Slicer-3.6-QA
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- This page contains our assessment of the Slicer 3.6 modules
- See also the module culling event at the end of April 2010
Contents
Testing Status
Core Modules
| 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 |
Application CLI Modules
| 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 | ||
| 7?? | RegisterImages (RegisterImagesMultiRes) | complete | yes and yes | yes and yes | 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/ | ||
| 7?? | BRAINSDemonWarp | complete | yes and no | yes and no | 0.0% | Unknown | Hans Johnson, Greg Harris | same | ||
| 7?? | BRAINSFit | complete | yes and yes | yes and yes | 0.0% | Unkown | Eun Young Kim | same | ||
| 7?? | 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 | ||
| 7?? | EMSegment BatchMake | complete | yes and yes | yes and yes | 0.0% | Unknown | Julien Jomier, Stephen Aylward, Brad Davis | EM Segmenter batch | ||
| 7?? | Gaussian Blur BatchMake | complete | yes and yes | yes and yes | 0.0% | Unknown | Julien Jomier, Stephen Aylward, Julien Finet | Gaussian Blur batch | ||
| 7?? | RegisterImages BatchMake | complete | yes and yes | yes and yes | 0.0% | Unknown | Stephen Aylward, Julien Finet | Register Images batch | ||
| 7?? | 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 | ||
| 7?? | ResampleDTIVolume | complete | yes and yes | yes and yes | 37.0% | 0 | Francois Budin | same | ||
| 7?? | Rician LMMSE Image Filter | complete | yes and no | yes and yes | 0.0% | Unknown | Antonio Tristan Vega, Santiago Aja Fernandez, Marc Niethammer | same | ||
| 7?? | 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 | ||
| 7?? | 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 | Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward | n/a | |||
| 7?? | MRI Bias Field Correction | complete | yes and yes | yes and yes | 0 | Sylvain Jaume | same | |||
| 6Hazard | N4ITK MRI Bias Correction | no | yes and no | yes and yes | 0 | Nick Tustison, Andriy Fedorov | same | |||
| 7?? | ACPC Transform | complete | yes and yes | yes and yes | 0 | Nicole Aucoin | same | |||
| 7?? | Mesh Contour Segmentation | complete | yes and yes | yes and yes | 0 | Peter Karasev, Karol Chudy, Allen Tannenbaum | same | |||
| 6Hazard | Utah BSpline Deformable registration | no | yes and no | yes and yes | 0 | Sam Gerber, Jim Miller, Steve Pieper, Ross Whitaker | n/a | |||
| 6Hazard | Calculate Volume Statistics | no | no | no | 0 | Tri Ngo | n/a | |||
| 6Hazard | Generate Connectivity Map | no | no | no | 0 | Tri Ngo | n/a | |||
| 6Hazard | ROI Tract Filter | no | no | no | 0 | Tri Ngo | n/a | |||
| 6Hazard | Stochastic Tractography Filter | no | no | no | 0 | Tri Ngo | n/a | |||
| 6Hazard | MIDAS Data and Slicer Tutorials | no | yes and no | yes and no | 0 | Patrick Reynolds, Stephen Aylward | n/a |
- ↑ including link to website documentation
- ↑ including name of author and of supervisor
- ↑ in % for non-interactive part
- ↑ Test coverage percentage determined by: [# lines code covered / total # lines of code (covered and non-covered) *100] of relevant .cxx and .h files
- ↑ 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:
| 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.
