Slicer-3.6-QA

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  • This page contains our assessment of the Slicer 3.6 modules

Testing Status

Core Modules

Slicer 3.6 Quality Assurance
Score Name Documentation Help [1] Acknowledgment [2] Current Owner
?? Camera complete yes, no link no Sebastien Barre
?? Volumes complete yes and yes yes and yes Steve Pieper
?? Diffusion Editor complete yes and yes no CF Westin
?? Models complete yes and yes yes and yes Alex Yarmarkovich
?? Measurements complete yes and yes yes and yes Nicole Aucoin
?? Fiducials complete yes and yes yes and yes Nicole Aucoin
?? Data complete yes and yes yes and yes Steve Pieper
?? Slices complete yes and yes yes and yes Jim Miller
?? Colors complete yes and yes yes and yes Nicole Aucoin
?? Interactive Editor complete no and yes yes and no Steve Pieper
?? ROI Module complete no and yes no and yes Alex Yarmarkovich
?? Volume Rendering complete yes and yes no and yes Yanling Liu
?? PET/CT Fusion complete yes and yes yes and yes Wendy Plesniak
  1. including link to website documentation
  2. including name of author and of supervisor

Application CLI Modules

Slicer 3.6 Quality Assurance
Score Name Documentation Help [1] Acknowledgment [2] Test coverage [3] valgrind errors Current Owner Comments [4] 3.6 Documentation Name [5]
1Gold my module complete yes and yes yes, yes, yes 80% 0
6Hazard DiffusionWeightedTest no no yes and yes 69.8% 0 CF Westin n/a
2Silver DiffusionTensorEstimation complete yes and no yes and yes 79.7% 9 CF Westin same
6Hazard DiffusionTensorMathematics no yes and no yes and yes 56.2% 5 CF Westin Diffusion Tensor Scalar Measurements
1Gold OrientImage complete yes and yes yes and yes 85.7% 0 Bill Lorensen OrientImages
3Bronze LinearRegistration complete yes and no yes and yes 66.7% 4 Daniel Blezek same
5Coal RigidRegistration complete yes and yes yes and yes 1.0% 92 Daniel Blezek same
1Gold RegisterImages (RegisterImagesMultiRes) complete yes and yes yes and yes 83.5% Unknown Casey Goodlett, Stephen Aylward same
5Coal Fast Affine Registration complete yes and no yes and yes 1.4% 82 Daniel Blezek same
1Gold BSplineDeformableRegistration complete yes and yes yes and yes 82.3% 6 Bill Lorensen Fast Nonrigid BSpline Registration
6Hazard TestGridTransformRegistration no no yes and yes 90.7% 0 Yinglin Lee n/a
3Bronze CheckerBoard complete yes and yes yes and yes 67.4% 0 Bill Lorensen CheckerBoard Filter
4Clay ResampleVolume complete yes and yes yes and yes 57.1% 0 Bill Lorensen same
6Hazard PolyDataToLabelmap no yes and yes yes and yes 87.9% 0 Nicole Aucoin, Xiaodong Tao n/a
4Clay GaussianBlurImageFilter complete yes and no yes and yes 55.9% 0 Julien Jomier, Stephen Aylward Gaussian Blur
1Gold ConfidenceConnected complete yes and no yes and yes 87.5% 0 Jim Miller Simple region growing
6Hazard ExecutionModelTour no yes and yes yes and yes 87.2% 0 Daniel Blezek, Bill Lorensen n/a
6Hazard ImageReadDicomWrite no yes and yes yes and yes 86.1% 0 Bill Lorensen Create a Dicom Series
3Bronze CurvatureAnisotropicDiffusion complete yes and yes yes and yes 64.3% 0 Bill Lorensen same
3Bronze GradientAnisotropicDiffusion complete yes and yes yes and yes 63.4% 0 Bill Lorensen GradientAnisotropicFilter
4Clay MedianImageFilter complete yes and yes yes and yes 51.1% 0 Bill Lorensen same
3Bronze HistogramMatching complete yes and yes yes and yes 65.0% 0 Bill Lorensen same
6Hazard OtsuThresholdImageFilter no yes and yes yes and yes 100% 0 Bill Lorensen OtsuThreshold
1Gold OtsuThresholdSegmentation complete yes and no yes and yes 90.9% 0 Bill Lorensen same
2Silver Subtract complete yes and yes yes and yes 71.7% 0 Bill Lorensen SubtractImages
6Hazard Multiply no yes and no yes and yes 77.6% 0 Bill Lorensen n/a
1Gold Add complete yes and yes yes and yes 84.9% 0 Bill Lorensen AddImages
3Bronze Threshold complete yes and no yes and yes 55.8% 0 Nicole Aucoin ThresholdImage
1Gold Mask complete yes and no yes and yes 80.0% 0 Nicole Aucoin Mask Image
5Coal Cast complete yes and no yes and yes 14.6% 0 Nicole Aucoin Cast Image
1Gold VotingBinaryHoleFillingImageFilter complete yes and yes yes and yes 100% 0 Bill Lorensen Voting Binary Hole Filling
4Clay ModelMaker complete yes and yes yes and yes 57.4% 1 Nicole Aucoin same
6Hazard MultipleModelsExample no yes and no yes and yes 1.9% 50 Nicole Aucoin n/a
6Hazard GrayscaleModelMaker no yes and no yes and yes 82.1% 1 Bill Lorensen same
6Hazard MergeModels no yes and yes yes and yes 62.7% 0 Nicole Aucoin, Daniel Haehn same
4Clay GrayscaleFillHoleImageFilter complete yes and yes yes and yes 57.1% 0 Bill Lorensen Grayscale Fill Hole
3Bronze GrayscaleGrindPeakImageFilter complete yes and yes yes and yes 64.5% 0 Bill Lorensen Grayscale Grind Peak
