[Insight-users] need help using itk with python
Matei Stroila
matei.stroila at gmail.com
Thu Mar 15 18:18:55 EST 2007
On 3/15/07, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
>
> That's bad :-/
Yes, it looks like the whole dynamic build is bad since I tried some
examples and they crashed.
I did a clean Release build. I guess, I will have to clean somehow my
environment.
>
> Do you have built all ITK with the Release configuration ?
> Can you give the result of
>
> ctest -C Release -R PythonTestDirectory -V
Here it is:
D:\build\InsightToolkit-3.2.0-bin>ctest -C Release -R PythonTestDirectory -V
Add coverage exclude regular expressions.
Start processing tests
Test project D:/build/InsightToolkit-3.2.0-bin
Constructing a list of tests
Done constructing a list of tests
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Wrapping/WrapITK/Pytho
n/Tests
1/240 Testing PythonTestDirectory
Test command: D:\build\InsightToolkit-3.2.0-bin\bin\Release\itkTestDriver.exe --
add-before-env PYTHONPATH D:/build/InsightToolkit-3.2.0-bin/Wrapping/WrapITK/Pyt
hon/Release --add-before-env PYTHONPATH D:/build/InsightToolkit-3.2.0-bin/bin/Re
lease C:/Python25/python.exe D:/src/InsightToolkit-3.2.0/Wrapping/WrapITK/Python
/Tests/TestDirectory.py
Loading VXLNumerics...Traceback (most recent call last):
File "D:/src/InsightToolkit-3.2.0/Wrapping/WrapITK/Python/Tests/TestDirectory.
py", line 4, in <module>
d = itk.Directory.New()
File "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkLaz
y.py", line 18, in __getattribute__
itkBase.LoadModule(module, namespace)
File "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkBas
e.py", line 77, in LoadModule
LoadModule(dep, namespace)
File "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkBas
e.py", line 85, in LoadModule
if not swigModuleName in sys.modules: module = loader.load(swigModuleName)
File "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkBas
e.py", line 192, in load
return imp.load_module(name, fp, pathname, description)
File "D:\build\InsightToolkit-3.2.0-bin\bin\Release\VXLNumericsPython.py", lin
e 5, in <module>
import _VXLNumericsPython
ImportError: No module named _VXLNumericsPython
-- Process completed
***Failed
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/Iterators
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/DataRepresent
ation/Image
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/DataRepresent
ation/Mesh
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/DataRepresent
ation/Path
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/Filtering
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/Registration
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/Segmentation
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/Statistics
Changing directory into D:/build/InsightToolkit-3.2.0-bin/Examples/Patented
0% tests passed, 1 tests failed out of 1
The following tests FAILED:
1 - PythonTestDirectory (Failed)
Errors while running CTest
Thanks for help,
Matei
>
> Thanks,
>
> Gaetan
>
>
> Le Thu, 15 Mar 2007 23:20:19 +0100, Matei Stroila
> <matei.stroila at gmail.com> a écrit:
>
> > On 3/15/07, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
> >>
> >> can you run the command
> >>
> >> ctest -C Release -R Python
> >>
> >> and send the result ?
