Difference between revisions of "2009 Winter Project Week Command Line Program Testing"

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# Regression tests run the program and compare the resulting output with a baseline output. Currently only image regression testing is available. Each command line program that produces an image should have a regression test.
 
# Regression tests run the program and compare the resulting output with a baseline output. Currently only image regression testing is available. Each command line program that produces an image should have a regression test.
  
−
Documentation: TODO
+
Documentation: [[Slicer3:Execution Model Testing|Slicer3 Execution Model Testing]]
  
  
Line 49: Line 49:
 
== Status ==
 
== Status ==
  
−
The table shows each command line program and its testing status. Under '''Test Type''', the item in ''parentheses'' is a test that has been added as part of this project.
+
Starting (current) status:
 +
# 5 (20) regression tests
 +
# 3 (9) smoke tests
 +
# 30 (9) with no tests
 +
 
 +
During Project Week, I'll work with those folks responsible for programs whose status is untested.
 +
 
 +
The table shows each command line program and its testing status. Under '''Test Type''', the item in ''parentheses'' is a test that has been added as part of this project. Even the untested programs have at a minimum test that runs the program with ''--help''. We still consider these programs untested since every CLP program responds to ''--help''. However, at least these test programs can link and run.
  
 
{| border="1"
 
{| border="1"
Line 59: Line 66:
 
Add
 
Add
 
|
 
|
−
<span style="color:#98fb98">Regression</span>
+
<span style="color:#00ff00">Regression</span>
 
|
 
|
−
  ${TEST_DATA}/CTHeadAxial.nhdr ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/AddTest.nhdr
+
  ${TEST_DATA}/CTHeadAxial.nhdr
 +
${TEST_DATA}/CTHeadAxial.nhdr
 +
${TEMP}/AddTest.nhdr
 
|-
 
|-
 
| style="background:#fa8072; color:black"|
 
| style="background:#fa8072; color:black"|
Line 72: Line 81:
 
BSplineDeformableRegistration
 
BSplineDeformableRegistration
 
|
 
|
−
<span style="color:#c0c0c0">Smoke</span>
+
<span style="color:#000000">Smoke</span>
 
|
 
|
 
  --resampledmovingfilename  ${TEMP}/BSplineDeformableRegistrationTest00.nhdr
 
  --resampledmovingfilename  ${TEMP}/BSplineDeformableRegistrationTest00.nhdr
Line 89: Line 98:
 
CheckerBoard
 
CheckerBoard
 
|
 
|
−
<span style="color:#98fb98">Regression</span>
+
<span style="color:#00ff00">Regression</span>
 
|
 
|
 
  --checkerPattern 5,3,2
 
  --checkerPattern 5,3,2
Line 99: Line 108:
 
ConfidenceConnected
 
ConfidenceConnected
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#98fb98">Regression</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 
  --smoothingIterations 1
 
  --smoothingIterations 1
Line 114: Line 123:
 
CurvatureAnisotropicDiffusion
 
CurvatureAnisotropicDiffusion
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#98fb98">Regression</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 
  --conductance 2
 
  --conductance 2
Line 125: Line 134:
 
DicomToNrrdConverter
 
DicomToNrrdConverter
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#c0c0c0">Smoke</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#000000">Smoke</span>)
 
|
 
|
 
  ${TEST_DATA}/CTHeadAxialDicom
 
  ${TEST_DATA}/CTHeadAxialDicom
 
  ${TEMP} CTHeadAxialFromDicom.nhdr
 
  ${TEMP} CTHeadAxialFromDicom.nhdr
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#c0c0c0; color:black"|
 
DiffusionTensorEstimation
 
DiffusionTensorEstimation
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#000000">Smoke</span>)
 
|
 
|
 +
--otsuomegathreshold 0.5
 +
${MRML_TEST_DATA}/helix-DWI.nhdr
 +
${TEMP}/DiffusionTensorEstimationTest_dti.nhdr
 +
${TEMP}/DiffusionTensorEstimationTest_baseline.nhdr
 +
${TEMP}/DiffusionTensorEstimationTest_otsu.nhdr
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#c0c0c0; color:black"|
 
