original authors, who are also part of the nifticlib upstream team, disclaimed there copyright in those files. From a request on the debian-legal mailing list it arose that the new copyright statements should be acceptable for Debian main, but there might be difficulties for upstream to place this software into the public domain. http://lists.debian.org/debian-legal/2006/09/msg00026.html Please note, that all code is simply left in the source tarball, but is not compiled and hence not part of the binary packages. Files: fsliolib/dbh.h Copyright: (c) Copyright 1986-1995, Biomedical Imaging Resource, Mayo Foundation. Incorporation License: other Use of the ANALYZE 7.5 file header by permission of the Mayo Foundation. Changes from the ANALYZE 7.5 file header in this file are released to the public domain, including the functional comments and any amusing asides. Files: debian/* Copyright: Copyright 2006-2008, Michael Hanke License: Expat 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 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. debian/libnifti-dev.install0000644000000000000000000000004411421375100013122 0ustar usr/include/nifti usr/lib/*.{so,a} debian/libnifti-doc.examples0000644000000000000000000000003611421372005013263 0ustar real_easy/nifti1_read_write.c debian/libnifti.10000644000000000000000000000357411421372005011054 0ustar .TH "NIFTI" "1" "August 2006" "Michael Hanke" "" .SH "NAME" nifti \- IO libraries and tools for the NIFTI\-1 data format .SH "DESCRIPTION" The NIfTI\-1 data format is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. The NIfTI format is an extension of the widely used ANALYZE 7.5 format. The goals of this modified data format are (1) to add information to the header that will be useful for functional neuroimaging data analysis and display. These additions include: .IP \- More basic data types. .br \- Two affine transformations to specify voxel coordinates. .br \- "Intent" codes and parameters to describe the meaning of the data. .br \- Affine scaling of the stored data values to their "true" values. .br \- Optional storage of the header and image data in one file (.nii). .br .PP And (2) To maintain compatibility with non\-NIFTI\-aware ANALYZE 7.5 compatible software (i.e., such a program should be able to do something useful with a NIFTI\-1 dataset \-\- at least, with one stored in a traditional .img/.hdr file pair). .PP The NIfTI library package consists of two libraries: .TP \fBznzlib\fR \-\- low level library for handling read/write of compressed files. .TP \fBniftilib\fR \-\- core i/o routines for reading and writing nifti\-1 format files. Primarily routines to read/write and manipulate the header field information, including orientation matrices. Volume\-wise, timecourse\-wise, access to image data. .SH "SEE ALSO" .BR nifti_tool (1), .BR nifti1_test (1), .BR nifti_stats (1). .PP Homepage: .I http://niftilib.sourceforge.net .SH "AUTHOR" The \fBNIfTI\fR libraries were written by the NIfTI Data Format Working Group (DFWG, .I http://nifti.nimh.nih.gov/ ). .PP This manual page was written by Michael Hanke , for the Debian project (but may be used by others). debian/control0000644000000000000000000000513011421375701010571 0ustar Source: nifticlib Priority: optional Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), cmake, zlib1g-dev, doxygen, python Standards-Version: 3.9.0 Section: libs Homepage: http://niftilib.sourceforge.net Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/nifticlib.