6Hazard LabelMapSmoothing no yes and no yes and yes 87.9% 0 Dirk Padfield, Josh Cates, Ross Whitaker n/a
5Coal ImageLabelCombine complete yes and no yes and no 7.5% 50 Alex Yarmarkovich same
6Hazard ResampleVolume2 no yes and yes yes and yes 46.8% 0 Francois Budin Resample Scalar/Vector/DWI Volume
6Hazard ZeroCrossingBasedEdgeDetectionImageFilter no yes and no yes and yes 62.5% 0 Elliot Uvero n/a
6Hazard FreesurferSurfaceSectionExtraction no yes and no yes and yes 60.0% 62 Sylvain Bouix n/a/
6Hazard BRAINSDemonWarp complete yes and no yes and no 0.0% Unknown Hans Johnson, Greg Harris same
6Hazard BRAINSFit complete yes and yes yes and yes 0.0% Unkown Eun Young Kim same
6Hazard BRAINSMush complete no no 0.0% Unknown Hans Johnson same
6Hazard BRAINSResample no yes and yes yes and no 0.0% Unknown Hans Johnson n/a
6Hazard BRAINSROIAuto no yes and no yes and no 0.0% Unknown Hans Johnson n/a
6Hazard DiffusionTensorEstimation BatchMake no yes and no yes and no 0.0% Unknown Lauren O'Donnell n/a
6Hazard EMSegment BatchMake complete yes and yes yes and yes 0.0% Unknown Julien Jomier, Stephen Aylward, Brad Davis EM Segmenter batch
6Hazard Gaussian Blur BatchMake complete yes and yes yes and yes 0.0% Unknown Julien Jomier, Stephen Aylward, Julien Finet Gaussian Blur batch
6Hazard RegisterImages BatchMake complete yes and yes yes and yes 0.0% Unknown Stephen Aylward, Julien Finet Register Images batch
6Hazard ResampleScalarVolume BatchMake complete yes and yes yes and yes 0.0% Unknown Julien Finet Resample Volume batch
6Hazard Diffeomorphic Demons Algorithm no no yes and yes 0.0% Unknown Tom Vercauteren, Ender Konukoglu, Kilian Pohl n/a
5Coal ResampleDTIVolume complete yes and yes yes and yes 37.0% 0 Francois Budin same
6Hazard Rician LMMSE Image Filter complete yes and no yes and yes 0.0% Unknown Antonio Tristan Vega, Santiago Aja Fernandez, Marc Niethammer same
6Hazard Unbiased Non Local Means filter for DWI complete yes and no yes and yes 0.0% Unknown Antonio Tristán Vega, Santiago Aja-Fernandez n/a
6Hazard Joint Rician LMMSE Image Filter complete yes and no yes and yes 0.0% Unknown Antonio Tristán Vega, Santiago Aja Fernández same
6Hazard Extract Skeleton no yes and no no and yes 0.0% Unknown Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward n/a
6Hazard MRI Bias Field Correction complete yes and yes yes and yes 0.0% Unknown Sylvain Jaume same
6Hazard N4ITK MRI Bias Correction no yes and no yes and yes 0.0% Unknown Nick Tustison, Andriy Fedorov same
6Hazard ACPC Transform complete yes and yes yes and yes 0.0% Unknown Nicole Aucoin same
6Hazard Mesh Contour Segmentation complete yes and yes yes and yes 0.0% Unknown Peter Karasev, Karol Chudy, Allen Tannenbaum same
6Hazard Utah BSpline Deformable registration no yes and no yes and yes 0.0% Unknown Sam Gerber, Jim Miller, Steve Pieper, Ross Whitaker n/a
6Hazard Calculate Volume Statistics no no no 0.0% 0 Tri Ngo n/a
6Hazard Generate Connectivity Map no no no 0.0% Unknown Tri Ngo n/a
6Hazard ROI Tract Filter no no no 0.0% Unknown Tri Ngo n/a
6Hazard Stochastic Tractography Filter no no no 0.0% Unknown Tri Ngo n/a
6Hazard MIDAS Data and Slicer Tutorials no yes and no yes and no 0.0% Patrick Reynolds, Stephen Aylward n/a
  1. including link to website documentation
  2. including name of author and of supervisor
  3. in % for non-interactive part
  4. Test coverage percentage determined by: [# lines code covered / total # lines of code (covered and non-covered) *100] of relevant .cxx and .h files
  5. http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6

Testing Partition

Most Slicer modules have a GUI component and a Data Processing component.

Testing GUI components is still a challenge, so we will focus here on testing the Data Processing components. This can be done in most cases by partitioning the module into a GUI section and a Data Processing section, where the second one usually takes the form of a C++ class (although that is not a requirement).

The data processing section can be tested by using standard CTest/CMake mechanisms. Basically by adding ADD_TEST() entries to the CMakeLists.txt file of the module.

Luis Ibanez' scoring system

The following scoring will be applied to the data processing sections of all modules:

Slicer 3.6 Quality Assurance Scoring
Score Code Coverage Valgrind Errors Documentation Tutorial
1Gold > 80% 0 yes yes
2Silver > 70% < 10 yes yes
3Bronze > 60% < 50 yes yes
4Clay > 50% < 100 yes yes
5Coal < 50% > 100 yes yes
6Hazard unknown unknown no no

The code coverage and Valgrind error must be the ones reported on the Nightly Slicer Dashboard. Anecdotal data is not acceptable.