README for Excel spreadsheet file r/w access scripts for octave (> 3.8.x)
Copyright (C) 2009 - 2017 Philip Nienhuis <prnienhuis at users.sf.net>
February 4, 2017
EXCEL .XLS SUPPORT FILES
doc/README-XLS.html
This file.
xlsread.m
All-in-one function for reading data from one specific worksheet in an Excel spreadsheet file. This script has Matlab-compatible functionality.
xlswrite.m
All-in-one function for writing data to one specific worksheet in an Excel spreadsheet file. This script has Matlab-compatible functionality.
xlsfinfo.m
All-in-one function for exploring basic properties of an Excel spreadsheet file. This script has Matlab-compatible functionality.
xlsopen.m
Function for "opening" (= providing a handle to) an Excel spreadsheet file ("workbook"). This function sorts out which interface to use for .xls access (i.e.,COM; Java & Apache POI; JexcelAPI; OpenXLS; etc.), but it's choice can be overridden.
xls2oct.m
Function for reading data from a specific worksheet pointed to in a struct created by xlsopen.m. xls2oct can be called multiple times consecutively using the same pointer struct, each time allowing to read data from different ranges and/or worksheets. Data are returned in the form of a 2D heterogeneous cell array that can be parsed by parsecell.m. xls2oct is a mere wrapper for interface-dependent scripts that do the actual low-level reading.
oct2xls.m
Function for writing data to a specific worksheet pointed to in a struct created by xlsopen.m. octxls can be called multiple times consecutively using the same pointer struct, each time allowing to write data to different ranges and/or worksheets. oct2xls is a mere wrapper for interface-dependent scripts that do the actual low-level writing.
xlsclose.m
Function for closing (the handle to) an Excel workbook. When data have been written to the workbook oct2xls will write the workbook to disk. Otherwise, the file pointer is simply closed and possibly used interfaces for Excel access (COM/ActiveX/Excel.exe) will be shut down properly.
parsecell.m
Function for separating the data in raw arrays returned by xls2oct, into numerical/logical and text (cell) arrays.
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.
calccelladdress.m,Support function called by the script functions; calculates spreadsheet type row/column address based on 1-based row/column numbers.
test_spsh.m, io_xls_testscript.m
Undocumented scripts for testing basic features of the spreadsheet scripts. Meant for testers and developers, but I don't mind ordinary users to give it a try.
REQUIRED SUPPORT SOFTWARE
- For the native Octave interface (OCT)
(read/write support for OOXML (Excel 2007+), ODS 1.2 (LibreOffice/OpenOffice.org Calc), and Gnumeric)
NO external support software is required!
For the Excel/COM interface:
- A windows computer with Excel installed
- Octave-forge Windows-1.2.1 (Windows-1.2.2 for Octave 4.0+)
For the Java / Apache POI / JExcelAPI / OpenXLS / LibreOffice | OpenOffice.org interfaces (general):
- Octave 3.7.2 or later with Java support compiled in
- Java JRE or JDK > 1.6.0 (hasn't been tested with earlier versions)
- Apache POI specific:
and here:
- for OOXML support with Apache POI:
poi-ooxml-schemas-<version>.jar, + either xbean.jar or xmlbeans.jar, + dom4j-1.6.1.jar in javaclasspath.
Get them here:
http://poi.apache.org/download.html ("xmlbeans" and poi-ooxml-schemas)
http://sourceforge.net/projects/dom4j/files (dom4j-<version>)
Starting with POI-3.15, another Java class lib is required: commons-collections4-.jar
Recent releases of Apache POI provide zipped / tar.gz'd archives with all required files inside.
- JExcelAPI specific:
- OpenXLS specific:
- class .jar: OpenXLS.jar in classpath
- Get it here:
http://sourceforge.net/projects/openxls/ (Be sure to get version 10)
class .jar: gwt-servlet-deps.jar in classpath
Get it here: http://www.gwtproject.org/download.html ("Download GWT SDK")
- These class libs must be referenced with full pathnames in your javaclasspath.
When the io package gets loaded, a utility function (PKG_ADD) invokes an initiaization function that 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.
On MinGW the required Java class libs had best be put in /<libdir>/java (where <libdir> on MinGW 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.
