io/ 0000755 0000764 0001040 00000000000 12636612671 012545 5 ustar philip Administrators io/COPYING 0000644 0000764 0001040 00000104513 12431415112 013564 0 ustar philip Administrators GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
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THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
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If the disclaimer of warranty and limitation of liability provided
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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
state 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 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 .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
Copyright (C)
This program 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, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
.
The GNU 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 Lesser General
Public License instead of this License. But first, please read
.
io/DESCRIPTION 0000644 0000764 0001040 00000000756 12636612546 014264 0 ustar philip Administrators Name: io
Version: 2.4.0
Date: 2015-12-23
Author: various authors
Maintainer: Philip Nienhuis
Title: Input/Output
Description: Input/Output in external formats.
Categories: IO
Problems: Default initial Java memory probably too small, increase with java.opts (see documentation). UNO support experimental.
Depends: octave (>= 3.8.0), Octave (< 4.2.0)
Suggested: windows (>= 1.2.1); Java JRE (> 1.6)
Autoload: no
License: GPLv3+, simplified BSD
Url: http://octave.sf.net
io/doc/ 0000755 0000764 0001040 00000000000 12636612671 013312 5 ustar philip Administrators io/doc/READ-ODS.html 0000644 0000764 0001040 00000120304 12476634745 015346 0 ustar philip Administrators
ODS support for Octave
Copyright © 2009 - 2015 Philip Nienhuis <prnienhuis at users.sf.net>
This version March 7, 2015
(ODS = Open Document Format spreadsheet data format, used by e.g., OpenOffice.org.)
-
Files content
odsread.m
No-hassle read script for reading from an ODS file and parsing the numeric
and text data into separate arrays.
odswrite.m
No-hassle write script for writing to an ODS file.
- odsopen.m
- Get a file pointer to an ODS spreadsheet file.
ods2oct.m
Read raw data from an ODS spreadsheet file using the file pointer handed by odsopen.
-
oct2ods.m
Write data to an ODS spreadsheet file using the file pointer handed by odsopen.
-
odsclose.m
Close file handle made by odsopen and -if data have been transfered to a spreadsheet- save
data.
-
odsfinfo.m
Explore sheet names and optionally estimated data size of ods files with unknown content.
-
calccelladdress.m
Utility function, can be used to compute a spreadsheet-type cell adress from 1-based row and column numbers.
-
parsecell.m
(contained in Excel xlsread scripts, but works also for ods support) parse raw data (cell array) into separate numeric array and text (cell) array.)
-
chk_spreadsheet_support.m
Internal function for (1) checking, (2) setting up, (3) debugging spreadsheet support. While
not specifically meant for direct invocation from the Octave prompt (it
is more useful during initialization of Octave itself) it can be very
helpful when hunting down issues with spreadsheet support in Octave.
-
test_spsh.m, io_ods_testscript.m
Undocumented scripts for testing basic operation of ODS spreadsheet functions. Meant for testers and developers, but I don't mind if mere mortal users give it a try as well ;-)
REQUIRED
SUPPORT SOFTWARE
- For the native Octave interface (OCT)
(read/write support for ODS 1.2 (LibreOffice/OpenOffice.org Calc), OOXML (Excel 2007+), and Gnumeric)
NO external support software is required!
Octave >= 3.8.0 will do just fine but maybe a bit slow. If you want faster I/O, Java support need to be compiled in, a Java JRE > 1.6.0 must be installed, and one or more of the following is required:
odfdom.jar (for the OTK interface, currently the preferred option)
(only versions 0.7.5,
0.8.6, 0.8.7 and 0.8.8 (the latter from incubator v. 0.5, see download URL below) work OK!) & xercesImpl.jar (watch out here too! only version 2.9.1 (2007-sep-14) works OK with odfdom). Get them here:
http://odftoolkit.org/projects/odfdom/pages/Home
http://incubator.apache.org/odftoolkit/downloads.html (preferred)
Google for xerces-2.9.1 download
and/or
jopendocument<version>.jar (for the JOD interface)
(jOpenDocument 1.3 (final) is the most recent stable one and recommended for Octave)
and/or
OpenOffice.org (or clones like LibreOffice, Go-Office, ...) (for the UNO interface)
Get it from http://www.openoffice.org. The relevant Java class libs are unoil.jar,
unoloader.jar, jurt.jar, juh.jar and ridl.jar (which are scattered around the OOo installation directory), while also the <OOo>/program/
directory needs to be in the classpath.
NOTE: OOo's / LO's arch type (32-bit or 64-bit) must match Octave's arch. In other words, 64-bit Octave won't work with 32-bit LibreOffice, and vice versa.
