<div dir="ltr"><div><div><div><div>Hello Bradley,<br><br></div>here is what ldd gives:<br><br>sami@PAM-deb:~/Programming/Build/ITK451$ ldd /usr/local/lib/libitkSCIFIO-4.5.so.1 <br> linux-vdso.so.1 => (0x00007fff9c1ff000)<br>
libITKIOImageBase-4.5.so.1 => /usr/local/lib/libITKIOImageBase-4.5.so.1 (0x00007fc93f7fc000)<br> libITKCommon-4.5.so.1 => /usr/local/lib/libITKCommon-4.5.so.1 (0x00007fc93f530000)<br> libitksys-4.5.so.1 => /usr/local/lib/libitksys-4.5.so.1 (0x00007fc93f2eb000)<br>
libITKVNLInstantiation-4.5.so.1 => /usr/local/lib/libITKVNLInstantiation-4.5.so.1 (0x00007fc93f059000)<br> libitkvnl_algo-4.5.so.1 => /usr/local/lib/libitkvnl_algo-4.5.so.1 (0x00007fc93ede5000)<br> libitkv3p_lsqr-4.5.so.1 => /usr/local/lib/libitkv3p_lsqr-4.5.so.1 (0x00007fc93ebdf000)<br>
libitkvnl-4.5.so.1 => /usr/local/lib/libitkvnl-4.5.so.1 (0x00007fc93e5cf000)<br> libitkvcl-4.5.so.1 => /usr/local/lib/libitkvcl-4.5.so.1 (0x00007fc93e3cd000)<br> libitkv3p_netlib-4.5.so.1 => /usr/local/lib/libitkv3p_netlib-4.5.so.1 (0x00007fc93e0d2000)<br>
libitkdouble-conversion-4.5.so.1 => /usr/local/lib/libitkdouble-conversion-4.5.so.1 (0x00007fc93dec7000)<br> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fc93dcab000)<br> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fc93daa6000)<br>
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc93d824000)<br> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fc93d51d000)<br> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fc93d306000)<br>
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc93cf7b000)<br> /lib64/ld-linux-x86-64.so.2 (0x00007fc93fc5a000)<br><br></div>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)<br>
<br></div>Best,<br><br></div>Sami<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Feb 18, 2014 at 3:48 PM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello,<div><br></div><div>What is the output of "ldd /usr/local/libitkSCIFIO-4.5.so.1"?</div>
<div><br></div><div>Do all the ITK tests pass? If you run WrapITK out of the build directory does it work?</div><div><br></div><div>Brad</div><div><div class="h5"><div><br><div><div>On Feb 18, 2014, at 6:16 AM, Sami Koho <<a href="mailto:sami.koho@gmail.com" target="_blank">sami.koho@gmail.com</a>> wrote:</div>
<br><blockquote type="cite"><div dir="ltr"><div><div><div>Hello again,<br><br>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 <i>.so</i> 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:<br>
<br>Traceback (most recent call last):<br> File "itk_image_load_test.py", line 13, in <module><br> image = itkutils.itk_read_image(image_path, image_type='IUC2')<br> File "/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line 18, in itk_read_image<br>
itk_image_reader = getattr(itk.ImageFileReader, image_type).New()<br> File "/usr/local/lib/ITK-4.5/Python/itkLazy.py", line 37, in __getattribute__<br> itkBase.LoadModule(module, namespace)<br> File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 95, in LoadModule<br>
LoadModule(dep, namespace)<br> File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 103, in LoadModule<br> if not swigModuleName in sys.modules: module = loader.load(swigModuleName)<br> File "/usr/local/lib/ITK-4.5/Python/itkBase.py", line 214, in load<br>
return imp.load_module(name, fp, pathname, description)<br> File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 30, in <module><br> _ITKCommonPython = swig_import_helper()<br> File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in swig_import_helper<br>
_mod = imp.load_module('_ITKCommonPython', fp, pathname, description)<br><b>ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No such file or directory</b><br><br></div>Yet, as I reported last time around, the libitkSCIFIO-4.5.so.1 is there in <i>/usr/local/lib </i>with all the other ITK shared object files. Is there something I may still be doing wrong, or is this a bug? <br>
<br></div><div>I will just have to use ITK without SCIFIO for now...<br></div><div><br></div>Best,<br><br></div>Sami<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Feb 14, 2014 at 8:41 PM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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><div><div>
On Feb 14, 2014, at 4:00 AM, Sami Koho <<a href="mailto:sami.koho@gmail.com" target="_blank">sami.koho@gmail.com</a>> wrote:</div><br></div></div><blockquote type="cite"><div><div><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></div></div>
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