- UNO specific (invoking OpenOffice.org (or clones) behind the scenes):
NOTE: EXPERIMENTAL!! A working OpenOffice.org installation. The utility function chk_spreadsheet_support can be used to add the needed entries to the javaclasspath.
Be aware that OpenOffice.org/LibreOffice arch type (32-bit or 64-bit) must match Octave's arch type.
USAGE
xlsread and xlswrite are mere wrappers for xlsopen-xls2oct-xlsclose-parsecell and xlsopen-oct2xls-xlsclose sequences, resp. They exist for the sake of Matlab compatibility.
xlsfinfo can be used for finding out what worksheet names exist in the file. For OOXML files you either need MS-Excel 2007 for Windows (or later version) installed, and/or the input parameter REQINTF should be specified with a value of 'poi', 'oxs' or 'uno' (case-insensitive) and -obviously- either the complete POI interface must have been installed, and/or OpenXLS, and/or LibreOffice/OpenOffice.org.
Invoking xlsopen/..../xlsclose directly provides for much more flexibility, speed, and robustness than xlsread / xlswrite. Indeed, using the same file handle (pointer struct) you can mix reading & writing before writing the workbook out to disk using xlsclose.
And: xlsopen / xlsclose hide the gory interface details from the user.
Currently only .xls files (BIFF8) can be read/written; using JExcelAPI BIFF5 can be read as well. For OOXML files either Excel 2007 for Windows (or higher) and/or the complete Apache POI interface, and/or OpenXLS v 10, or LibreOffice must be installed (and probably the REQINTF parameter specified with a value of 'poi', 'oxs', or 'uno').
When using xlsopen....xlsclose be sure to keep track of the file handle struct.
A possible scenario:
xlh = xlsopen (<excel_filename> , [rw], [<requested interface>])
# Set rw to 1 if you want to write to a workbook immediately.
# In that case the check for file existence is skipped and
# -if needed- a new workbook created.
# If you really want an other interface than auto-selected
# by xlsopen you can request that. But xlsopen still checks
# proper support for your choice.
# Read some data
[ rawarr1, xlh ] = xls2oct (xlh, <SomeWorksheet>, <Range>)
# Be sure to specify xlh as output argument as xls2oct keeps
# track of changes and the need to write the workbook to disk
# in the xlhstruct. And the origin range is conveyed through
# the xlh pointer struct.
# Separate data into numeric and text data
[ numarr1, txtarr1, lim1 ] = parsecell (rawarr1)
# Get more data from another worksheet in the same workbook
[ rawarr2, xlh ] = xls2oct (xlh, <SomeOtherWorksheet>, <Range>)
[ numarr2, txtarr2, lim2 ] = parsecell (rawarr2)
# <... Analysis and preparation of new data in cell array Newdata....>
# Add new data to spreadsheet
xlh = oct2xls (Newdata, xlh, <AnotherWorksheet>, <Range>)
# Close the workbook and write it to disk; then clear the handle
xlh = xlsclose (xlh)
clear xlh
- When not using the COM interface, specify a value of 'POI' for parameter REQINTF when accessing OOXML files in xlsread, xlswrite, xlsopen, xlsfinfo (and be sure the complete Apache POI interface is installed). If you haven't got ActiveX installed (i.e., not having MS-Excel under Windows) specifying 'POI' may not be needed as in such cases Apache POI is the next default interface.
- When using JExcelAPI (JXL), after writing into a worksheet you MUST save the file – adding data to the same or another worksheet is no more possible after the first call to oct2xls(). This is a limitation of JExcelAPI.
SPREADSHEET FORMULA SUPPORT, STRIPPING AND ENCODING
When using the COM, POI, JXL, OXS, UNO and OCT interfaces you can:
- (When reading, xls2oct) either read evaluated spreadsheet formula results, or the literal formula text strings;
- (When writing, oct2xls) either enter text strings in the form of spreadsheet 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
which has some fields ("flags") that can be set to TRUE or FALSE:
= 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 JExcelAPI (JXL). So if you create formulas in your spreadsheet using oct2xls or xlswrite with 'JXL', do not expect meaningful results when reading those files later on unless you open them in Excel and write them back to disk.
While both Apache POI and JExcelAPI feature a formula validator, not all spreadsheet functions present in Excel have been implemented (yet).