-
Whatever Java option, these class libs must be referenced with full pathnames in your javaclasspath.
When the io package gets loaded, a utility function (PKG_ADD) tries to automatically find the Java class libs and adds the ones it found to the javaclasspath; When the io package gets unloaded, these same class libs will be removed from the javaclasspath.
Except for the UNO (OOo) classes, on MinGW the jar files had best be put in /<libdir>/java where <libdir> on MinGW it is usually /lib; on Linux system supplied Java class libs usually reside in /usr/share/java. Alternatively, you can put them in your HOME directory in a subdirectory java (mind case!) - on *nix that would be ~./java, on Windows %USERPROFILE%/java (same level as My Documents). The PKG_ADD routine, that gets run each time the io package is loaded, expects the class libs there; if they are elsewhere, add them in ./share/octave/<version>/m/startup/octaverc using appropriate javaaddpath statements or a chk_spreadsheet_support() call.
In addition, you can specify a subdirectory using the environment variable OCTAVE_IO_JAVALIBS.
Once a particular Java class lib has been added to the javaclasspath, it won't be searched anymore nor reloaded from the next search location. The search order is:
- Specified by the environment variable OCTAVE_IO_JAVALIBS
- <HOME_DIR>/java
- /usr/share/java (*nix) or /lib/java (MinGW)
If you do not want PKG_ADD to load the Java class libs, specify a value of "no", "false" or "0" for the OCTAVE_IO_JAVALIBS environment variable before starting Octave.
USAGE
(see “help
ods<function_filename>” in octave terminal.)
odsread
is a sort of analog to
xlsread and works more or less the same. odsread
is a
mere wrapper for the functions odsopen,
ods2oct,
and odsclose
that do file access and
the actual reading, plus parsecell
for post-processing.
odswrite
works similar to
xlswrite. It too is a wrapper for scripts which do the actual work
and invoke other scripts, a.o. oct2ods.
odsfinfo
can be used to explore
odsfiles with unknown content for sheet names and to get an
impression of the data content sizes.
When you need
data from just one sheet, odsread is for you. But when you need
data from multiple sheets in the same spreadsheet file, or if you
want to process spreadsheet data by limited-size chunks at a time,
odsopen / ods2oct [/parsecell] / … /
odsclose sequences provides for much more speed and
flexibility as the spreadsheet needs to be read just once rather
than repeatedly for each call to odsread.
Same reasoning goes for
odswrite.
Also, if you use
odsopen / …../, you can process multiple spreadsheets
simultaneously – just use odsopen repeatedly to get
multiple spreadsheet file pointers.
Moreover, after
adding data to an existing spreadsheet file, you can fiddle with the
filename in the ods file pointer struct to save the data into
another, possibly new spreadsheet file.
If you use
odsopen / ods2oct / … / oct2ods / ….
/ odsclose, DO NOT FORGET to invoke odsclose in the
end. The file pointers can contain an enormous amount of data and
may needlessly keep precious memory allocated. In case of the UNO interface, the hidden OpenOffice.org invocation (soffice.bin) can even block proper closing of
Octave.
SPREADSHEET
FORMULA SUPPORT
-
When using the OTK, UNO, and/or OCT
interface you can:
-
(When reading, ods2oct)
either read spreadsheet formula results, or the literal formula text
strings;
-
(When writing, oct2ods)
either enter formulas in the worksheet as formulas, or enter them as
literal text strings.
In short, you can
enter spreadsheet formulas and in a later stage read them back,
change them and re-enter them in the worksheet. The behaviour is
controlled by an option structure options
(as last argument to
oct2ods.m
and ods2oct.m)
which for now has only one (logical) field:-
options.formulas_as_text
= 0 (the default)
implies enter formulas as formulas and read back formula results
-
options.formulas_as_text
=1 (or
any positive integer) means enter formulas as text strings and read
them back as text strings.
- Be aware that
there's no formula evaluator in ODS java, not even a formula
validator. So if you create formulas in your spreadsheet using
oct2ods
or odswrite,
do not expect meaningful results when reading those files later on
unless
you open them in
OpenOffice.org Calc and write them back to disk.
-
You can write all kind
of junk as a formula into a spreadsheet cell. There's not much
validity checking built into odfdom.jar. I didn't bother to try
OpenOffice.org Calc to read such faulty spreadsheets, so I don't
know what will happen with spreadsheets containing invalid formulas.
But using the above options, you can at least repair them using
octave....
The only exception is if you select the UNO interface, as that invokes
OpenOffice.org behind the scenes, and OOo obviously has a validator and
evaluator built-in.