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/nifticlib.git XS-DM-Upload-Allowed: yes Package: libnifti2 Section: libs Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: IO libraries for the NIfTI-1 data format Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. . This package contains the shared library of the low-level IO library niftiio, low-level IO library znzlib and the nifticdf shared library that provides functions to compute cumulative distributions and their inverses. Package: libnifti-dev Section: libdevel Architecture: any Depends: libnifti2 (= ${binary:Version}), ${misc:Depends} Conflicts: libnifti1-dev, libniftiio-dev, libnifti0-dev, libfslio-dev Replaces: libnifti1-dev Description: IO libraries for the NIfTI-1 data format Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. . This package provides the header files and static libraries of libniftiio, znzlib and libnifticdf. Package: nifti-bin Section: utils Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: tools shipped with the NIfTI library Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. . This package provides the tools that are shipped with the library (nifti_tool, nifti_stats and nifti1_test). Package: libnifti-doc Section: doc Architecture: all Depends: ${misc:Depends} Description: NIfTI library API documentation Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. . This package provides the library API reference documentation. debian/nifti1_test.10000644000000000000000000000334711421372005011503 0ustar .TH "NIFTI1_TEST" "1" "September 2007" "Michael Hanke" "User Commands" .SH NAME \fBnifti1_test\fR \- NIfTI file conversion .SH SYNOPSIS .B nifti1_test [\fI-n2|-n1|-na|-a2\fR] \fIinfile \fR[\fIprefix\fR] .SH DESCRIPTION Converts NIfTI files from and to ANALYZE 7.5 format, compressed or uncompressed NIfTI files (pair or single file). Additionally one can convert NIfTI headers into ASCII format for convenient manipulation of header data. If prefix is given, then the options mean: .HP \fB\-a2\fR ==> write an ANALYZE 7.5 file pair: prefix.hdr/prefix.img .HP \fB\-n2\fR ==> write a NIFTI\-1 file pair: prefix.hdr/prefix.img .HP \fB\-n1\fR ==> write a NIFTI\-1 single file: prefix.nii .HP \fB\-na\fR ==> write a NIFTI\-1 ASCII+binary file: prefix.nia .HP \fB\-za2\fR => write an ANALYZE 7.5 file pair: .IP prefix.hdr.gz/prefix.img.gz .HP \fB\-zn2\fR => write a NIFTI\-1 file pair: prefix.hdr.gz/prefix.img.gz .HP \fB\-zn1\fR => write a NIFTI\-1 single file: prefix.nii.gz .HP \fB\-zna\fR => write a NIFTI\-1 ASCII+binary file: prefix.nia.gz .IP The default is '\-n1'. .PP If prefix is not given, then the header info from infile file is printed to stdout. .PP Please note that the '.nia' format is NOT part of the NIFTI\-1 specification, but is provided mostly for ease of visualization (e.g., you can edit a .nia file and change some header fields, then rewrite it as .nii) .SH "SEE ALSO" .BR libnifti (1), .BR nifti_tool (1), .BR nifti_stats (1). .PP Homepage: .I http://niftilib.sourceforge.net .SH "AUTHOR" The \fBNIfTI\fR libraries were written by the NIfTI Data Format Working Group (DFWG, .I http://nifti.nimh.nih.gov/ ). .PP This manual page was written by Michael Hanke , for the Debian project (but may be used by others). debian/nifti-bin.dirs0000644000000000000000000000003311421372005011717 0ustar usr/bin usr/share/man/man1 debian/patches/0000755000000000000000000000000011421375100010607 5ustar debian/patches/no_fslio0000644000000000000000000000064611421372005012351 0ustar --- a/docs/Doxy_nifti.txt +++ b/docs/Doxy_nifti.txt @@ -36,7 +36,7 @@ # directories like "/usr/src/myproject". Separate the files or directories # with spaces. -INPUT = ../fsliolib ../niftilib ../znzlib +INPUT = ../niftilib ../znzlib # 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 debian/patches/build_setup0000644000000000000000000000321111421372005013047 0ustar --- a/Testing/CMakeLists.txt +++ b/Testing/CMakeLists.txt @@ -3,5 +3,5 @@ PROJECT(TESTING) SUBDIRS(niftilib) -SUBDIRS(nifti_regress_test) +#SUBDIRS(nifti_regress_test) --- a/nifticdf/CMakeLists.txt +++ b/nifticdf/CMakeLists.txt @@ -6,8 +6,11 @@ SET(NIFTI_CDFLIB_NAME ${PACKAGE_PREFIX}nifticdf) -ADD_LIBRARY(${NIFTI_CDFLIB_NAME} ${NIFTICDFLIB_SRC} ) +# Debian: enable 'unused' function as the AFNI package needs them +ADD_DEFINITIONS( -D__COMPILE_UNUSED_FUNCTIONS__ ) +ADD_LIBRARY(${NIFTI_CDFLIB_NAME} ${NIFTICDFLIB_SRC} ) +TARGET_LINK_LIBRARIES(${NIFTI_CDFLIB_NAME} m ) IF (BUILD_SHARED_LIBS) SET_TARGET_PROPERTIES(${NIFTI_CDFLIB_NAME} PROPERTIES ${NIFTI_LIBRARY_PROPERTIES}) ENDIF (BUILD_SHARED_LIBS) --- a/utils/CMakeLists.txt +++ b/utils/CMakeLists.txt @@ -7,7 +7,7 @@ ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti_stats nifti_stats.c) ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti_tool nifti_tool.c) ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti1_test nifti1_test.c) -TARGET_LINK_LIBRARIES( nifti_stats ${PACKAGE_PREFIX}niftiio ${PACKAGE_PREFIX}nifticdf) +TARGET_LINK_LIBRARIES( nifti_stats ${PACKAGE_PREFIX}nifticdf) TARGET_LINK_LIBRARIES( nifti_tool ${PACKAGE_PREFIX}niftiio) TARGET_LINK_LIBRARIES( nifti1_test ${PACKAGE_PREFIX}niftiio) --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,6 +1,13 @@ #File Generated by Hans J. Johnson #Please contact hans-johnson@uiowa.edu for making enhancments/corrections PROJECT(NIFTI) + +# address warnings by cmake 2.6 +cmake_minimum_required(VERSION 2.4) +if(COMMAND cmake_policy) + cmake_policy(SET CMP0003 NEW) +endif(COMMAND cmake_policy) + # Configure Dart testing support. INCLUDE(${CMAKE_ROOT}/Modules/Dart.cmake) debian/patches/series0000644000000000000000000000002511421375100012021 0ustar no_fslio build_setup debian/changelog0000644000000000000000000002367311421401630011043 0ustar nifticlib (2.0.0-1) unstable; urgency=low * New release. Library changed API, hence bumped SO version to 2.0 (Closes: #587912). * Switch to dpkg-source 3.0 (quilt) format. Split git feature branches into quilt patch series. * Drop versioned -dev package. * Change maintainer to NeuroDebian Team . * Switch from verbose debhelper rules to 'dh'. * Removed ECODE patch (merged with upstream). * Bumped Standards-version to 3.9.0. Now supports 'nocheck'. -- Michael Hanke Tue, 20 Jul 2010 16:12:57 -0400 nifticlib (1.1.0-3) unstable; urgency=low * Disable building libfslio and remove the associated patches. The library is deprecated upstream. The affected Debian packages fsl and fslview will both build and use this library from fslview source code. * Included upstream-approved patch to add an ECODE for the PYPICKLE extension that is needed by PyNIfTI. Adjusted shlibdeps accordingly. * Added 'XS-DM-Upload-Allowed: yes' to debian/control. -- Michael Hanke Thu, 19 Feb 2009 19:13:54 +0100 nifticlib (1.1.0-2) unstable; urgency=low * Added patch to libfslio from FSL 4.1: Removal of ANALYZE support. Additionally, FSL 4.1 changed the signature of FslSeekVolume(). This patch is not imported as it has to be coordinated with upstream (ABI change). But as fslio will be remove from the package with the next version, there is little need to do so. * Added shlibsdeps info with (<= 1.1.0-2) for the upcoming removal of fslio. This is only needed for fsl and fslview packages (the only ones using fslio), to prevent them from being broken, once a new stripped nifticlib package is uploaded. -- Michael Hanke Fri, 24 Oct 2008 15:43:45 +0200 nifticlib (1.1.0-1) unstable; urgency=low * New upstream release. libniftiio1 contains some additional symbols -- keeping SONAME and let dh_makeshlibs note dependency information (>= 1.1). * Do not install fsliolib scripts (im*,remove_ext,*.tcl) anymore. This part will most likely be removed from the package