> >
> > Yes, here it is:
> >
> > D:\build\InsightToolkit-3.2.0-bin>ctest -C Release -R Python
> > Start processing tests
> > Test project D:/build/InsightToolkit-3.2.0-bin
> > 1/240 Testing PythonTestDirectory ***Failed
> > 2/240 Testing PythonTestObject ***Failed
> > 3/240 Testing PythonFilterCoverage Passed
> > 4/240 Testing PythonFindEmptyClasses ***Failed
> > 5/240 Testing PythonTypemaps ***Failed
> > 6/240 Testing PythonTemplate ***Failed
> > 7/240 Testing PythonExtras ***Failed
> > 8/240 Testing PythonModuleToModule ***Failed
> > 9/240 Testing PythonBinaryDilateImageFilter ***Failed
> > 10/240 Testing PythonBinaryErodeImageFilter ***Failed
> > 11/240 Testing PythonBinaryThresholdImageFilt***Failed
> > 12/240 Testing PythonCastImageFilter ***Failed
> > 13/240 Testing PythonGrayscaleDilateImageFilt***Failed
> > 14/240 Testing PythonBoxGrayscaleDilateImageF***Failed
> > 15/240 Testing PythonGrayscaleErodeImageFilte***Failed
> > 16/240 Testing PythonMeanImageFilter ***Failed
> > 17/240 Testing PythonMedianImageFilter ***Failed
> > 18/240 Testing PythonSigmoidImageFilter ***Failed
> > 19/240 Testing PythonThresholdImageFilter ***Failed
> > 20/240 Testing PythonResampleImageFilterTest1***Failed
> > 21/240 Testing PythonResampleImageFilterTest2***Failed
> > 22/240 Testing PythonResampleImageFilterTest3***Failed
> > 23/240 Testing PythonResampleImageFilterTest4***Failed
> > 24/240 Testing PythonCurvatureAnisotropicDiff***Failed
> > 25/240 Testing PythonCurvatureFlowImageFilter***Failed
> > 26/240 Testing PythonSmoothingRecursiveGaussi***Failed
> > 27/240 Testing PythonLaplacianImageFilter ***Failed
> > 28/240 Testing PythonFFTImageFilter ***Failed
> > 29/240 Testing PythonGradientMagnitudeRecursi***Failed
> > 30/240 Testing PythonGradientAnisotropicDiffu***Failed
> > 31/240 Testing PythonGeodesicActiveContourLef***Failed
> > 32/240 Testing PythonFastMarchingLeftVentricl***Failed
> > 33/240 Testing PythonFastMarchingRightVentric***Failed
> > 34/240 Testing PythonFastMarchingWhiteMatterT***Failed
> > 35/240 Testing PythonFastMarchingGrayMatterTe***Failed
> > 36/240 Testing PythonThresholdSegmentationLev***Failed
> > 37/240 Testing PythonThresholdSegmentationLev***Failed
> > 38/240 Testing PythonThresholdSegmentationLev***Failed
> > 39/240 Testing PythonCannyEdgeDetectionImageF***Failed
> > 40/240 Testing PythonWatershedSegmentation1 ***Failed
> > 41/240 Testing PythonSpatialObject ***Failed
> > 42/240 Testing PythonAntiAliasBinaryImageFilt***Failed
> > 43/240 Testing PythonSimplePipelineUC2 ***Failed
> > 44/240 Testing PythonSimplePipelineUS2 ***Failed
> > 45/240 Testing PythonSimplePipelineF2 ***Failed
> > 46/240 Testing PythonSimplePipelineUC3 ***Failed
> > 47/240 Testing PythonSimplePipelineUS3 ***Failed
> > 48/240 Testing PythonSimplePipelineF3 ***Failed
> >
> > 2% tests passed, 47 tests failed out of 48
> >
> > The following tests FAILED:
> > 1 - PythonTestDirectory (Failed)
> > 2 - PythonTestObject (Failed)
> > 4 - PythonFindEmptyClasses (Failed)
> > 5 - PythonTypemaps (Failed)
> > 6 - PythonTemplate (Failed)
> > 7 - PythonExtras (Failed)
> > 8 - PythonModuleToModule (Failed)
> > 9 - PythonBinaryDilateImageFilter (Failed)
> > 10 - PythonBinaryErodeImageFilter (Failed)
> > 11 - PythonBinaryThresholdImageFilter (Failed)
> > 12 - PythonCastImageFilter (Failed)
> > 13 - PythonGrayscaleDilateImageFilter (Failed)
> > 14 - PythonBoxGrayscaleDilateImageFilter (Failed)
> > 15 - PythonGrayscaleErodeImageFilter (Failed)
> > 16 - PythonMeanImageFilter (Failed)
> > 17 - PythonMedianImageFilter (Failed)
> > 18 - PythonSigmoidImageFilter (Failed)
> > 19 - PythonThresholdImageFilter (Failed)
> > 20 - PythonResampleImageFilterTest1 (Failed)