Worse, older Excel versions feature less functions than newer versions. So be wary as this may make for interesting confusion.
options.strip_array = 1 (the default) instructs Octave to strip the output arrays resulting from reading a spreadsheet from empty outer rows and columns.
options.strip_array = 0 will return the complete requested output range.
options.convert_utf = 0 (the default) leave UTF-8 encoded text strings read from a spreadsheet untouched. Usually this works well as the Octave terminal usually knows how to display UTF-8 encoded strings - but note that Octve itself has limited support for processing multibyte-character strings. Windows 10 has proper support for UTF-8 in the cmd.exe terminal (used by Octave); but older Windows versions may need a conversion step:
options.convert_utf = 1 currently invokes conversion functions utf82unicode.m (when reading from spreadsheet) or unicode2utf8 (when writing to spreadsheet). This can be useful when the strings in Octave that are intended to be written to spreadsheet file contain characters outside the range [32:127]; Excel and LibreOffice cannot process spreadsheets containing single characters outside that range.
Note that when invoking xlsread.m and xlswrite.m, these options are not available. To use these options you need to invoke xls2oct.m / oct2xls.m as outlined above under USAGE
MATLAB COMPATIBILITY
xlsread, xlswrite and xlsfinfo are for the most part Matlab-compatible. Some small differences are mentioned below. When using the Java interfaces octave supplies some formula manipulation support.
xlsread
Matlab's xlsread supports invoking extra functions while reading ("passing function handle"); octave not. But this can be simulated outside xlsread.
Matlab's xlsread flags some spreadsheet errors, octave-forge just returns blank cells.
Octave's xlsread (and for that matter, xlsfinfo as well) returns info about the actual (rather than the requested) cell range where the data came from. Personally I find it very useful to know from what part of a worksheet the data originate so I've put quite some effort in it :-)
- Matlab can't, due to Excel automatically trimming returned arrays from empty outer columns and rows. Octave is more clever but the Visual Basic call used for determining the actually used range has some limitations: (1) it relies on cached range values and thus may be out-of-date, and (2) it counts empty formatted cells too. When using ActiveX/COM, if octave's xlsfinfo.m returns wrong data ranges it is most often an overestimation.
- Matlab's xlsread ignores all non-numeric data values outside the smallest rectangle encompassing all numerical values. Octave's xlsread doesn't. This means that Matlab ignores all row/column headers, not very user-friendly IMO.
When using the Java interface, reading and writing xls-files by octave's xlsread is platform-independent. On systems w/o installed Excel, Matlab can only read Excel 95 formatted .xls files (written using ML xlswrite's 'Basic" option) – and then differently than under Windows.....
- Matlab's xlsread returns strings for cells containing date values. This makes for endless if-then-elseif-else-end constructs to catch all expected date formates. Octave returns numerical data (where 0 = 1/1/1900 – you can easily transfer them into proper octave date values yourself using e.g. datestr(), see bottom of this document for more info).
xlswrite
Octave's xlswrite works on systems w/o Excel support, Matlab's doesn't (properly).
- When specifying a sheet number larger than the number of existing sheets in an .xls file, Matlab's xlswrite adds empty sheets until the new sheet number is created; Octave's xlswrite only adds one sheet called "Sheet<number>" where <number> is the specified sheet number.
- Even better (IMO) while M's xlswrite always creates Sheet1/Sheet2/Sheet3 when creating a new spreadsheet, octave's xlswrite only creates the requested worksheet. (Did you know that you can instruct Excel to create spreadsheets with just one, or any number of, worksheets? Look in Tools | Options, General tab.)
- Oh and octave doesn't touch the "active sheet" - but that's not automatically an advantage.
- If the specified write range is larger than the actual data array, Matlab's xlswrite adds #N/A cells to fill up the lowermost rows and rightmost columns; octave-forge's xlswrite doesn't.
xlsfinfo
When invoking Excel/COM interface, Octave's xlsfinfo also echoes the type of sheet (worksheet, chart), not just the sheet names. Using Java I haven't found similar functionality (yet).
Octave's xlsfinfo also shows (and returns) the range of the smallest rectangle encompassing all occupied data ranges in each sheet.