GOTCHAS
I know of one big
gotcha: i.e. reading dates (& time). A less obvious one is Java
memory pool allocation size.
Date and time
in ODS
Octave (as does Matlab)
stores dates as a number representing the number of days since
January 1, 0 (and as an aside ignores a.o. Pope Gregorius'
intervention in 1582 when 10 days were simply skipped).
OpenOffice.org stores
dates as text strings like “yyyy-mm-dd”.
MS-Excel stores dates as
a number representing the number of days since January 1, 1900 (and
as an aside, erroneously assumes 1900 to be a leap year).
Now, converting
OpenOffice.org date cell values (actually, character strings flagged
by “date” attributes) into Octave looks pretty
straightforward. But when the ODS spreadsheet was originally an
Excel spreadsheet converted by OpenOffice.org, the date cells can
either be OOo date values (i.e.,strings) OR old numerical values
from the Excel spreadsheet.
So: you should
carefully check what happens to date cells.
As octave has no
”date” or “time” data type, octave date
values (usually numerical data) are simply transferred as “floats”
to ODS spreadsheets. You'll have to convert the values into dates
yourself from within OpenOffice.org.
While adding data and
time values has been implemented in the write scripts, the wait is
for clever solutions to distinguish dates from floats in octave cell
arrays.
Java memory
pool allocation size
The Java virtual machine
(JVM) initializes one big chunk of your computer's RAM in which all
Java classes and methods etc. are to be loaded: the Java memory
pool. It does this because Java has a very sophisticated “garbage
collection” system. At least on Windows, the initial size is
2MB and the maximum size is 64MB. On Linux this allocated size is
much bigger. This part of memory is where the Java-based ODS octave
routines (and the Java-based ods routines) live and keep their
variables etc.
For transferring large
pieces of information to and from spreadsheets you might hit the
limits of this pool. E.g. to be able to handle I/O of an array of
around 50,000 cells I needed a memory pool size of 512 MB.
The memory size can be
increased by inserting a file called “java.opts”
(without quotes) in the directory
./share/octave/packages/java-<version> (where the script file
javaclasspath.m is located), containing just the following lines:
-Xms16m
-Xmx512m
(where 16 = initial
size, 512 = maximum size (in this example), m stands for Megabyte.
This number is system-dependent).
After processing a large
chunk of spreadsheet information you might notice that octave's
memory footprint does not shrink so it looks like Java's memory pool
does not shrink back; but rest assured, the memory footprint is the
allocated (reserved) memory size, not the actual used size.
After the JVM has done its garbage collection, only the so-called
“working set” of the memory allocation is really in use
and that is a trimmed-down part of the memory allocation pool. On
Windows systems it often suffices to minimize the octave terminal
for a few seconds to get a more reasonable memory footprint.
Reading cells
containing errors
Spreadsheet cells
containing erroneous stuff are transferred to Octave as NaNs. But
not all errors can be catched. Cells showing #Value# in
OpenOffice.org Calc often contain invalid formulas but may have a 0
(null) value stored in the value fields. It is impossible to catch
this as there is no run-time formula evaluator (yet) in ODF Toolkit
nor jOpenDocument (like there is in Apache POI for Excel).
Smaller gotcha's
(only with jOpenDocument 1.2b2, fixed in 1.2b3+ and
1.2 final):
While reading, empty
cells are sometimes not skipped but interpreted with numerical value
0 (zero).
A valid range MUST be
specified, I haven't found a way to discover the actual occupied
rows and columns (jOpenDocument can give the physical ones (=
capacity) but that doesn't help).
NOT fixed in
version 1.2 final nor 1.3b1:
MATLAB
COMPATIBILITY
Depending on the MS-Excel version on the same computer,
Matlab may read/write ODS files using xlsread/xlswrite. Note that decent ODS 1.2 support only started with Excel 2013.
odsread is fairly
function-compatible to xlsread, however.
Same goes for odswrite,
odsfinfo and xlsfinfo – however odsfinfo
has better functionality IMO.
COMPARISON
OF INTERFACES
The ODFtoolkit is
the one that gives the best (but slow) results at present. However,
parsing xml trees into rectangular arrays is not quite
straightforward and the other way round is a real nightmare;
odftoolkit up til 0.7.5. did little to hide the gory details for the
developers.
While reading ODS is
still OK, writing implies checking whether cells already exist
explicitly (in table:table-cells) or implicitly (in
number-columns-repeated or number-rows-repeated nodes) or not at all
yet in which case you'll need to add various types of parent nodes.