DiffusionTensorMathematics
 
DiffusionTensorMathematics
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#000000">Smoke</span>)
 
|
 
|
 +
--enumeration FractionalAnisotropy
 +
${MRML_TEST_DATA}/helix-DWI.nhdr
 +
${TEMP}/DiffusionTensorMathematicsTest.nhdr
 
|-
 
|-
 
| style="background:#fa8072; color:black"|
 
| style="background:#fa8072; color:black"|
Line 163: Line 180:
 
ExecutionModelTour
 
ExecutionModelTour
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#c0c0c0">Smoke</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#000000">Smoke</span>)
 
|
 
|
 
  --integer 30
 
  --integer 30
Line 175: Line 192:
 
  ${TEST_DATA}/MRHeadResampled.nhdr
 
  ${TEST_DATA}/MRHeadResampled.nhdr
 
  ${TEST_DATA}/CTHeadAxial.nhdr
 
  ${TEST_DATA}/CTHeadAxial.nhdr
−
|-
 
−
| style="background:#fa8072; color:black"|
 
−
ExtractSkeleton/ExtractSkeleton
 
−
|
 
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
 
−
|
 
 
|-
 
|-
 
| style="background:#fa8072; color:black"|
 
| style="background:#fa8072; color:black"|
Line 191: Line 202:
 
GaussianBlurImageFilter
 
GaussianBlurImageFilter
 
|
 
|
−
<span style="color:#98fb98">Regression</span>
+
<span style="color:#00ff00">Regression</span>
 
|
 
|
−
  --sigma 2.5 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/GaussianBlurImageFilterTest.nhdr
+
  --sigma 2.5
 +
${TEST_DATA}/CTHeadAxial.nhdr
 +
${TEMP}/GaussianBlurImageFilterTest.nhdr
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
 
GradientAnisotropicDiffusion
 
GradientAnisotropicDiffusion
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
--conductance 2
 +
--timeStep 0.0625
 +
--iterations 2
 +
${TEST_DATA}/MRHeadResampled.nhdr
 +
${TEMP}/GradientAnisotropicDiffusionTest.nhdr
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
 
GrayscaleFillHoleImageFilter
 
GrayscaleFillHoleImageFilter
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
${TEST_DATA}/MRHeadResampled.nhdr
 +
${TEMP}/GrayscaleFillHoleTest.nhdr
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
|-
 +
| style="background:#98fb98; color:black"|
 
GrayscaleGrindPeakImageFilter
 
GrayscaleGrindPeakImageFilter
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
${TEST_DATA}/MRHeadResampled.nhdr
 +
${TEMP}/GrayscaleGrindPeakTest.nhdr
 +
|-
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#c0c0c0; color:black"|
 
GrayscaleModelMaker
 
GrayscaleModelMaker
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#000000">Smoke</span>)
 
|
 
|
 +
--threshold 300
 +
--name CTFace
 +
--smooth 15
 +
--decimate 0.95
 +
--splitnormals
 +
--pointnormals
 +
${TEST_DATA}/CTHeadAxial.nhdr
 +
${TEMP}GrayscaleModelMakerTest.vtp
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
 
HistogramMatching
 
HistogramMatching
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
--numberOfHistogramLevels 64
 +
--numberOfMatchPoints 10
 +
${TEST_DATA}/CTHeadAxial.nhdr
 +
${TEST_DATA}/MRHeadResampled.nhdr
 
|-
 
|-
 
| style="background:#fa8072; color:black"|
 
| style="background:#fa8072; color:black"|
Line 234: Line 270:
 
ImageReadDicomWrite
 
ImageReadDicomWrite
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#98fb98">Regression</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 
  --patientName Austrialian
 
  --patientName Austrialian
Line 252: Line 288:
 
  ${TEST_DATA}/CTHeadAxial.nhdr
 
  ${TEST_DATA}/CTHeadAxial.nhdr
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
 
