[Insight-users] Problems with SCIFIO
Sami Koho
sami.koho at gmail.com
Fri Feb 21 04:22:53 EST 2014
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
> >>>
> >>> _____________________________________
> >>> Powered by www.kitware.com
> >>>
> >>> Visit other Kitware open-source projects at
> >>> http://www.kitware.com/opensource/opensource.html
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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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> > http://www.itk.org/mailman/listinfo/insight-users
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