Inserting new cells (“nodes”) or deleting nodes implies
rebuilding possibly large parts of the tree in memory - nothing for
the faint-of-heart. Only with ODFToolkit (odfdom) 0.8.6, 0.8.7 and 0.8.8 things have
been simplified for developers.
Unfortunately, with odftoolkit-0.6.0-incubating and odftoolkit-0.6.1-incubating
(corresponding to odfdom-0.8.9 and 0.8.10) unresolved dependencies ("jenasin") have been introduced that
break their functionality for Octave.
The jOpenDocument
interface is more promising, as it does shield the xml tree
details and presents developers something which looks like a
spreadsheet model.
However, unfortunately
the developers decided to shield essential methods by making them
'protected' (e.g. the vital getCellType). JopenDocument does support
writing. But OTOH many obvious methods are still lacking and formula
support is absent (although announced for future version 1.4).
And last (but not least)
the jOpenDocument developers state that their development is
primarily driven by requests from customers who pay for support. I
do sympathize with this business model but for Octave needs this may
hamper progress for a while.
In addition, jOpenDocument 1.2 and 1.3b1 still have bugs here and there. For
one, it doesn't write appropriate OfficeValueType attributes to the cells, so
there's no way to reliably read and distinguish boolean, string and integer
values.
The (still experimental)
UNO interface, based on a Java/UNO bridge linking a hidden OpenOffice.org
invocation to Octave, is the most promising:
-
Admittedly OOo needs some tens of seconds to start for the first time,
but once OOo is in the operating system's disk cache, it operates much
faster than ODF or JOD;
-
It has built-in formula validator and evaluator;
-
It has a much more reliable data parser;
-
It can read much more spreadsheet formats than just ODS; .sxc (older OOo and
StarOffice), but also .xls, .xlsx (Excel), .wk1 (Lotus 123), dbf, etc.
-
It consumes only a fraction of the JVM heap memory that the other Java ODS
spreadsheet solutions need because OOo reads the spreadsheet in its own memory
chunk in RAM. The other solutions read, expand, parse and manipulate
all data in the JVM. In addition, OOo's code is outside the JVM (and
Octave) while the ODF Toolkit and jOpenDocument classes also reside in the
JVM.
However, UNO is not stable yet (see below).
As stated above, the arch type (32-bit or 64-bit) must match that of Octave..
The OCT (native Octave)
interface is also promising as it is completely under control of Octave (-Forge) developers.
Currently it only offers read and -experimental- write support for ODS (relatively slow), gnumeric (faster) and OOXML (very fast). An immense advantage is that no other external software is required. Write support has not extensively tested yet, however.
TROUBLESHOOTING
Some hints for
troubleshooting ODS support are given here.
Since April 2011 the function chk_spreadsheet_support() has been included in
the io package. Calling it with arguments ('', 3) (empty string and debug level 3)
will echo a lot of diagnostics to the screen. Large parts of the steps
outlined below have been automated in this script.
Problems with UNO are too complicated to treat them here; most of the troubleshooting has been
implemented in chk_spreadsheet_support.m, only some general guidelines are
given below.
Check
if Java
works. Do a pkg
list and
see
a. If there's a Java
package mentioned (then it's installed). If not, install it.
b. If there's an
asterisk on the java package line (then the package is loaded). If
not, do a pkg
rebuild-auto java
Check
Java
memory settings. Try javamem
a. If it works, check if
it reports sufficiently large max memory (had better be 200 MiB, the
bigger the better)
b. If it
doesn't work, do:
rt = java_invoke
('java.lang.Runtime', 'getRuntime')
rt.gc
rt.maxMemory
().doubleValue () / 1024 / 1024
The last command will
show MaxMemory in MiB.
c. In case
you have insufficient memory, see in “GOTCHAS”, “Java
memory pool allocation size”, how to increase java's memory
pre-reservation.
Check if all classes
(.jarfiles) are in class path. Do a 'jcp = javaclasspath (-all)' (under unix/linux, do 'jcp
= javaclasspath; strsplit (jcp,”:”)'
(w/o quotes). See above under “REQUIRED SUPPORT SOFTWARE”
what classes should be mentioned.
If classes (.jar files)
are
missing, download and put them somewhere and add them to the
javaclass path with their fully qualified pathname (in quotes) using
javaaddpath().
Once all classes
are present and in the javaclasspath, the ods interfaces should just
work. The only remaining showstoppers are insufficient write
privileges for the working directory, a wrecked up octave or some
other problems outside octave.
Try
opening an ods file:
ods1
= odsopen ('test.ods', 1, 'otk').
