<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;"><div>To hide the warnings I found some code on the web to catch the stderr and to hide it. Here is my code for ITK : <a href="https://gist.github.com/iMichka/9131352">https://gist.github.com/iMichka/9131352</a></div>We are currently working on fixing these warnings.<div><br></div><div>Ideally they should be triggered with the python warnings module, were it is much easier to enable/disable warnings.</div><div>I am currently cleaning up a little bit ITK’s python code, I’ll try to replace the sys stderr warnings with <a href="http://docs.python.org/2/library/warnings.html">http://docs.python.org/2/library/warnings.html</a></div><div>This won’t happen until the next ITK release so you’ll have to go with my solution for the moment.</div><div><br></div><div>Michka<br><div><br></div><div><br><div><div>On 21 févr. 2014, at 10:22, Sami Koho <<a href="mailto:sami.koho@gmail.com">sami.koho@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div><div><div>Hi Matt & Bradley,<br><br></div>I am currently reviewing these patches. My intention is to build ITK with the patches enabled one by one and see whether they help. Now that I have built the library around 10 times in a week I noticed that every time I change the source code or change something in the cmakecache.txt, the whole Python wrapping gets rebuilt from the start (whereas on the C++ side only the modified modules get updated). Is this the normal behavior? It takes quite a bit of time to start from the "beginning" every time.<br>
<br></div>Another question related to the Python wrapping: is there a way for suppressing the Warning messages that appear when using ITK? I know that in Python in general one can ignore certain types of warnings, but I don't know how to block the ones from ITK. <br>
<br></div>Best,<br><br></div>Sami<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Feb 19, 2014 at 5:28 PM, Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Sami,<br>
<br>
Please review [1] this patch [2], which may also fix your problem (I<br>
have not tested it for your case where it is installed) and this patch<br>
[3], which should also fix the issue by wrapping the SCIFIO module.<br>
<br>
Thanks,<br>
Matt<br>
<br>
[1] <a href="http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html" target="_blank">http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/CommunitySoftwareProcess/PerformAGerritReview/index.html</a><br>
<br>
[2] <a href="http://review.source.kitware.com/#/c/14492/" target="_blank">http://review.source.kitware.com/#/c/14492/</a><br>
<br>
[3] <a href="http://review.source.kitware.com/#/c/14493/" target="_blank">http://review.source.kitware.com/#/c/14493/</a><br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, Feb 19, 2014 at 6:19 AM, Sami Koho <<a href="mailto:sami.koho@gmail.com">sami.koho@gmail.com</a>> wrote:<br>
> Hello Bradley,<br>
><br>
> here is what ldd gives:<br>
><br>
> sami@PAM-deb:~/Programming/Build/ITK451$ ldd<br>
> /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<br>
> (0x00007fc93f7fc000)<br>
> libITKCommon-4.5.so.1 => /usr/local/lib/libITKCommon-4.5.so.1<br>
> (0x00007fc93f530000)<br>
> libitksys-4.5.so.1 => /usr/local/lib/libitksys-4.5.so.1<br>
> (0x00007fc93f2eb000)<br>
> libITKVNLInstantiation-4.5.so.1 =><br>
> /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<br>
> (0x00007fc93ede5000)<br>
> libitkv3p_lsqr-4.5.so.1 => /usr/local/lib/libitkv3p_lsqr-4.5.so.1<br>
> (0x00007fc93ebdf000)<br>
> libitkvnl-4.5.so.1 => /usr/local/lib/libitkvnl-4.5.so.1<br>
> (0x00007fc93e5cf000)<br>
> libitkvcl-4.5.so.1 => /usr/local/lib/libitkvcl-4.5.so.1<br>
> (0x00007fc93e3cd000)<br>
> libitkv3p_netlib-4.5.so.1 => /usr/local/lib/libitkv3p_netlib-4.5.so.1<br>
> (0x00007fc93e0d2000)<br>
> libitkdouble-conversion-4.5.so.1 =><br>
> /usr/local/lib/libitkdouble-conversion-4.5.so.1 (0x00007fc93dec7000)<br>
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0<br>
> (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<br>
> (0x00007fc93d51d000)<br>
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1<br>
> (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>
> I will comment on the tests tomorrow, as I did not build the testing modules<br>
> previously (usually saves me a lot of time when compiling)<br>
><br>
> Best,<br>
><br>
> Sami<br>
><br>
><br>
><br>
> On Tue, Feb 18, 2014 at 3:48 PM, Bradley Lowekamp <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
> wrote:<br>
>><br>
>> Hello,<br>
>><br>
>> What is the output of "ldd /usr/local/libitkSCIFIO-4.5.so.1"?<br>
>><br>
>> Do all the ITK tests pass? If you run WrapITK out of the build directory<br>
>> does it work?<br>
>><br>
>> Brad<br>
>><br>
>> On Feb 18, 2014, at 6:16 AM, Sami Koho <<a href="mailto:sami.koho@gmail.com">sami.koho@gmail.com</a>> wrote:<br>
>><br>
>> Hello again,<br>
>><br>
>> I finally had some time to dedicate to this SCIFIO problem. Just to make<br>
>> sure that I did not do anything stupid, I made a clean build of the whole<br>
>> ITK (with the new 4.5.1 version), with SCIFIO module enabled. Then I removed<br>
>> my old installation from /usr/local/lib - by manually deleting the .so<br>
>> files, the ITK4.5 directory and the cmake directory containing some ITK<br>
