[ITK Community] [Insight-users] Problems with SCIFIO
Sami Koho
sami.koho at gmail.com
Wed Feb 19 06:19:36 EST 2014
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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