If this works and ods1 is a struct with various fields containing
objects, ODF toolkit interface (OTK) works. Do an ods1
= odsclose (ods1) to
close the file.
ods2 = odsopen
('test.ods', 1, 'jod').
If this works and ods2 is a struct with various fields containing
objects, jOpenDocument interface (JOD) works as well. Do ods2
= odsclose (ods2) to
close the file.
For the UNO
interface, at least version 1.2.8 of the Java package is needed plus the following
Java class libs (jars) and directory:
* unoil.jar (usually found in subdirectory Basis<version>/program/classes/
or the like of the OpenOffice.org (<OOo>) installation directory;
* juh.jar, jurt.jar, unoloader.jar and ridl.jar, usually
found in the subdirectory URE/share/java/ (or the like) of OOo's installation directory;
* The subdirectory program/ (where soffice[.exe] (or ooffice) resides).
The exact case (URE or ure, Basis or basis), name ("Basis3.2" or just "basis") and
subdirectory tree (URE/java or URE/share/java) varies across OOo versions and -clones,
so chk_spreadsheet_support.m can have a hard time finding all needed classes. In
particularly bad cases, when chk_spreadsheet_support cannot find them, you might need
to add one or more of these these classes manually to the javaclasspath.
DEVELOPMENT
As with the Excel
r/w stuff, adding new interfaces should be easy and straightforward.
Add relevant stanzas for your new interface INTF in odsopen, odsclose, odsfinfo, oct2ods, ods2oct, getusedrange and add new subfunctions (for the real work) in subdir ./private; you'll need a total of six interface-dependent private functions (see the various examples for each interface in subdir ./private).
Suggestions for
future development:
Speeding up (ODS is 10 X
slower than e.g. OOXML !!!). jOpenDocument is much faster but still
immature.
For large spreadsheets, UNO *is* MUCH faster than jOpenDocument but starting up OpenOffice.org
for the first time can take tens of seconds...
Note that UNO is still experimental. The issue is that odsclose() will simply
kill ALL other OpenOffice.org invocations, also those that were not opened
through Octave! This is related to UNO-Java limitations.
The underlying issue is that when Octave starts an OpenOffice.org invocation,
OpenOffice.org must be closed for Octave to be able to exit; otherwise Octave will
wait for OOo to shut down before it can terminate itself. So Octave must kill
OOo to be able to terminate.
A way out hasn't been found yet.
“Passing function
handle” a la Matlab's xlsread
Adding styles (borders,
cell lay-out, font, etc.)
Some notes on the
choice for Java (becoming less relevant as the OCT interface gets more mature):
-
It saves a LOT of
development time to use ready-baked Java classes rather than
developing your own routines and thus effectively reinvent the
wheel.
-
A BIG advantage is that
a Java-based solution is platform-independent (“portable”).
-
The Java classes offer much more options than just reading and writing. Formatting, recalculation options, hiding/merging cell ranges, etc.
-
But Java is known to be
not very conservative with resources, especially not when processing
XML-based formats.
- So Java is a
compromise between portability and rapid development time versus
capacity (and speed).
-
But IMO data sets larger
than 5.105 cells should not be kept in spreadsheets
anyway. Use real databases for such data sets.
-
- ODFDOM versions
-
- I have tried various
odfdom versions. As to 0.8 & 0.8.5, while the API has been
simplified enormously (finally one can address cells by spreadsheet
address rather than find out yourself by parsing the
table-column/-row/-cell structure), many irrecoverable bugs have
been introduced :-((
- In addition
processing ODS files became significantly slower (up to 7 times!).
-
- End of August 2010
there's implemented support for odfdom-0.8.6.jar – that version
is at last sufficiently reliable to use. The few remaining bugs and
limitations could easily be worked around by diving in the older
TableTable API. Later on (early 2011) version 0.8.7 has been tested
too - this needed a few adjustments. Early 2012 odfdom-0.8.8 (from odfdom-0.5-incubator)
was accepted. In March 2015 odfdom-0.8.10 (odfdom-0.6.1-incubator) was tested but
alas, it doesn't work (needs extraneous dependencies); clearly the odfdom API (currently at main
version 0) is not stable yet.
-
So at the moment
(August 2012 = last I looked) only odfdom versions 0.7.5,
0.8.6, 0.8.7 and 0.8.8(-incubator) are supported.
0.7.5 is deprecated, however.
- If you want to
experiment with odfdom 0.8 & 0.8.5, you can try:
-
odsopen.m (revision
7157)
-
ods2oct.m (revision
7158)
-
oct2ods.m (revision
7159)
Enjoy!
Philip Nienhuis, March 7, 2015