[Insight-users] Problems with SCIFIO

[Sami Koho]

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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