in future releases. So far, it has not been exposed in the default search path, but is only used internally by the fsl package. However, FSL itself comes with a more up-to-date copy of these scripts. The included ones are outdated and cannot be used as a dependency for FSL. * Convert debian/copyright into a machine-readable format and merge debian/README.legal into it. * Bump Standards-version to 3.8.0, no changes necessary. * Manpage generator for 'nifti_tool' now replaces all single-quotes with double-quotes to prevent confusing them with groff commands, if they are first character on a line (addressed lintian warning). -- Michael Hanke Mon, 29 Sep 2008 12:38:07 +0200 nifticlib (1.0.0-1) unstable; urgency=low * New Upstream Version. New versioning scheme follows SO versions. All libraries in the package are no synchronized with respect to SO name and version. * Merged filename memory leak patch and ARM alignment patch (modified) with upstream. * Merged libfslio* packages with libniftiio*. As all library versions are now synchronized there is no need to keep libfslio separated. Especially as libfslio depends on libniftiio and is only a non-significant addition to the libniftiio package. Furthermore upstream is planning to merge libfslio with libniftiio in one of the next releases. * Renamed the only remaining library package pair to libnifti1. This is necessary to move all sub-libraries into one package without changing the SO name of libniftiio1 (with properly added conflicts to old libniftiio1 package). * Removed build-dep to d-shlibs as it cannot deal with new package name and install is now done manually. * Fixed some missing and some unnecessary symbols with correct linking. * Bumped Standards-version to 3.7.3, no changes necessary. -- Michael Hanke Wed, 02 Jan 2008 20:46:21 +0100 nifticlib (0.6-3) unstable; urgency=low * Fix half-broken dependency of libfslio0-dev on no longer existing libniftiio0-dev. -- Michael Hanke Wed, 28 Nov 2007 13:32:14 +0100 nifticlib (0.6-2) unstable; urgency=low * Compile 'unused' functions in nifticdf, because the prospective AFNI package depends on them. Set SO version of linifticdf to 0debian.1.0, because symbols were added. * Added new-style 'Hompage' and Vcs* fields to debian/control source stanza. * Included patch that fixes an illegal memory read that could occur when handling short filenames. Thanks to Yaroslav Halchenko. * Included patch that fixes a complicated issue that caused the library to fail on ARM. The reason was byte-swapping code that did not take the 4-byte alignment on ARM into account. Please see http://netwinder.osuosl.org/users/b/brianbr/public_html/alignment.html for more info about this topic. The Debian maintainer is grateful to Dominique Belhachemi for starting the investigation and Yaroslav Halchenko for finally spotting and fixing this bug (Closes: #446893). -- Michael Hanke Tue, 06 Nov 2007 20:01:05 +0100 nifticlib (0.6-1) unstable; urgency=low * New Upstream Version. This release introduces a new SO name for libniftiio. This was necessary to be able to handle NIfTI files larger than 2GB. * SO names of libznz and libnifticdf where set to a debian specific string ('0debian'). This was done to be able to keep them in one package with libniftiio1, without having to conflict with the previous libnifti0 package. The Debian maintainer decided against the alternative solution of a package split (one package for each library), because upstream wants to adopt a VTK like versioning scheme in future release (syncronize library interface versions across all libs). The Debian package will then merge all libraries into one package, as each one alone isn't really useful. * Install the TCL wrapper for the image