Proposals:Updating Nrrd library 2009

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Nrrd Library

This page describes the procedure for synchronizing the NrrdIO parts of Teem, with the one in Insight/Utilities/NrrdIO

Note that patches may have to be moved in both directions.

Background

  • Nrrd started as one of the libraries in Teem <http://teem.sf.net>
  • NrrdIO is a subset of Teem containing only the IO functionalities (basically, parts of the air, biff, and nrrd libraries).
  • The only part of Teem that's in ITK is in NrrdIO. Also, while Teem has a weakened LGPL license, NrrdIO is licensed identically to ITK.
  • Creating NrrdIO from Teem is done by a GNUMakefile (NrrdIO/pre-GNUmakefile) and a perl script (NrrdIO/unteem.pl)
  • The back-propagation that should happen is from ITK's NrrdIO back to Teem, because the idea is that NrrdIO should be periodically regenerated from Teem, and ITK's NrrdIO should be an up-to-date copy of the NrrdIO automatically regenerated from Teem

Checking out Teem and NrrdIO

The way that Sourceforge names things makes this a little confusing. The sourceforge "project name" Teem includes multiple directories, or multiple separate SVN repositories. One directory, called Teem, this is the main source tree, where all the NrrdIO sources are copied from. There is also a NrrdIO directory.

Use the following SVN command to check out all of Teem:

  svn co http://teem.svn.sourceforge.net/svnroot/teem/teem/trunk teem

and the following to checkout NrrdIO:

  svn co http://teem.svn.sourceforge.net/svnroot/teem/NrrdIO/trunk NrrdIO

The contents of the NrrdIO directory are created automatically from the Teem directory. This is described in the comments in pre-GNUmakefile, reproduced here. To make a NrrdIO for ITK, which includes a header for name-mangling all the symbols, the steps are ("make" needs to be a GNU make) as follows. This assumes csh; environment variable commands will be different for bash.

  • rm -f itk_NrrdIO_mangle.h
  • touch itk_NrrdIO_mangle.h
  • make -f pre-GNUmakefile clean
  • setenv ITK_NRRDIO
  • make -f pre-GNUmakefile
  • unsetenv ITK_NRRDIO
  • make -f sample-GNUmakefile
  • perl mangle.pl itk >! itk_NrrdIO_mangle.h
  • make -f sample-GNUmakefile clean

The "pre-GNUmakefile" makefile copies files from a Teem checkout and modifies them slightly (through the action of unteem.py). Then "sample-GNUmakefile" builds a NrrdIO library (and a small test executable), and mangle.pl looks at all the symbols in the library in order to generate the name-mangling header file required for ITK. If we weren't making NrrdIO for ITK, the name mangling wouldn't be required, and the process would just be:

  • make -f pre-GNUmakefile clean
  • make -f pre-GNUmakefile
  • make -f sample-GNUmakefile
  • make -f sample-GNUmakefile clean

where we run make with "sample-GNUmakefile" just to make sure that everything compiles ok.

NrrdIO / Teem Dashboard

Update Procedure

Perform the following two tasks:

From ITK to NrrdIO

For all the changes made to

             Insight/Utilities/NrrdIO

after the last Nrrd batch commit (from G Kindlmann):

  • understand what the change was
  • apply the same change (or something equivalent) to the corresponding file in Teem
  • regenerate NrrdIO from Teem and update sourceforge's NrrdIO

For the .c files this should be easy; these are just copied directly from a Teem checkout, and then the headers are mangled a bit.

For NrrdIO.h; this is actually a concatenation of air/air.h, biff/biff.h, nrrd/nrrdDefines.h, nrrd/nrrdEnums.h, nrrd/nrrdMacros.h, and nrrd/nrrd.h (these are defined in the NEED_PUB_HDRS variable of NrrdIO/pre-GNUmakefile)

This is probably not a one-day project.

From Nrrd to ITK

Gradually or all at once, depending on our bravery, we copy sourceforge's NrrdIO to

           Insight/Utilities/NrrdIO 

and see what breaks,... and fix it

Progress

Table

The table below lists all the files in NrrdIO which are generated from a Teem checkout via NrrdIO/pre-GNUmakefile; these are marked with "*", and the originating directory in Teem is also indicated (the air, biff, and nrrd directories inside teem/src). Changes in these files in ITK's NrrdIO since GLK's last commits in 2005 should be back-propagated to the corresponding files in Teem, so that when NrrdIO is next regenerated from Teem, none of the improvements to ITK's NrrdIO are lost. Handling updates to these files is the hard/interesting part of this project.

The files not marked with a "*" are not generated from Teem via NrrdIO/pre-GNUmakefile; they exist only within NrrdIO. GLK doesn't see why there would have been any changes to these in files in ITK's NrrdIO, because it wouldn't effect how ITK uses Nrrd, but if there are changes they should also be reviewed and possibly back-propagated to Sourceforge's NrrdIO.

File Check ITK for Bug Fix Move from NrrdIO to ITK
000-README.txt
* air/754.c
* nrrd/accessors.c
* air/array.c
* nrrd/arraysNrrd.c
* nrrd/axis.c
* biff/biffbiff.c
* biff/biffmsg.c
CMakeLists.txt
* nrrd/comment.c
* nrrd/defaultsNrrd.c
* air/dio.c
* nrrd/encodingAscii.c
encodingBzip2.c
* nrrd/encoding.c
* nrrd/encodingGzip.c
* nrrd/encodingHex.c
* nrrd/encodingRaw.c
* air/endianAir.c
* nrrd/endianNrrd.c
* air/enum.c
* nrrd/enumsNrrd.c
* nrrd/format.c
formatEPS.c
* nrrd/formatNRRD.c
formatPNG.c
formatPNM.c
formatText.c
formatVTK.c
* nrrd/gzio.c
* nrrd/keyvalue.c
mangle.pl
* nrrd/methodsNrrd.c
* air/miscAir.c
* air/mop.c
* air,biff,nrrd/NrrdIO.h
NrrdIO_Srcs.txt
NrrIOLIst.txt
* air/parseAir.c
* nrrd/parseNrrd.c
preamble.c
pre-GNUmakefile
* air/privateAir.h
* nrrd/privateNrrd.h
qnanhibit.c
* nrrd/read.c
* nrrd/reorder.c
sample-GNUmakefile
sampleIO.c
* air/sane.c
* nrrd/simple.c
* air/string.c
* nrrd/subset.c
* include/teem32bit.h
* include/teemDio.h
* include/teemEndian.h
* include/teemPng.h
* include/teemQnanhibit.h
unteem.pl
* nrrd/write.c