[Insight-users] Problems with SCIFIO

Sami Koho sami.koho at gmail.com
Thu Feb 27 08:19:35 EST 2014 

Hello,

thank you Michka for the warnings suppress code. Regarding the patches Matt provided, the SCIFIO module works now with Python. I am a bit late for reviewing the two patches, as I had some problems getting ITK working on my new computer — for some reason I needed to enable the USE SYSTEM SWIG option on Ubuntu 12.04. In any case, the patches seem to have fixed the problem and SCIFIO now works with Python in git head version of ITK from a couple of day back, installed to /usr/local/lib. Thank you for your help!

Best,

Sami

On 21 Feb 2014, at 11:38, Michka Popoff <michkapopoff at gmail.com> wrote:

> To hide the warnings I found some code on the web to catch the stderr and to hide it. Here is my code for ITK : https://gist.github.com/iMichka/9131352
> We are currently working on fixing these warnings.
> 
> Ideally they should be triggered with the python warnings module, were it is much easier to enable/disable warnings.
> I am currently cleaning up a little bit ITK’s python code, I’ll try to replace the sys stderr warnings with http://docs.python.org/2/library/warnings.html
> This won’t happen until the next ITK release so you’ll have to go with my solution for the moment.
> 
> Michka
> 
> 
> On 21 févr. 2014, at 10:22, Sami Koho <sami.koho at gmail.com> wrote:
> 
>> Hi Matt & Bradley,
>> 
>> I am currently reviewing these patches. My intention is to build ITK with the patches enabled one by one and see whether they help. Now that I have built the library around 10 times in a week I noticed that every time I change the source code or change something in the cmakecache.txt, the whole Python wrapping gets rebuilt from the start (whereas on the C++ side only the modified modules get updated). Is this the normal behavior? It takes quite a bit of time to start from the "beginning" every time.
>> 
>> Another question related to the Python wrapping: is there a way for suppressing the Warning messages that appear when using ITK? I know that in Python in general one can ignore certain types of warnings, but I don't know how to block the ones from ITK. 
>> 
>> Best,
>> 
>> Sami
>> 
>> 
>> On Wed, Feb 19, 2014 at 5:28 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>> Hi Sami,
>> 
>> Please review [1] this patch [2], which may also fix your problem (I
>> have not tested it for your case where it is installed) and this patch
>> [3], which should also fix the issue by wrapping the SCIFIO module.
>> 
>> Thanks,
>> Matt
>> 
>> [1] http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html
>> 
>> [2] http://review.source.kitware.com/#/c/14492/
>> 
>> [3] http://review.source.kitware.com/#/c/14493/
>> 
>> On Wed, Feb 19, 2014 at 6:19 AM, Sami Koho <sami.koho at gmail.com> wrote:
>> > Hello Bradley,
>> >
>> > here is what ldd gives:
>> >
>> > sami at PAM-deb:~/Programming/Build/ITK451$ ldd
>> > /usr/local/lib/libitkSCIFIO-4.5.so.1
>> >     linux-vdso.so.1 =>  (0x00007fff9c1ff000)
>> >     libITKIOImageBase-4.5.so.1 => /usr/local/lib/libITKIOImageBase-4.5.so.1
>> > (0x00007fc93f7fc000)
>> >     libITKCommon-4.5.so.1 => /usr/local/lib/libITKCommon-4.5.so.1
>> > (0x00007fc93f530000)
>> >     libitksys-4.5.so.1 => /usr/local/lib/libitksys-4.5.so.1
>> > (0x00007fc93f2eb000)
>> >     libITKVNLInstantiation-4.5.so.1 =>
>> > /usr/local/lib/libITKVNLInstantiation-4.5.so.1 (0x00007fc93f059000)
>> >     libitkvnl_algo-4.5.so.1 => /usr/local/lib/libitkvnl_algo-4.5.so.1
>> > (0x00007fc93ede5000)
>> >     libitkv3p_lsqr-4.5.so.1 => /usr/local/lib/libitkv3p_lsqr-4.5.so.1
>> > (0x00007fc93ebdf000)
>> >     libitkvnl-4.5.so.1 => /usr/local/lib/libitkvnl-4.5.so.1
>> > (0x00007fc93e5cf000)
>> >     libitkvcl-4.5.so.1 => /usr/local/lib/libitkvcl-4.5.so.1
>> > (0x00007fc93e3cd000)
>> >     libitkv3p_netlib-4.5.so.1 => /usr/local/lib/libitkv3p_netlib-4.5.so.1
>> > (0x00007fc93e0d2000)
>> >     libitkdouble-conversion-4.5.so.1 =>
>> > /usr/local/lib/libitkdouble-conversion-4.5.so.1 (0x00007fc93dec7000)
>> >     libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>> > (0x00007fc93dcab000)
>> >     libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fc93daa6000)
>> >     libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc93d824000)
>> >     libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>> > (0x00007fc93d51d000)
>> >     libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>> > (0x00007fc93d306000)
>> >     libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc93cf7b000)
>> >     /lib64/ld-linux-x86-64.so.2 (0x00007fc93fc5a000)
>> >
>> > I will comment on the tests tomorrow, as I did not build the testing modules
>> > previously (usually saves me a lot of time when compiling)
>> >
>> > Best,
>> >
>> > Sami
>> >
>> >
>> >
>> > On Tue, Feb 18, 2014 at 3:48 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
>> > wrote:
>> >>
>> >> Hello,
>> >>
>> >> What is the output of "ldd /usr/local/libitkSCIFIO-4.5.so.1"?
>> >>
>> >> Do all the ITK tests pass? If you run WrapITK out of the build directory
>> >> does it work?
>> >>
>> >> Brad
>> >>
>> >> On Feb 18, 2014, at 6:16 AM, Sami Koho <sami.koho at gmail.com> wrote:
>> >>
>> >> Hello again,
>> >>
>> >> I finally had some time to dedicate to this SCIFIO problem. Just to make
>> >> sure that I did not do anything stupid, I made a clean build of the whole