LabelMapSmoothing
 
LabelMapSmoothing
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
--labelToSmooth 1
 +
--numberOfIterations 50
 +
--maxRMSError 0.01
 +
--gaussianSigma 3
 +
${TEST_DATA}/CTHeadResampledOtsuSegmented.nhdr
 +
${TEMP}/LabelMapSmoothingTest.nhdr
 
|-
 
|-
 
| style="background:#c0c0c0; color:black"|
 
| style="background:#c0c0c0; color:black"|
 
LinearRegistration
 
LinearRegistration
 
|
 
|
−
<span style="color:#c0c0c0">Smoke</span>
+
<span style="color:#000000">Smoke</span>
 
|
 
|
 
  --resampledmovingfilename  ${TEMP}/LinearRegistrationTest00.nhdr
 
  --resampledmovingfilename  ${TEMP}/LinearRegistrationTest00.nhdr
Line 277: Line 319:
 
MedianImageFilter
 
MedianImageFilter
 
|
 
|
−
<span style="color:#98fb98">Regression</span>
+
<span style="color:#00ff00">Regression</span>
 
|
 
|
 
  --neighborhood 1,2,3 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/MedianImageFilterTest.nhdr
 
  --neighborhood 1,2,3 ${TEST_DATA}/CTHeadAxial.nhdr ${TEMP}/MedianImageFilterTest.nhdr
Line 284: Line 326:
 
ModelMaker
 
ModelMaker
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#c0c0c0">Smoke</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#000000">Smoke</span>)
 
|
 
|
 
  --labels 2
 
  --labels 2
Line 299: Line 341:
 
OrientImage
 
OrientImage
 
|
 
|
−
<span style="color:#98fb98">Regression</span>
+
<span style="color:#00ff00">Regression</span>
 
|
 
|
 
  --orientation Axial ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestAxial.nrrd
 
  --orientation Axial ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestAxial.nrrd
Line 305: Line 347:
 
  --orientation Sagittal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestSagittal.nrrd
 
  --orientation Sagittal ${MRML_DATA}/fixed.nrrd ${TEMP}/OrientImageTestSagittal.nrrd
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
 
OtsuThresholdImageFilter
 
OtsuThresholdImageFilter
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
−
 
 
 
|
 
|
 +
--insideValue 0
 +
--outsideValue 255
 +
--numberOfBins 128
 +
${TEST_DATA}/CTHeadResampled.nhdr
 +
${TEMP}/OtsuThresholdImageFilterTest.nhdr
 
|-
 
|-
 
| style="background:#98fb98; color:black"|
 
| style="background:#98fb98; color:black"|
 
OtsuThresholdSegmentation
 
OtsuThresholdSegmentation
 
|
 
|
−
<span style="color:#773333">None</span> (<span style="color:#98fb98">Regression</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 
  --brightObjects
 
  --brightObjects
Line 322: Line 368:
 
  --minimumObjectSize 1000
 
  --minimumObjectSize 1000
 
  ${TEST_DATA}/CTHeadResampled.nhdr
 
  ${TEST_DATA}/CTHeadResampled.nhdr
−
  ${TEMP}/OtsuThresholdImageFilterTest.nhdr  
+
  ${TEMP}/OtsuThresholdSegmentationTest.nhdr  
 
|-
 
|-
 
| style="background:#fa8072; color:black"|
 
| style="background:#fa8072; color:black"|
Line 330: Line 376:
 
|
 
|
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
−
Realign/Realign
 
−
|
 
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
 
−
|
 
−
|-
 
−
| style="background:#fa8072; color:black"|
 
 
ResampleVolume2
 
ResampleVolume2
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
--Reference ${TEST_DATA}/MRHeadResampled.nhdr
 +
--number_of_thread 0
 +
--transform_matrix 1,0,0,0,1,0,0,0,1,0,0,0
 +
--transform rt
 +
--space LPS
 +
--interpolation linear
 +
--window_function c
 +
--spline_order 3
 +
--spacing 0,0,0
 +
--size 0,0,0
 +
--direction_matrix 0,0,0,0,0,0,0,0,0
 +
${TEST_DATA}/MRHeadResampled.nhdr
 +
${TEMP}/ResampleVolume2Test.nhdr
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
 
