Difference between revisions of "2009 Winter Project Week Command Line Program Testing"
Line 50: | Line 50: | ||
Regression | Regression | ||
| | | | ||
− | ${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/AddTest.nhdr | + | ${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/AddTest.nhdr |
|- | |- | ||
| | | | ||
Line 63: | Line 63: | ||
Smoke | Smoke | ||
| | | | ||
− | --resampledmovingfilename ${TEMP}/BSplineDeformableRegistrationTest00.nhdr | + | --resampledmovingfilename ${TEMP}/BSplineDeformableRegistrationTest00.nhdr |
− | --outputtransform ${TEMP}/BSplineDeformableRegistrationTest00Transform.txt | + | --outputtransform ${TEMP}/BSplineDeformableRegistrationTest00Transform.txt |
− | --default 0 | + | --default 0 |
− | --maximumDeformation 1.0 | + | --maximumDeformation 1.0 |
− | --constrain | + | --constrain |
− | --spatialsamples 10000 | + | --spatialsamples 10000 |
− | --histogrambins 32 | + | --histogrambins 32 |
− | --gridSize 5 | + | --gridSize 5 |
− | --iterations 50 | + | --iterations 50 |
− | ${TEST_DATA}/CTHeadAxial.nhdr | + | ${TEST_DATA}/CTHeadAxial.nhdr |
− | ${TEST_DATA}/CTHeadAxial.nhdr | + | ${TEST_DATA}/CTHeadAxial.nhdr |
|- | |- | ||
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Line 80: | Line 80: | ||
Regression | Regression | ||
| | | | ||
− | --checkerPattern 5,3,2 ${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxialDoubled.nhdr ${TEMP}/CheckerBoardTest.nhdr | + | --checkerPattern 5,3,2 |
+ | ${TEST_DATA}/CTHeadAxial.nhdr | ||
+ | ${TEST_DATA}/CTHeadAxialDoubled.nhdr | ||
+ | ${TEMP}/CheckerBoardTest.nhdr | ||
|- | |- | ||
| | | | ||
ConfidenceConnected | ConfidenceConnected | ||
| | | | ||
− | None | + | 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 | ||
|- | |- | ||
| | | | ||
Line 153: | Line 165: | ||
Regression | Regression | ||
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− | --sigma 2.5 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/GaussianBlurImageFilterTest.nhdr | + | --sigma 2.5 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/GaussianBlurImageFilterTest.nhdr |
|- | |- | ||
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Line 208: | Line 220: | ||
Smoke | Smoke | ||
| | | | ||
− | --resampledmovingfilename ${TEMP}/LinearRegistrationTest00.nhdr | + | --resampledmovingfilename ${TEMP}/LinearRegistrationTest00.nhdr |
− | --outputtransform ${TEMP}/LinearRegistrationTest00Transform.txt | + | --outputtransform ${TEMP}/LinearRegistrationTest00Transform.txt |
− | --initialtransform ${TEST_DATA}/itkAffineTransform00.txt | + | --initialtransform ${TEST_DATA}/itkAffineTransform00.txt |
− | --spatialsamples 10000 | + | --spatialsamples 10000 |
− | --histogrambins 32 | + | --histogrambins 32 |
− | --iterations 50 | + | --iterations 50 |
− | --learningrate 0.01 | + | --learningrate 0.01 |
− | --translationscale 100 | + | --translationscale 100 |
− | ${TEST_DATA}/CTHeadAxial.nhdr | + | ${TEST_DATA}/CTHeadAxial.nhdr |
− | ${TEST_DATA}/CTHeadAxial.nhdr | + | ${TEST_DATA}/CTHeadAxial.nhdr |
|- | |- | ||
| | | | ||
Line 224: | Line 236: | ||
Regression | Regression | ||
| | | | ||
− | --neighborhood 1,2,3 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/MedianImageFilterTest.nhdr | + | --neighborhood 1,2,3 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/MedianImageFilterTest.nhdr |
|- | |- | ||
| | | | ||
Line 243: | Line 255: | ||
Regression | Regression | ||
| | | | ||
− | --orientation Axial ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestAxial.nrrd | + | --orientation Axial ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestAxial.nrrd |
<br> | <br> | ||
− | --orientation Coronal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestCoronal.nrrd | + | --orientation Coronal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestCoronal.nrrd |
<br> | <br> | ||
− | --orientation Sagittal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestSagittal.nrrd | + | --orientation Sagittal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestSagittal.nrrd |
|- | |- | ||
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Line 302: | Line 314: | ||
Smoke | Smoke | ||
| | | | ||
− | --gridSize 5 --outputtransform ${TEMP}/TestGridTransformRegistrationTest00Transform.txt ${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxial.nhdr | + | --gridSize 5 |
+ | --outputtransform ${TEMP}/TestGridTransformRegistrationTest00Transform.txt | ||
+ | ${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxial.nhdr | ||
|- | |- | ||
| | | | ||
VotingBinaryHoleFillingImageFilter | VotingBinaryHoleFillingImageFilter | ||
| | | | ||
− | None | + | None (Regression) |
| | | | ||
+ | --radius 3,3,3 | ||
+ | --majorityThreshold 1 | ||
+ | --background 0 | ||
+ | --foreground 1 | ||
+ | ${TEST_DATA}/CTHeadResampledOtsuSegmented.nhdr | ||
+ | ${TEMP}/VotingBinaryHoleFillingImageFilterTest.nhdr | ||
|- | |- | ||
| | | | ||
ZeroCrossingBasedEdgeDetectionImageFilter.xml | ZeroCrossingBasedEdgeDetectionImageFilter.xml | ||
| | | | ||
− | None | + | None (Regression) |
| | | | ||
+ | ${TEST_DATA}/CTHeadResampled.nhdr | ||
+ | ${TEMP}/ZeroCrossingBasedEdgeDetectionImageFilterTest.nhdr | ||
|- | |- | ||
|} | |} |
Revision as of 18:35, 2 January 2009
Home < 2009 Winter Project Week Command Line Program Testing
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 |
|
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 |
|
DicomToNrrdConverter |
None |
|
DiffusionTensorEstimation |
None |
|
DiffusionTensorMathematics |
None |
|
DiffusionTensorTest |
None |
|
DiffusionWeightedTest |
None |
|
DWIDicomLoad |
None |
|
ExecutionModelTour |
None |
|
ExtractSkeleton/ExtractSkeleton |
None |
|
FreesurferSurfaceSectionExtraction |
None |
|
GaussianBlurImageFilter |
Regression |
--sigma 2.5 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/GaussianBlurImageFilterTest.nhdr |
GradientAnisotropicDiffusion |
None |
|
GrayscaleFillHoleImageFilter |
None |
|
GrayscaleGrindPeakImageFilter |
None |
|
GrayscaleModelMaker |
None |
|
HistogramMatching |
None |
|
ImageLabelCombine |
None |
|
ImageReadDicomWrite |
None |
|
LabelMapSmoothing |
None |
|
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 |
|
MultipleModelsExample |
None |
|
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 |
|
ProbeVolumeWithModel |
None |
|
Realign/Realign |
None |
|
ResampleVolume2 |
None |
|
ResampleVolume |
None |
|
RigidRegistration |
None |
|
Subtract |
None |
|
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 |