>> >> ITK (with the new 4.5.1 version), with SCIFIO module enabled. Then I removed
>> >> my old installation from /usr/local/lib - by manually deleting the .so
>> >> files, the ITK4.5 directory and the cmake directory containing some ITK
>> >> files - after which I installed my new build of the ITK4.5.1. I still have
>> >> the same problem:
>> >>
>> >> Traceback (most recent call last):
>> >>   File "itk_image_load_test.py", line 13, in <module>
>> >>     image = itkutils.itk_read_image(image_path, image_type='IUC2')
>> >>   File
>> >> "/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line
>> >> 18, in itk_read_image
>> >>     itk_image_reader = getattr(itk.ImageFileReader, image_type).New()
>> >>   File "/usr/local/lib/ITK-4.5/Python/itkLazy.py", line 37, in
>> >> __getattribute__
>> >>     itkBase.LoadModule(module, namespace)
>> >>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 95, in LoadModule
>> >>     LoadModule(dep, namespace)
>> >>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 103, in LoadModule
>> >>     if not swigModuleName in sys.modules: module =
>> >> loader.load(swigModuleName)
>> >>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 214, in load
>> >>     return imp.load_module(name, fp, pathname, description)
>> >>   File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 30, in
>> >> <module>
>> >>     _ITKCommonPython = swig_import_helper()
>> >>   File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in
>> >> swig_import_helper
>> >>     _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)
>> >> ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No
>> >> such file or directory
>> >>
>> >> Yet, as I reported last time around, the libitkSCIFIO-4.5.so.1 is there in
>> >> /usr/local/lib with all the other ITK shared object files. Is there
>> >> something I may still be doing wrong, or is this a bug?
>> >>
>> >> I will just have to use ITK without SCIFIO for now...
>> >>
>> >> Best,
>> >>
>> >> Sami
>> >>
>> >>
>> >>
>> >> On Fri, Feb 14, 2014 at 8:41 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
>> >> wrote:
>> >>>
>> >>> Hello Sami,
>> >>>
>> >>> This sounds like an installation issue.
>> >>>
>> >>> Did you reinstall ITK w/ WrapITK after rebuilding? Are you running out of
>> >>> the build directory? Where is the libitkSCIFIO-4.5.so.1 file?
>> >>>
>> >>> Brad
>> >>>
>> >>> On Feb 14, 2014, at 4:00 AM, Sami Koho <sami.koho at gmail.com> wrote:
>> >>>
>> >>> Hello,
>> >>>
>> >>> I have been having some problems with reading my image data with ITK. My
>> >>> images are microscope images, originally from a Leica confocal, saved as 3D
>> >>> tiff volumes in ImageJ. When I open such a file with ITK (version 4.5), I
>> >>> get a complaint about unknown tags and lose all my metadata (such as voxel
>> >>> size information). SImilarly. when I save a tiff file with ITK, I seem to
>> >>> lose all the metadata - at least ImageJ does not understand it.
>> >>>
>> >>> I ended up installing MetaImage plugin to ImageJ, allowing me to export
>> >>> to mhd format, which seems to work, for reading data into my ITK application
>> >>> at least. I still have problems showing the results in ImageJ, as the voxel
>> >>> sizes go wrong on save.
>> >>>
>> >>> Last night I compiled ITK with SCIFIO module enabled, as I thought that
>> >>> this would make handling microscope images a bit more easy. Everything
>> >>> compiled nicely, but now I get a following error:
>> >>>
>> >>> python rescaling_test.py psf_red.tif
>> >>> Traceback (most recent call last):
>> >>>   File "rescaling_test.py", line 18, in <module>
>> >>>     image = itkio.itk_read_image(image_path)
>> >>>   File
>> >>> "/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line
>> >>> 18, in itk_read_image
>> >>>     itk_image_reader = getattr(itk.ImageFileReader, image_type).New()
>> >>>   File "/usr/local/lib/ITK-4.5/Python/itkLazy.py", line 37, in
>> >>> __getattribute__
>> >>>     itkBase.LoadModule(module, namespace)
>> >>>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 95, in LoadModule
>> >>>     LoadModule(dep, namespace)
>> >>>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 103, in
>> >>> LoadModule
>> >>>     if not swigModuleName in sys.modules: module =
>> >>> loader.load(swigModuleName)
>> >>>   File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 214, in load
>> >>>     return imp.load_module(name, fp, pathname, description)
>> >>>   File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 30, in
>> >>> <module>
>> >>>     _ITKCommonPython = swig_import_helper()
>> >>>   File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in
>> >>> swig_import_helper
>> >>>     _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)
>> >>> ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No
>> >>> such file or directory
>> >>>
>> >>> I am using ITK on 64bit Debian Wheezy (with Python wrapping). I checked,
>> >>> and there is a file called  libitkSCIFIO-4.5.so.1 in /usr/local/lib. Does
>> >>> someone have an idea, what is going wrong here?
>> >>>
>> >>> Best,
>> >>>
>> >>> Sami
>> >>>
>> >>> _____________________________________
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>> >>>
>> >>
>> >>
>> >
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
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>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
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