>> files - after which I installed my new build of the ITK4.5.1. I still have<br>
>> 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<br>
>> "/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line<br>
>> 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<br>
>> __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 =<br>
>> 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<br>
>> <module><br>
>> _ITKCommonPython = swig_import_helper()<br>
>> File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in<br>
>> swig_import_helper<br>
>> _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)<br>
>> ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No<br>
>> such file or directory<br>
>><br>
>> Yet, as I reported last time around, the libitkSCIFIO-4.5.so.1 is there in<br>
>> /usr/local/lib with all the other ITK shared object files. Is there<br>
>> something I may still be doing wrong, or is this a bug?<br>
>><br>
>> I will just have to use ITK without SCIFIO for now...<br>
>><br>
>> Best,<br>
>><br>
>> Sami<br>
>><br>
>><br>
>><br>
>> On Fri, Feb 14, 2014 at 8:41 PM, Bradley Lowekamp <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
>> wrote:<br>
>>><br>
>>> Hello Sami,<br>
>>><br>
>>> This sounds like an installation issue.<br>
>>><br>
>>> Did you reinstall ITK w/ WrapITK after rebuilding? Are you running out of<br>
>>> the build directory? Where is the libitkSCIFIO-4.5.so.1 file?<br>
>>><br>
>>> Brad<br>
>>><br>
>>> On Feb 14, 2014, at 4:00 AM, Sami Koho <<a href="mailto:sami.koho@gmail.com">sami.koho@gmail.com</a>> wrote:<br>
>>><br>
>>> Hello,<br>
>>><br>
>>> I have been having some problems with reading my image data with ITK. My<br>
>>> images are microscope images, originally from a Leica confocal, saved as 3D<br>
>>> tiff volumes in ImageJ. When I open such a file with ITK (version 4.5), I<br>
>>> get a complaint about unknown tags and lose all my metadata (such as voxel<br>
>>> size information). SImilarly. when I save a tiff file with ITK, I seem to<br>
>>> lose all the metadata - at least ImageJ does not understand it.<br>
>>><br>
>>> I ended up installing MetaImage plugin to ImageJ, allowing me to export<br>
>>> to mhd format, which seems to work, for reading data into my ITK application<br>
>>> at least. I still have problems showing the results in ImageJ, as the voxel<br>
>>> sizes go wrong on save.<br>
>>><br>
>>> Last night I compiled ITK with SCIFIO module enabled, as I thought that<br>
>>> this would make handling microscope images a bit more easy. Everything<br>
>>> compiled nicely, but now I get a following error:<br>
>>><br>
>>> python rescaling_test.py psf_red.tif<br>
>>> Traceback (most recent call last):<br>
>>> File "rescaling_test.py", line 18, in <module><br>
>>> image = itkio.itk_read_image(image_path)<br>
>>> File<br>
>>> "/usr/local/lib/python2.7/dist-packages/iocbio/io/itk_io_utilites.py", line<br>
>>> 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<br>
>>> __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<br>
>>> LoadModule<br>
>>> if not swigModuleName in sys.modules: module =<br>
>>> 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<br>
>>> <module><br>
>>> _ITKCommonPython = swig_import_helper()<br>
>>> File "/usr/local/lib/ITK-4.5/Python/ITKCommonPython.py", line 26, in<br>
>>> swig_import_helper<br>
>>> _mod = imp.load_module('_ITKCommonPython', fp, pathname, description)<br>
>>> ImportError: libitkSCIFIO-4.5.so.1: cannot open shared object file: No<br>
>>> such file or directory<br>
>>><br>
>>> I am using ITK on 64bit Debian Wheezy (with Python wrapping). I checked,<br>
>>> and there is a file called libitkSCIFIO-4.5.so.1 in /usr/local/lib. Does<br>
>>> someone have an idea, what is going wrong here?<br>
>>><br>
>>> Best,<br>
>>><br>
>>> Sami<br>
>>><br>
>>> _____________________________________<br>
>>> Powered by <a href="http://www.kitware.com/" target="_blank">www.kitware.com</a><br>
>>><br>
>>> Visit other Kitware open-source projects at<br>
>>> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>>><br>
>>> Kitware offers ITK Training Courses, for more information visit:<br>
>>> <a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
>>><br>
>>> Please keep messages on-topic and check the ITK FAQ at:<br>
>>> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>>><br>
>>> Follow this link to subscribe/unsubscribe:<br>
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>>><br>
>>><br>
>><br>
>><br>
><br>
><br>
> _____________________________________<br>
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><br>
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</div></div></blockquote></div><br></div>
_____________________________________<br>Powered by <a href="http://www.kitware.com">www.kitware.com</a><br><br>Visit other Kitware open-source projects at<br><a href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><br><br>Kitware offers ITK Training Courses, for more information visit:<br>http://www.kitware.com/products/protraining.php<br><br>Please keep messages on-topic and check the ITK FAQ at:<br>http://www.itk.org/Wiki/ITK_FAQ<br><br>Follow this link to subscribe/unsubscribe:<br>http://www.itk.org/mailman/listinfo/insight-users<br></blockquote></div><br></div></div></body></html>