> > 21 - PythonResampleImageFilterTest2 (Failed)
> > 22 - PythonResampleImageFilterTest3 (Failed)
> > 23 - PythonResampleImageFilterTest4 (Failed)
> > 24 - PythonCurvatureAnisotropicDiffusionImageFilter (Failed)
> > 25 - PythonCurvatureFlowImageFilter (Failed)
> > 26 - PythonSmoothingRecursiveGaussianImageFilter (Failed)
> > 27 - PythonLaplacianImageFilter (Failed)
> > 28 - PythonFFTImageFilter (Failed)
> > 29 - PythonGradientMagnitudeRecursiveGaussianImageFilterTest
> > (Failed)
> > 30 - PythonGradientAnisotropicDiffusionImageFilterTest (Failed)
> > 31 - PythonGeodesicActiveContourLeftVentricleTest (Failed)
> > 32 - PythonFastMarchingLeftVentricleTest (Failed)
> > 33 - PythonFastMarchingRightVentricleTest (Failed)
> > 34 - PythonFastMarchingWhiteMatterTest (Failed)
> > 35 - PythonFastMarchingGrayMatterTest (Failed)
> > 36 - PythonThresholdSegmentationLevelSetVentricleTest (Failed)
> > 37 - PythonThresholdSegmentationLevelSetWhiteMatterTest (Failed)
> > 38 - PythonThresholdSegmentationLevelSetGrayMatterTest (Failed)
> > 39 - PythonCannyEdgeDetectionImageFilterTest (Failed)
> > 40 - PythonWatershedSegmentation1 (Failed)
> > 41 - PythonSpatialObject (Failed)
> > 42 - PythonAntiAliasBinaryImageFilterTest (Failed)
> > 43 - PythonSimplePipelineUC2 (Failed)
> > 44 - PythonSimplePipelineUS2 (Failed)
> > 45 - PythonSimplePipelineF2 (Failed)
> > 46 - PythonSimplePipelineUC3 (Failed)
> > 47 - PythonSimplePipelineUS3 (Failed)
> > 48 - PythonSimplePipelineF3 (Failed)
> > Errors while running CTest
> >
> > D:\build\InsightToolkit-3.2.0-bin>
> >
> > Thanks,
> >
> > Matei
> >
> >
> >
> >
> >>
> >> Thanks,
> >>
> >> Gaetan
> >>
> >>
> >> Le Thu, 15 Mar 2007 21:04:04 +0100, Matei Stroila
> >> <matei.stroila at gmail.com> a écrit:
> >>
> >> > I did a clean build in Release mode (InsightToolkit-3.2.0) with
> >> > WrapITK ON, VS 2005.
> >> > Using WrapITK, it gives the same error:
> >> >
> >> > D:\Documents and Settings\mstroila>python
> >> > Python 2.5 (r25:51908, Sep 19 2006, 09:52:17) [MSC v.1310 32 bit
> >> > (Intel)] on win
> >> > 32
> >> > Type "help", "copyright", "credits" or "license" for more information.
> >> >>>> import itk
> >> >>>> reader = itk.ImageFileReader[itk.UC,2].New()
> >> > Traceback (most recent call last):
> >> > File "<stdin>", line 1, in <module>
> >> > File
> >> >
> >> "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkLaz
> >> > y.py", line 18, in __getattribute__
> >> > itkBase.LoadModule(module, namespace)
> >> > File
> >> >
> >> "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkBas
> >> > e.py", line 77, in LoadModule
> >> > LoadModule(dep, namespace)
> >> > File
> >> >
> >> "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkBas
> >> > e.py", line 77, in LoadModule
> >> > LoadModule(dep, namespace)
> >> > File
> >> >
> >> "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkBas
> >> > e.py", line 85, in LoadModule
> >> > if not swigModuleName in sys.modules: module =
> >> > loader.load(swigModuleName)
> >> > File
> >> >
> >> "D:\build\InsightToolkit-3.2.0-bin\Wrapping\WrapITK\Python\Release\itkBas
> >> > e.py", line 192, in load
> >> > return imp.load_module(name, fp, pathname, description)
> >> > File
> >> > "D:\build\InsightToolkit-3.2.0-bin\bin\Release\VXLNumericsPython.py",
> >> lin
> >> > e 5, in <module>
> >> > import _VXLNumericsPython
> >> > ImportError: No module named _VXLNumericsPython
> >> >
> >> > Thanks for help,
> >> >
> >> > Matei
> >> >
> >> > On 3/15/07, Matei Stroila <matei.stroila at gmail.com> wrote:
> >> >> On 3/15/07, Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
> >> >> > Can you verify that your PYTHONPATH contain the path to the dll
> >> files
> >> >> ?
