<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hello Sami,<div><br></div><div>This sounds like an installation issue.</div><div><br></div><div>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?</div><div><br></div><div>Brad</div><div><br><div><div>On Feb 14, 2014, at 4:00 AM, Sami Koho <<a href="mailto:sami.koho@gmail.com">sami.koho@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><div dir="ltr">Hello,<div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>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:</div><div>
<br></div><div><div>python rescaling_test.py psf_red.tif</div><div>Traceback (most recent call last):</div><div> File "rescaling_test.py", line 18, in <module></div><div> image = itkio.itk_read_image(image_path)</div>
<div> File "/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line 18, in itk_read_image</div><div> itk_image_reader = getattr(itk.ImageFileReader, image_type).New()</div><div> File "/usr/local/lib/ITK-4.5/Python/itkLazy.py", line 37, in __getattribute__</div>
<div> itkBase.LoadModule(module, namespace)</div><div> File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 95, in LoadModule</div><div> LoadModule(dep, namespace)</div><div> File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 103, in LoadModule</div>
<div> if not swigModuleName in sys.modules: module = loader.load(swigModuleName)</div><div> File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 214, in load</div><div> return imp.load_module(name, fp, pathname, description)</div>
<div> File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 30, in <module></div><div> _ITKCommonPython = swig_import_helper()</div><div> File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in swig_import_helper</div>
<div> _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)</div><div><b>ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No such file or directory</b></div></div><div><b><br>
</b></div><div>I am using ITK on 64bit Debian Wheezy (with Python wrapping). I checked, and there is a file called <b> </b>libitkSCIFIO-4.5.so.1 in /usr/local/lib. Does someone have an idea, what is going wrong here?</div>
<div><br></div><div>Best,</div><div><br></div><div>Sami</div><div><br></div></div>
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