handling scripts in nifti-bin (fslio.tcl). * Updated package descriptions. * Include patch for fslio from FSL4. This patch introduces a number of new symbols, but doesn't change the API or ABI of the public interface. Therefore the SO name is kept constant. * Wrote individual manpages for the nifti-bin tools. * Disabled parts of the regression tests at build time, as they depend on datasets that are not part of the sources (have to be downloaded first). -- Michael Hanke Wed, 5 Sep 2007 18:17:48 +0200 nifticlib (0.5-2) unstable; urgency=low * Add a patch to fslio to make it suitable for FSL 4.0. Bumped libfslio SO version due to some added symbols, but keeping SO name as only one internal function vanished (not previously exposed in the header file). * Removed leftover lintian override (Upstream does not include the CVS dirs anymore). * Added a little script to transform the help output of nifti_tool into a manpage (help2man does not work properly in this case). Added Python to the build-dependencies. * Removed custom SO-version setting from debian/rules as upstream sets proper SO-versions now. * Install fslio scripts into /usr/share/nifti to prevent naming conflicts with e.g. the 'im' package, but still let users and other packages make use of them. * Switch from ${Source-Version} to ${binary:Version} in debian/control. -- Michael Hanke Mon, 23 Jul 2007 11:30:50 +0200 nifticlib (0.5-1) unstable; urgency=low * New upstream release. * Shared library patch merged with upstream. * The nifticdf library is now part of upstream sources. This make the AFNI nifticdf patch obsolete. * Currently no Debian-specific patches left, but keeping dpatch dependency. * Enable verbose compiler output by default. * Add .NOTPARALLEL flag to debian/rules (required by dpatch). * Listing which libraries are part of which package in the package description. * Use "-Wl,--as-needed" as linker flags to address problems reported by checklib. -- Michael Hanke Tue, 5 Jun 2007 14:26:38 +0200 nifticlib (0.4+cvs20070424-1) unstable; urgency=low * New upstream CVS snapshot. No library interface changes, hence keeping current soversion. * Split nifti_stats sources into nifticdf library and nifti_stats application, to let the afni package use this library instead of using a copy of the sourcecode. libnifticdf is now part of the libniftiio* packages. * Perform tests at package build time. * Modified shared_lib support patch to match new upstream makefiles. -- Michael Hanke Wed, 25 Apr 2007 20:17:04 +0200 nifticlib (0.4-1) unstable; urgency=low * New upstream release. This release mostly changes the copyright statements of fsliolib source code files to explicitely mention that they were previously part of FSL, but are now placed into the public domain. * Debian patches merged with upstream. -- Michael Hanke Wed, 6 Sep 2006 21:47:35 +0200 nifticlib (0.3-2) unstable; urgency=low * Added appropriate 'Replaces' directives to debian/control to reflect the renaming of libnifti0 to libniftiio0 (and the separation of libfslio). -- Michael Hanke Mon, 4 Sep 2006 09:59:32 +0200 nifticlib (0.3-1) unstable; urgency=low * Initial release. (Closes: #383349) * Added shared library support. * Added a lintian override concerning a single CVS directory in the upstream sources. * Added a lintian override that the library package is not named after the contained library. The NIFTI interfaces consists of three different libraries (compression, low-level and high-level) and it make no sense to me to split them into three binary packages. * Added manpage. -- Michael Hanke Thu, 10 Aug 2006 22:14:20 +0200 debian/nifti-bin.install0000644000000000000000000000001711421372005012426 0ustar usr/bin/nifti* debian/makeniftitoolmanpage.py0000644000000000000000000000661311421372005013737 0ustar #!