> >> >>
> >> >> I did add it with no success. Same error message.
> >> >>
> >> >> I will look at WrapITK.
> >> >>
> >> >> Thanks,
> >> >>
> >> >> Matei
> >> >>
> >> >> >
> >> >> > Thanks,
> >> >> >
> >> >> > Gaetan
> >> >> >
> >> >> > PS: It will not fix your problem, but if your intersted in using
> >> itk
> >> >> with
> >> >> > python, you should look at WrapITK, which is also included in ITK
> >> >> 3.2.0
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Wed, 14 Mar 2007 20:43:48 +0100, Matei Stroila
> >> >> > <matei.stroila at gmail.com> wrote:
> >> >> >
> >> >> > > I built the new ITK release (3.2.0) with Visual Studio 2005 and
> >> no
> >> >> > > errors.
> >> >> > > I set the PYTHONPATH to the CSwig dir:
> >> >> > > D:\build\InsightToolkit-3.2.0-bin\Wrapping\CSwig\Python\Release
> >> >> > > and added to the PATH the build dir:
> >> >> > > D:\build\InsightToolkit-3.2.0-bin\bin\release
> >> >> > >
> >> >> > > When I try to use Python I get the following:
> >> >> > >
> >> >> > > Python 2.5 (r25:51908, Sep 19 2006, 09:52:17) [MSC v.1310 32 bit
> >> >> > > (Intel)] on win
> >> >> > > 32
> >> >> > > Type "help", "copyright", "credits" or "license" for more
> >> >> information.
> >> >> > >>>> from InsightToolkit import *
> >> >> > > Traceback (most recent call last):
> >> >> > > File "<stdin>", line 1, in <module>
> >> >> > > File
> >> >> > >
> >> >>
> >> "D:/build/InsightToolkit-3.2.0-bin/Wrapping/CSwig/Python\Release\InsightT
> >> >> > > oolkit.py", line 1, in <module>
> >> >> > > from itkalgorithms import *
> >> >> > > File
> >> >> > >
> >> >>
> >> "D:/build/InsightToolkit-3.2.0-bin/Wrapping/CSwig/Python\Release\itkalgor
> >> >> > > ithms.py", line 1, in <module>
> >> >> > > from itknumerics import *
> >> >> > > File
> >> >> > >
> >> >>
> >> "D:/build/InsightToolkit-3.2.0-bin/Wrapping/CSwig/Python\Release\itknumer
> >> >> > > ics.py", line 1, in <module>
> >> >> > > from itkcommon import *
> >> >> > > File
> >> >> > >
> >> >>
> >> "D:/build/InsightToolkit-3.2.0-bin/Wrapping/CSwig/Python\Release\itkcommo
> >> >> > > n.py", line 1, in <module>
> >> >> > > from vxlnumerics import *
> >> >> > > File
> >> >> > >
> >> >>
> >> "D:/build/InsightToolkit-3.2.0-bin/Wrapping/CSwig/Python\Release\vxlnumer
> >> >> > > ics.py", line 4, in <module>
> >> >> > > from VXLNumericsPython import *
> >> >> > > File "VXLNumericsPython.py", line 5, in <module>
> >> >> > > import _VXLNumericsPython
> >> >> > > ImportError: No module named _VXLNumericsPython
> >> >> > >
> >> >> > > I checked the build dir and _VXLNumericsPython.dll is there. I
> >> don't
> >> >> > > understand why is not finding that module.
> >> >> > >
> >> >> > > Thanks a lot for help,
> >> >> > >
> >> >> > > Matei
> >> >> > > _______________________________________________
> >> >> > > Insight-users mailing list
> >> >> > > Insight-users at itk.org
> >> >> > > http://www.itk.org/mailman/listinfo/insight-users
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Gaëtan Lehmann
> >> >> > Biologie du Développement et de la Reproduction
> >> >> > INRA de Jouy-en-Josas (France)
> >> >> > tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
> >> >> > http://voxel.jouy.inra.fr
> >> >> >
> >> >>
> >>
> >>
> >>
> >> --
> >> Gaëtan Lehmann
> >> Biologie du Développement et de la Reproduction
> >> INRA de Jouy-en-Josas (France)
> >> tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
> >> http://voxel.jouy.inra.fr
> >>
>
>
>
> --
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr
>
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