2009 Winter Project Week Command Line Program Testing
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Key Investigators
- Bill Lorensen (His Basement)
Objective
There is NA-MIC funded infrastructure in place to regression test the command line programs found in Applications/CLI. Surprisingly, of the over 50 command line programs in the current Slicer3 distribution, only 11 have tests. This project will illustrate the importance of testing and show how easy it is to create tests for command line programs using the existing infrastructure. The project will document the process, create tests and help others to create tests.
Approach, Plan
Using the existing infrastructure, the project will create regression tests for many of the existing command line programs in Applications/CLI. The project will provide expert assistance to those who feel that creating a test is difficult. A Wiki page will provide step-by-step procedures to test the command line programs.
Progress
There is really no excuse for the lack of testing in Applications/CLI. The infrastructure that has been in place for a few years makes it almost painless to test command line programs. Better documentation and peer pressure will help improve the situation.
Working Notes
| Program | Test Type | Command Line |
|---|---|---|
|
Add |
Regression |
${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/AddTest.nhdr
|
|
AffineRegistration |
None (--help) |
|
|
BSplineDeformableRegistration |
Smoke |
--resampledmovingfilename ${TEMP}/BSplineDeformableRegistrationTest00.nhdr
--outputtransform ${TEMP}/BSplineDeformableRegistrationTest00Transform.txt
--default 0
--maximumDeformation 1.0
--constrain
--spatialsamples 10000
--histogrambins 32
--gridSize 5
--iterations 50
${TEST_DATA}/CTHeadAxial.nhdr
${TEST_DATA}/CTHeadAxial.nhdr
|
|
CheckerBoard |
Regression |
--checkerPattern 5,3,2
${TEST_DATA}/CTHeadAxial.nhdr
${TEST_DATA}/CTHeadAxialDoubled.nhdr
${TEMP}/CheckerBoardTest.nhdr
|
|
ConfidenceConnected |
None (Regression) |
--smoothingIterations 1
--timestep 0.0625
--iterations 5
--multiplier 2.5
--neighborhood 1
--labelvalue 2
--seed 9.71622,-8.1,14.2189 --seed -12.9459,-8.1,18.577
${TEST_DATA}/MRHeadResampled.nhdr
${TEMP}/ConfidenceConnectedTest.nhdr
|
|
CurvatureAnisotropicDiffusion |
None (Regression) |
--conductance 2
--timeStep 0.0625
--iterations 2
${TEST_DATA}/MRHeadResampled.nhdr
${TEMP}/CurvatureAnisotropicDiffusionTest.nhdr
|
|
DicomToNrrdConverter |
None (--help) |
|
|
DiffusionTensorEstimation |
None (--help) |
|
|
DiffusionTensorMathematics |
None (--help) |
|
|
DiffusionTensorTest |
None (--help) |
|
|
DiffusionWeightedTest |
None (--help) |
|
|
DWIDicomLoad |
None (--help) |
|
|
ExecutionModelTour |
None (Smoke) |
--integer 30
--double 30
-f 1.3,2,-14
--string_vector foo,bar,foobar
--enumeration Bill
--boolean1
--transform1 ${TEST_DATA}/ExecutionModelTourTest.mrml\#vtkMRMLLinearTransformNode1
--transform2 ${TEST_DATA}/ExecutionModelTourTest.mrml\#vtkMRMLLinearTransformNode2
${TEST_DATA}/MRHeadResampled.nhdr
${TEST_DATA}/CTHeadAxial.nhdr
|
|
ExtractSkeleton/ExtractSkeleton |
None (--help) |
|
|
FreesurferSurfaceSectionExtraction |
None (--help) |
|
|
GaussianBlurImageFilter |
Regression |
--sigma 2.5 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/GaussianBlurImageFilterTest.nhdr
|
|
GradientAnisotropicDiffusion |
None (--help) |
|
|
GrayscaleFillHoleImageFilter |
None (--help) |
|
|
GrayscaleGrindPeakImageFilter |
None (--help) |
|
|
GrayscaleModelMaker |
None (--help) |
|
|
HistogramMatching |
None (--help) |
|
|
ImageLabelCombine |
None (--help) |
|
|
ImageReadDicomWrite |
None (--help) |
|
|
LabelMapSmoothing |
None (--help) |
|
|
LinearRegistration |
Smoke |
--resampledmovingfilename ${TEMP}/LinearRegistrationTest00.nhdr
--outputtransform ${TEMP}/LinearRegistrationTest00Transform.txt
--initialtransform ${TEST_DATA}/itkAffineTransform00.txt
--spatialsamples 10000
--histogrambins 32
--iterations 50
--learningrate 0.01
--translationscale 100
${TEST_DATA}/CTHeadAxial.nhdr
${TEST_DATA}/CTHeadAxial.nhdr
|
|
MedianImageFilter |
Regression |
--neighborhood 1,2,3 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/MedianImageFilterTest.nhdr
|
|
ModelMaker |
None (Smoke) |
--labels 2
--modelSceneFile ${TEMP}/ModelMakerTest.mrml\#vtkMRMLModelHierarchyNode1
${MRML_TEST_DATA}/helix-roi-lable2.nrrd
|
|
MultipleModelsExample |
None (--help) |
|
|
OrientImage |
Regression |
--orientation Axial ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestAxial.nrrd
--orientation Coronal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestCoronal.nrrd
--orientation Sagittal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestSagittal.nrrd
|
|
OtsuThresholdImageFilter |
None |
|
|
OtsuThresholdSegmentation |
None (Smoke) |
--brightObjects
--numberOfBins 128
--faceConnected
--minimumObjectSize 1000
${TEST_DATA}/CTHeadResampled.nhdr
${TEMP}/OtsuThresholdImageFilterTest.nhdr
|
|
ProbeVolumeWithModel |
None (--help) |
|
|
Realign/Realign |
None (--help) |
|
|
ResampleVolume2 |
None (--help) |
|
|
ResampleVolume |
None (--help) |
|
|
RigidRegistration |
None (--help) |
|
|
Subtract |
None (--help) |
|
|
TestGridTransformRegistration |
Smoke |
--gridSize 5
--outputtransform ${TEMP}/TestGridTransformRegistrationTest00Transform.txt
${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxial.nhdr
|
|
VotingBinaryHoleFillingImageFilter |
None (Regression) |
--radius 3,3,3
--majorityThreshold 1
--background 0
--foreground 1
${TEST_DATA}/CTHeadResampledOtsuSegmented.nhdr
${TEMP}/VotingBinaryHoleFillingImageFilterTest.nhdr
|
|
ZeroCrossingBasedEdgeDetectionImageFilter.xml |
None (Regression) |
${TEST_DATA}/CTHeadResampled.nhdr
${TEMP}/ZeroCrossingBasedEdgeDetectionImageFilterTest.nhdr
|
