[Insight-developers] changing ITK data

Nicholas Tustison ntustison at gmail.com
Sun Jul 24 07:31:37 EDT 2011 

THanks so much, Cory.  I'll give that a try.


On Jul 23, 2011, at 10:54 PM, Cory Quammen wrote:

> Nick,
> 
> Ah, okay. So, no linking will occur with what you are doing. You are actually overwriting the test data in the "old" Data repository. To use the new procedure for adding data, you will have to do a bit more work.
> 
> First, create a new Baseline directory in ITK/Modules/Core/Transform/test/
> 
> cd ITK/Modules/Core/Transform/test/
> mkdir Baseline
> 
> Then, copy your new data file to the Baseline repository
> 
> cp itkBSplineDeformableTransformTest2PixelCentered.png ITK/Modules/Core/Transform/test/Baseline
> 
> Then, you need to change the entry for the test in the ITK/Modules/Core/Transform/test/CMakeLists.txt file from
> 
> itk_add_test(NAME itkBSplineDeformableTransformTest2
>       COMMAND ITKTransformTestDriver
>     --compare ${ITK_DATA_ROOT}/Baseline/Common/itkBSplineDeformableTransformTest2PixelCentered.png
>               ${ITK_TEST_OUTPUT_DIR}/itkBSplineDeformableTransformTest2PixelCentered.png
>     itkBSplineDeformableTransformTest2 ${ITK_EXAMPLE_DATA_ROOT}/BSplineDisplacements5.txt ${ITK_EXAMPLE_DATA_ROOT}/DiagonalLines.png ${ITK_EXAMPLE_DATA_ROOT}/DiagonalLines.png ${ITK_TEST_OUTPUT_DIR}/itkBSplineDeformableTransformTest2PixelCentered.png ${ITK_TEST_OUTPUT_DIR}/itkBSplineDeformableTransformTest2DeformationFieldPixelCentered.mhd 1)
> 
> to
> 
> itk_add_test(NAME itkBSplineDeformableTransformTest2
>       COMMAND ITKTransformTestDriver
>     --compare DATA{Baseline/itkBSplineDeformableTransformTest2PixelCentered.png}
>               ${ITK_TEST_OUTPUT_DIR}/itkBSplineDeformableTransformTest2PixelCentered.png
>     itkBSplineDeformableTransformTest2 ${ITK_EXAMPLE_DATA_ROOT}/BSplineDisplacements5.txt ${ITK_EXAMPLE_DATA_ROOT}/DiagonalLines.png ${ITK_EXAMPLE_DATA_ROOT}/DiagonalLines.png ${ITK_TEST_OUTPUT_DIR}/itkBSplineDeformableTransformTest2PixelCentered.png ${ITK_TEST_OUTPUT_DIR}/itkBSplineDeformableTransformTest2DeformationFieldPixelCentered.mhd 1)
> 
> The DATA{} notation is what invokes the linking.
> 
> Be warned that after you run CMake, the original data file itkBSplineDeformableTransformTest2PixelCentered.png will be moved to a hidden location and replaced with a file named itkBSplineDeformableTransformTest2PixelCentered.png.md5. Presumably, you have a way to regenerate that file if needed. If not, you can access the hidden file by following the directions here:
> 
> http://www.itk.org/Wiki/ITK/Git/Develop/Data#Recover_Data_File
> 
> Hope that helps,
> Cory
> 
> On Sat, Jul 23, 2011 at 10:32 PM, Nicholas Tustison <ntustison at gmail.com> wrote:
> Thanks Cory.  So this is what I did
> 
> 1. One of the tests that's failing involves the image
> 
> ITK/Testing/Data/Baseline/Common/itkBSplineDeformableTransformTest2PixelCentered.png
> 
> so I took the correct image produced on my machine
> and copied over the incorrect one.
> 
> 2. I then changed to my build directory, and typed
> "cmake .".  It is my understanding that I should have
> gotten a message like 
> 
> Linked Modules/.../test/Baseline/MyTest.png.md5 to ExternalData MD5/...
> as shown on the wiki page but I don't see that.  Instead I got
> 
> $ cmake .
> -- Enabled ITKKWSys, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKVNL, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKVNLInstantiation, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKCommon, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKFiniteDifference, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageFilterBase, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKCurvatureFlow, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageAdaptors, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKNetlib, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKStatistics, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKZLIB, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKHDF5, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKTransform, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageFunction, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageGrid, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKAnisotropicSmoothing, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOBase, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOBMP, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKExpat, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKOpenJPEG, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKGDCM, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOGDCM, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOGIPL, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKJPEG, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOJPEG, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKMetaIO, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOMeta, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKNIFTI, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIONIFTI, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKNrrdIO, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIONRRD, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKPNG, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOPNG, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKTIFF, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOTIFF, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOVTK, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKTestKernel, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageCompose, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKMesh, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKSpatialObjects, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageStatistics, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKPath, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageIntensity, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageLabel, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKThresholding, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKConnectedComponents, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKMathematicalMorphology, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKLabelMap, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKBinaryMathematicalMorphology, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKNarrowBand, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKDistanceMap, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKQuadEdgeMesh, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKFastMarching, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageCompare, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKSmoothing, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageGradient, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKImageFeature, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKOptimizers, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKSignedDistanceFunction, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKLevelSets, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKAntiAlias, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKPolynomials, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKBiasCorrection, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKBioCell, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKClassifiers, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKDICOMParser, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKDeformableMesh, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKDeformationField, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKDiffusionTensorImage, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKEigen, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKRegistrationCommon, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKFEM, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKPDEDeformableRegistration, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKFEMRegistration, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKFFT, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOBioRad, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOIPL, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOGE, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOLSM, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIORAW, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOSiemens, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOXML, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOSpatialObjects, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOStimulate, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKKLMRegionGrowing, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKLabelVoting, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKMarkovRandomFieldsClassifiers, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKNeuralNetworks, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKQuadEdgeMeshFiltering, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKRegionGrowing, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKSpatialFunction, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKVTK, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKVoronoi, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKWatersheds, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKDeprecated, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOHDF5, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIOPhilipsREC, needed by [ITKGroup_IO].
> -- Enabled ITKImageFusion, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKIntegratedTest, requested by ITK_BUILD_ALL_MODULES.
> -- Enabled ITKReview, requested by Module_ITKReview.
> -- Filter ZLIB is ON
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /Users/ntustison/Pkg/ITK/bin
> 
> 
> 
> 
> Nick
> 
> 
> 
> 
> On Jul 23, 2011, at 9:37 PM, Nicholas Tustison wrote:
> 
>> Hi,
>> 
>> For the following patch, 
>> 
>> http://review.source.kitware.com/#change,1856
>> 
>> there were some fundamental changes to the output and
>> I need to update the data so that the tests don't fail.  I've
>> looked at the wiki page
>> 
>> http://www.itk.org/Wiki/ITK/Git/Develop/Data
>> 
>> which I haven't had much success with. I've gotten as far
>> as running CMake but the linking doesn't occur.  Is this 
>> wiki page restricted to adding data as opposed to changing 
>> data?  
>> 
>> Thanks,
>> Nick
> 
> 
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> 
> 
> -- 
> Cory Quammen
> Research Associate
> Department of Computer Science
> University of North Carolina at Chapel Hill
> http://www.cs.unc.edu/~cquammen

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