COMPARISON OF INTERFACES & USAGE
- Using Excel itself (through COM / ActiveX on Windows systems) is probably the most robust and versatile and especially FAST option (though for OOXML the OCT interface is probably faster). There's one gotcha: in case of some type of COM errors Excel will keep running invisibly; you can only end it through Task Manager.
A tiny problem is that one cannot find out easily through COM what file types are supported; xls, wks, wk1, xlsx, etc.
Another -obvious- limitation is that COM Excel access only works on Windows systems where Excel is installed.
JExcelAPI (Java-based and therefore platform-independent) is proven technology but switching between reading and writing is quite involved and memory-hungry when processing large spreadsheets. As the docs state, JExcelAPI is optimized for reading and it does do that well - but still slower than Excel/COM. The fact that upon a switch from reading to writing the existing spreadsheet is overwritten in place by a blank one and that you can only get the contents back wen writing out all of the changes is worrying - and any change after the first write() is lost as a next write() doesn't seem to work, worse yet, you may completely loose the spreadsheet in question. The first is by JExcelAPI design, the second is probably a bug (in octave-forge/Java or JExcelAPI ? I don't know). Adding data to existing spreadsheets does work, but IMO undue user confidence is needed.
- JExcelAPI supports BIFF5 (only reading) and BIFF8 (Excel 95 and Excel 97-2003, respectively). Upon overwriting, BIFF5 spreadsheets are converted silently to BIFF8.
- JexcelAPI, unlike ApachePOI, doesn't evaluate functions while reading but instead relies on cached results (i.e. results computed by Excel itself). Depending on Excel settings ("Automatic calculation" ON or OFF) this may or may not yield incorrect (or expected) results.
Apache POI (Java-based and platform-independent too) is based on the OpenOffice.org I/O Excel r/w routines. It is a more versatile than JExcelAPI, while it doesn't support BIFF5 it does support BIFF8 (Excel 97 – 2003) and OOXML (Excel 2007).
- It is slower than native JXL let alone Excel & COM but it features active formula evaluation, although at the moment (early 2015, v. 3.11) still not *all* Excel functions have been implemented (a daunting task for the POI devs, as it is hard to keep up with MS here). I've made the relevant subfunction (xls2jpoi2oct) fall back to cached formula results (and yield a suitable warning) for non-implemented Excel functions while reading Excel files.
OpenXLS (an open source version of Extentech's commercial Java-xls product) is still a bit experimental. It seems to work faster than JExcelAPI, but it has other issues - i.e., processing of OOXML files is still unreliable. In addition OpenXLS scatters Extentech.tmp files here and there. For .xls (BIFF8) it works OK.
UNO (invoking OpenOffice.org (OOo) or LibreOffice (LO) or clones behind the scenes, a la ActiveX) is experimental. It works FAST (i.e., once OOo itself is loaded and initialized which can take some time) and can process much larger spreadsheets than the other Java-based interfaces because the data are not entered in the JVM but in OOo's memory.
A big stumbling block is that odsclose() on a UNO xls struct will kill ALL OpenOffice.org invocations, also those that were not related to Octave! This is due 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.
All in all, of the three Java options I'd prefer Apache POI rather than OpenXLS or JexcelAPI. But the latter is indispensable for BIFF5 formats. Once UNO is stable it is to be preferred as it can read ALL file formats supported by OOo (viz. wk1, ods, xlsx, sxc, ...). If you need to process really large spreadsheets, UNO is by far the fastest option (behind COM on Windows systems), but for smaller spreadsheets you'll find that the other interfaces are more efficient.
- The OCT interface (native Octave calls) is by far the fastest for OOXML, the only Octave option for gnumeric, but for ODS it is still slower than COM/ActiveX or UNO. Experimental OCT write support is available for OOXML, ODS 1.2 and gnumeric but not extensively tested yet.
Some notes on the choice for Java:
- 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. Better use real databases for such data sets.
A NOTE ON JAVA MEMORY USAGE
Java memory pool allocation size
- The Java virtual machine (JVM), when initialized by octave, reserves 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 16 MB. On Linux this allocated size might differ (e.g., my Mandriva box with openJDK has a 512 MB default max setting). This part of memory is where the Java-based XLS/ODS octave 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 500,000 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//java (where the script file javaclasspath.m is located; try "which javaclasspath" in an Octave terminal to get the proper location), containing just the following lines:
- -Xms16m
-Xmx512m
- (where 16 = initial size, 512 = maximum size (in this example), m stands for Megabyte. This maximum is system-dependent. E.g., I have a 1 GB setting).