/usr/bin/python import sys import re sections = ['intro', 'usage', 'examples', 'checkoptions', 'createoptions', 'copyoptions', 'displayoptions', 'modoptions', 'addrmoptions', 'diffoptions', 'miscoptions', 'helpoptions', 'status' ] def prettyPrint( tlist, killcolon = False, markupcolon = False ): for line in tlist: line = re.sub("'", '"', line) if killcolon: parts=re.split(':',line) line = '.PP\n' + '\\fB' + parts[0].strip() + '\\fR ' + ' '.join(parts[1:]).strip() if markupcolon and line.find(':') >= 0: line = '\\fI' + line + '\\fR' if not line: print '.PP' continue elif line.startswith('- ') or line.startswith('o '): line = line[2:] print '.IP' elif line.startswith('-'): parts = re.split(' ', line) line = '\\fI' + parts[0] + '\\fR' + ' ' + ' '.join(parts[1:]) + '\n' elif line.startswith('one can'): print line[ :line.find('-')].strip() print '.IP' line = line[ line.find('-')+1:].strip() elif line.startswith('Note:'): print '\\fBNote:\\fR', line[6:] continue print line if __name__ == "__main__": sec_counter = 0 # initialize section dict info = {} for i in sections: info[i] = [] # fill section dict #print "Section:", sections[sec_counter] for line in sys.stdin: # strip useless stuff line = line.strip() if line.startswith('------'): sec_counter += 1 #print 'Section:', sections[sec_counter] info[sections[sec_counter]].append( line ) # transform section dict into a nice manpage print '.TH "NIFTI_TOOL" "1" "" "Michael Hanke" ""' print '.SH NAME' print 'nifti_tool - multipurpose manipulation tool for NIfTI files' print '.SH SYNOPSIS' prettyPrint( info['usage'][4:], killcolon=True) print '.BR' print '.SH DESCRIPTION' prettyPrint( ['This tool can'] + info['intro'][2:] ) print '.SH OPTIONS' print '\\fBCheck options\\fB\n.BR\n' prettyPrint( info['checkoptions'][4:]) print '\\fBCreate options\\fB\n.BR\n' prettyPrint( info['createoptions'][4:]) print '\\fBCopy options\\fB\n.BR\n' prettyPrint( info['copyoptions'][4:]) print '\\fBDisplay options\\fB\n.BR\n' prettyPrint( info['displayoptions'][4:]) print '\\fBModification options\\fB\n.BR\n' prettyPrint( info['modoptions'][4:]) print '\\fBAdd, remove options\\fB\n.BR\n' prettyPrint( info['addrmoptions'][4:]) print '\\fBDifference options\\fB\n.BR\n' prettyPrint( info['diffoptions'][4:]) print '\\fBMiscellaneous options\\fB\n.BR\n' prettyPrint( info['miscoptions'][4:]) print '\\fBHelp options\\fB\n.BR\n' prettyPrint( info['helpoptions'][4:]) print '.SH EXAMPLES' prettyPrint( info['examples'][4:], markupcolon=True) print """\ .SH "SEE ALSO" .BR libnifti (1), .BR nifti1_test (1), .BR nifti_stats (1). .PP Homepage: .I http://niftilib.sourceforge.net .SH "AUTHOR" The \\fBNIfTI\\fR libraries were written by the NIfTI Data Format Working Group (DFWG, .I http://nifti.nimh.nih.gov/ ). .PP This manual page was generated by a custom script, written by Michael Hanke (available within the Debian package) from the help output of the nifti_tool binary.' """ debian/nifti_stats.10000644000000000000000000000314311421372005011573 0ustar .TH NIFTI_STATS "1" "September 2007" "nifti_stats " "User Commands" .SH NAME nifti_stats \- compute NIfTI statistical functions .SH SYNOPSIS .B nifti_stats [\fI-q|-d|-1|-z\fR] \fIvalue CODE \fR[\fIp1 p2 p3\fR] .SH DESCRIPTION nifti_stats supports several distributions (normal, uniform, logistic, chi, etc.) and calculates density or cummulative distribution function (and many more). Values are printed to stdout and can be piped to other tools. .TP \fIvalue\fR can be a single number or in the form bot:top:step. default ==> output p = Prob(statistic < val). .TP \fB\-q\fR ==> output is 1\-p. .TP \fB\-d\fR ==> output is density. .TP \fB\-1\fR ==> output is x such that