ResampleVolume
 
ResampleVolume
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
--spacing 5,5,5
 +
--interpolation linear
 +
${TEST_DATA}/MRHeadResampled.nhdr
 +
${TEMP}/ResampleVolumeTest.nhdr
 
|-
 
|-
 
| style="background:#fa8072; color:black"|
 
| style="background:#fa8072; color:black"|
Line 354: Line 411:
 
|
 
|
 
|-
 
|-
−
| style="background:#fa8072; color:black"|
+
| style="background:#98fb98; color:black"|
 
Subtract
 
Subtract
 
|
 
|
−
<span style="color:#773333">None</span> (<span style="color:#fa8072">--help</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 +
${TEST_DATA}/CTHeadAxial.nhdr
 +
${TEST_DATA}/CTHeadAxialDoubled.nhdr
 +
${TEMP}/SubtractTest.nhdr
 
|-
 
|-
 
| style="background:#c0c0c0; color:black"|
 
| style="background:#c0c0c0; color:black"|
 
TestGridTransformRegistration
 
TestGridTransformRegistration
 
|
 
|
−
<span style="color:#c0c0c0">Smoke</span>
+
<span style="color:#000000">Smoke</span>
 
|
 
|
 
  --gridSize 5
 
  --gridSize 5
Line 372: Line 432:
 
VotingBinaryHoleFillingImageFilter
 
VotingBinaryHoleFillingImageFilter
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#98fb98">Regression</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 
  --radius 3,3,3  
 
  --radius 3,3,3  
Line 384: Line 444:
 
ZeroCrossingBasedEdgeDetectionImageFilter
 
ZeroCrossingBasedEdgeDetectionImageFilter
 
|
 
|
−
<span style="color:#ff0000">None</span> (<span style="color:#98fb98">Regression</span>)
+
<span style="color:#ff0000">None</span> (<span style="color:#00ff00">Regression</span>)
 
|
 
|
 
  ${TEST_DATA}/CTHeadResampled.nhdr
 
  ${TEST_DATA}/CTHeadResampled.nhdr

Latest revision as of 14:35, 9 January 2009

Home < 2009 Winter Project Week Command Line Program Testing
Return to Project Week Main Page



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.

Tests have been created for all of the command line programs in Applications/CLI (not including sub directories). Three types of tests exist:

  1. --help tests just run the command line program with the --help flag. These tests are as basic as a test can be. All they really test is whether or not the command line program can build, link and report help.
  2. Smoke tests run the program put do not check the results of the program. These are one step above the --help tests and should be the minimum test for each program.
  3. Regression tests run the program and compare the resulting output with a baseline output. Currently only image regression testing is available. Each command line program that produces an image should have a regression test.

Documentation: Slicer3 Execution Model Testing



Status

Starting (current) status:

  1. 5 (20) regression tests
  2. 3 (9) smoke tests
  3. 30 (9) with no tests

During Project Week, I'll work with those folks responsible for programs whose status is untested.

The table shows each command line program and its testing status. Under Test Type, the item in parentheses is a test that has been added as part of this project. Even the untested programs have at a minimum test that runs the program with --help. We still consider these programs untested since every CLP program responds to --help. However, at least these test programs can link and run.

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 (Smoke) 

${TEST_DATA}/CTHeadAxialDicom
${TEMP} CTHeadAxialFromDicom.nhdr

DiffusionTensorEstimation

None (Smoke) 

--otsuomegathreshold 0.5
${MRML_TEST_DATA}/helix-DWI.nhdr
${TEMP}/DiffusionTensorEstimationTest_dti.nhdr
${TEMP}/DiffusionTensorEstimationTest_baseline.nhdr
${TEMP}/DiffusionTensorEstimationTest_otsu.nhdr

DiffusionTensorMathematics

None (Smoke) 

--enumeration FractionalAnisotropy
${MRML_TEST_DATA}/helix-DWI.nhdr
${TEMP}/DiffusionTensorMathematicsTest.nhdr

