[Insight-users] Problems with SCIFIO
Matt McCormick
matt.mccormick at kitware.com
Wed Feb 19 10:28:08 EST 2014
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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>>
>>
>
>
> _____________________________________
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>
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>
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