Prob(statistic < x) = val. .TP \fB\-z\fR ==> output is z such that Normal cdf(z) = p(val). .TP \fB\-h\fR ==> output is z such that 1/2\-Normal cdf(z) = p(val). .PP Allowable CODEs: .TP CORREL, TTEST, FTEST, ZSCORE, CHISQ, BETA, BINOM, GAMMA, POISSON, NORMAL, FTEST_NONC, CHISQ_NONC, LOGISTIC, LAPLACE, UNIFORM, TTEST_NONC, WEIBULL, CHI, INVGAUSS, EXTVAL, PVAL, LOGPVAL and LOG10PVAL .IP Following CODE are distributional parameters, as needed. .PP Results are written to stdout, 1 number per output line. .SH EXAMPLE Piping output into AFNI program 1dplot: .IP nifti_stats \fB\-d\fR 0:4:.001 INVGAUSS 1 3 | 1dplot \fB\-dx\fR 0.001 \fB\-stdin\fR .SH SEE ALSO .BR libnifti (1), .BR nifti_tool (1), .BR nifti1_test (1). .PP Homepage: .I http://niftilib.sourceforge.net .SH AUTHOR RW Cox \- SSCC/NIMH/NIH/DHHS/USA/EARTH \- March 2004 .PP This manual page was written by Michael Hanke , for the Debian project (but may be used by others). debian/libnifti-dev.docs0000644000000000000000000000000711421375100012403 0ustar README debian/nifti-bin.manpages0000644000000000000000000000010211421372005012546 0ustar debian/tmp/nifti_tool.1 debian/nifti_stats.1 debian/nifti1_test.1 debian/watch0000644000000000000000000000010011421372005010201 0ustar version=3 http://sf.net/niftilib/nifticlib-([\d\.]*)\.tar\.gz debian/rules0000755000000000000000000000456011421375100010245 0ustar #!/usr/bin/make -f # -*- makefile -*- # This has to be exported to make some magic below work. export DH_OPTIONS STATIC_BUILD_PATH=DEB_build_static SHARED_BUILD_PATH=DEB_build_shared export CFLAGS = -Wall -g ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) export CFLAG += -O0 else export CFLAGS += -O2 endif CMAKE_FLAGS=-DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DNIFTI_INSTALL_INCLUDE_DIR:PATH=include/nifti \ -DCMAKE_SKIP_RPATH:BOOL=ON \ -DCMAKE_C_FLAGS:STRING="$$CFLAGS" \ -DCMAKE_SHARED_LINKER_FLAGS="-Wl,--as-needed" \ -DCMAKE_EXE_LINKER_FLAGS="-Wl,--as-needed" \ -DUSE_FSL_CODE:BOOL=OFF \ -DBUILD_TESTING:BOOL=TRUE # one ring to rule them all ... %: dh $@ --buildsystem=cmake override_dh_auto_clean: rm -rf $(STATIC_BUILD_PATH) $(SHARED_BUILD_PATH) rm -rf docs/html dh_clean override_dh_auto_configure: if [ ! -d $(STATIC_BUILD_PATH) ]; then mkdir $(STATIC_BUILD_PATH); fi if [ ! -d $(SHARED_BUILD_PATH) ]; then mkdir $(SHARED_BUILD_PATH); fi cd $(STATIC_BUILD_PATH) \ && cmake $(CURDIR) $(CMAKE_FLAGS) -DBUILD_SHARED_LIBS:BOOL=OFF \ -DBUILD_TESTING:BOOL=ON cd $(SHARED_BUILD_PATH) \ && cmake $(CURDIR) $(CMAKE_FLAGS) -DBUILD_SHARED_LIBS:BOOL=ON \ -DBUILD_TESTING:BOOL=OFF override_dh_auto_build: # build static libs cd $(STATIC_BUILD_PATH) && $(MAKE) VERBOSE=1 # build shared libs and binaries cd $(SHARED_BUILD_PATH) && $(MAKE) VERBOSE=1 # build api reference cd docs && doxygen Doxy_nifti.txt override_dh_auto_test: ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS))) cd $(STATIC_BUILD_PATH) && ctest endif override_dh_auto_install: # install binaries and shared libs cd $(SHARED_BUILD_PATH) && $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp # install static libs cd $(STATIC_BUILD_PATH)/znzlib \ && $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp cd $(STATIC_BUILD_PATH)/niftilib \ && $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp cd $(STATIC_BUILD_PATH)/nifticdf \ && $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp # install manpage $(STATIC_BUILD_PATH)/utils/nifti_tool -help | \ python debian/makeniftitoolmanpage.py > debian/tmp/nifti_tool.1 # Remove unecessary header file rm $(CURDIR)/debian/tmp/usr/include/nifti/nifti_tool.h override_dh_installchangelogs: dh_installchangelogs -k Updates.txt debian/libnifti2.install0000644000000000000000000000001711421375100012430 0ustar usr/lib/*.so.*