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

FreesurferSurfaceSectionExtraction

None (--help)

GaussianBlurImageFilter

Regression 

--sigma 2.5
${TEST_DATA}/CTHeadAxial.nhdr
${TEMP}/GaussianBlurImageFilterTest.nhdr

GradientAnisotropicDiffusion

None (Regression) 

--conductance 2
--timeStep 0.0625
--iterations 2
${TEST_DATA}/MRHeadResampled.nhdr
${TEMP}/GradientAnisotropicDiffusionTest.nhdr

GrayscaleFillHoleImageFilter

None (Regression) 

${TEST_DATA}/MRHeadResampled.nhdr
${TEMP}/GrayscaleFillHoleTest.nhdr

GrayscaleGrindPeakImageFilter

None (Regression) 

${TEST_DATA}/MRHeadResampled.nhdr
${TEMP}/GrayscaleGrindPeakTest.nhdr

GrayscaleModelMaker

None (Smoke) 

--threshold 300
--name CTFace
--smooth 15
--decimate 0.95
--splitnormals
--pointnormals
${TEST_DATA}/CTHeadAxial.nhdr
${TEMP}GrayscaleModelMakerTest.vtp

HistogramMatching

None (Regression) 

--numberOfHistogramLevels 64
--numberOfMatchPoints 10
${TEST_DATA}/CTHeadAxial.nhdr
${TEST_DATA}/MRHeadResampled.nhdr

ImageLabelCombine

None (--help)

ImageReadDicomWrite

None (Regression) 

--patientName Austrialian
--patientID 8775070
--patientComments "A volunteer"
--studyID 123456
--studyDate 20090102
--studyComments Resampled
--studyDescription None
--modality CT
--manufacturer "GE Medical Systems"
--model CT8800
--seriesNumber 123456
--seriesDescription None
--dicomDirectory ${TEMP}
--dicomPrefix CTHeadAxialDicom
${TEST_DATA}/CTHeadAxial.nhdr

LabelMapSmoothing

None (Regression) 

--labelToSmooth 1
--numberOfIterations 50
--maxRMSError 0.01
--gaussianSigma 3
${TEST_DATA}/CTHeadResampledOtsuSegmented.nhdr
${TEMP}/LabelMapSmoothingTest.nhdr

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 (Regression) 

--insideValue 0
--outsideValue 255
--numberOfBins 128 
${TEST_DATA}/CTHeadResampled.nhdr
${TEMP}/OtsuThresholdImageFilterTest.nhdr

OtsuThresholdSegmentation

None (Regression) 

--brightObjects
--numberOfBins 128
--faceConnected
--minimumObjectSize 1000
${TEST_DATA}/CTHeadResampled.nhdr
${TEMP}/OtsuThresholdSegmentationTest.nhdr

ProbeVolumeWithModel

None (--help)

ResampleVolume2

None (Regression) 

--Reference ${TEST_DATA}/MRHeadResampled.nhdr
--number_of_thread 0
--transform_matrix 1,0,0,0,1,0,0,0,1,0,0,0
--transform rt
--space LPS
--interpolation linear
--window_function c
--spline_order 3
--spacing 0,0,0
--size 0,0,0
--direction_matrix 0,0,0,0,0,0,0,0,0
${TEST_DATA}/MRHeadResampled.nhdr
${TEMP}/ResampleVolume2Test.nhdr

ResampleVolume

None (Regression) 

--spacing 5,5,5
--interpolation linear
${TEST_DATA}/MRHeadResampled.nhdr 
${TEMP}/ResampleVolumeTest.nhdr

RigidRegistration

None (--help)

Subtract

None (Regression) 

${TEST_DATA}/CTHeadAxial.nhdr
${TEST_DATA}/CTHeadAxialDoubled.nhdr
${TEMP}/SubtractTest.nhdr

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

None (Regression) 

${TEST_DATA}/CTHeadResampled.nhdr
${TEMP}/ZeroCrossingBasedEdgeDetectionImageFilterTest.nhdr
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