[Insight-users] Problems with SCIFIO
Bradley Lowekamp
blowekamp at mail.nih.gov
Fri Feb 14 13:41:29 EST 2014
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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