For further details consult the Octave manual, "Java Interface", "FAQ", "How can I handle memory limitations?"
- 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.
TROUBLESHOOTING
- Some hints for troubleshooting Excel support are contained in this thread:
http://sourceforge.net/mailarchive/forum.php?thread_name=4C61B649.9090802%40hccnet.nl&forum_name=octave-dev
dated August 10, 2010.
A more structured approach is below.
Since April 2011 a special purpose setup file has been included in the io package (chk_spreadsheet_support.m). Large parts of the approach below (starting at Step 2) have been automated in this script. When running it with the second input argument (debug level) set to 3 a lot of useful diagnostic output will be printed to screen.
- Check if COM / ActiveXworks (only under Windows OS). Do a
pkg list and see
a. If there's a windows package mentioned (then it's installed). If not, install it.
b. If there's an asterisk on the windows package line (then the package is loaded). If not, do a pkg load windows
Check if the ActiveX server works. Do:
exl = actxserver ('Excel.Application')
## Note the period between "Excel" and "Application"
If a COM object is returned, ActiveX / COM / Excel works. Do:
exl.Quit(); delete (exl) to shut down the (hidden) Excel invocation.
If you get an error message, your last resort is re-installing the windows package, or trying the Java-based interfaces.
Check if java works.
As of Octave-3.8, Java is usually built-in and step 3 does not apply anymore
Do a pkg list and see
a. If there's a java package mentioned (then it's installed). If not, install it. Don't do this in Octave 3.8 and higher!!
b. If there's an asterisk on the java package line (then the package is loaded). If not, do a pkg rebuild -auto java Don't do this in Octave 3.8 and higher!!
- 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 '
javaclasspath' (under unix/linux, do 'tmp = javaclasspath; strsplit (tmp,":")' (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 xls interfaces should just work. The only remaining showstoppers are insufficient write privileges for the working directory, a wrecked up octave or some other problem outside octave.
- Try opening an xls file:
xls1 = xlsopen ('test.xls', 1, 'poi')
. If this works and xls1 is a struct with various fields containing objects, the Apache POI interface (POI) works. Do an xls1 = xlsclose (xls1) to close the file.
xls2 = xlsopen ('test.xls', 1, 'jxl')
. If this works and xls2 is a struct with various fields containing objects, the JExcelAPI interface (JXL) works as well. Don't forget to do xls2 = xlsclose (xls2) to close the file.
DEVELOPMENT
- xlsopen
/xlsclose and friends have been written so that adding other interfaces (Perl? native octave? ...?) should be very easily accomplished. xlsopen.m merely needs two stanzas, xlsfinfo.m, xls2oct.m, oct2xls.m and getusedrange.m each need an additional elseif stanza, and xlsclose.m needs a small stanza for closing the pointer struct and writing to disk.
The real work lies in creating the relevant __<INTF>_spsh_open__.m & __<INTF>_spsh_close__.m, __<INTF>_spsh2oct__.m & __<INTF>_oct2spsh__.m, __<INTF>_spsh_info__.m, and __<INTF>_getusedrange__.m subfunction scripts in ./private subdir, but that shouldn't be really hard, depending on the interface support libraries' quality and documentation. The function scripts in the ./private subdir provide for ample examples.
Separating the file access functions and the actual reading/writing from/to the workbook in memory has made developer's life (I mean: my time developing this stuff) much easier.
Some other options for development (who?):
- Speeding up, especially Java worksheet/cell access. For cracks, not me.
- Automatic conversion of Excel date/time values into octave ones and vice versa (adding or subtracting 636960). But then again Excel's dates are 01-01-1900 based (octave's 0-0-0000) and buggy (Excel thinks 1900 is a leap year), and I sometimes have to use dates from before 1900. Maybe as an option?
- Creating Excel graphs (a significant enterprise to write from scratch).
- Support for "passing function handle" in xlsread.
Enjoy!
- Philip Nienhuis, February 4, 2017