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 and yes | yes and yes | Sebastien Barre |
| ?? | Welcome | complete | yes and yes | yes and yes | Wendy Plesniak |
| ?? | 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 | yes and yes | yes and yes | Steve Pieper |
| ?? | ROI Module | complete | no and yes | yes and yes | Alex Yarmarkovich |
| ?? | Volume Rendering | complete | yes and yes | yes and yes | Yanling Liu |
| ?? | PET/CT Fusion | complete | yes and yes | yes and yes | Wendy Plesniak |
Application CLI Modules
Version of 04-29-2010
Slicer 3.6 QA table 2010 04 29
Version of 05-2010
Part A
| Score | Name[1] | Documentation | Help [2] | Acknowledgment [3] | Test coverage [4] | valgrind errors | Current Owner | Comments [5] | - | 2Silver | ACPC Transform | complete | yes and yes | yes and yes | 75% | 1 | Nicole Aucoin | same | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1Gold | Add Images | complete | yes and yes | yes and yes | 84.9% | 0 | Bill Lorensen | AddImages | ||||||||||||
| 4Clay | Affine registration (Fast Affine Registration ?) | complete | yes and no | yes and yes | 68.4% | 82 | Daniel Blezek | same | ||||||||||||
| BRAINSDemonWarp | complete | yes and no | yes and no | 78.4% | Unknown | Hans Johnson, Greg Harris | same | |||||||||||||
| BRAINSFit | complete | yes and yes | yes and yes | 73.3% | Unknown | Eun Young Kim | same | |||||||||||||
| 6Hazard | BRAINSResample | no | yes and yes | yes and no | 76.7% | Unknown | Hans Johnson | same | ||||||||||||
| 6Hazard | BRAINSROIAuto | no | yes and no | yes and no | xx | Unknown | Hans Johnson | same | ||||||||||||
| 6Hazard | BRAINSVectorDemonWarping | no | yes and no | yes and no | xx | Unknown | Hans Johnson | same | ||||||||||||
| 5Coal | Cast Image | complete | yes and yes | yes and yes | 24.1% | 0 | Nicole Aucoin | Cast Image | ||||||||||||
| 3Bronze | CheckerBoard Filter | complete | yes and yes | yes and yes | 67.4% | 0 | Bill Lorensen | CheckerBoard Filter | ||||||||||||
| 5Coal | Create a DICOM Series | complete | yes and yes | yes and yes | 86.1% | 124 | Bill Lorensen | Create a Dicom Series | ||||||||||||
| 3Bronze | Curvature Anisotropic Diffusion | complete | yes and yes | yes and yes | 64.3% | 0 | Bill Lorensen | same | ||||||||||||
| Deformable BSpline registration | complete | yes and yes | yes and yes | 82.3% | xx | Bill Lorensen | Fast Nonrigid BSpline Registration | |||||||||||||
| 5Coal | Dicom to Nrrd Converter | complete | yes and yes | yes and yes | 35.8% | 0 | Xiaodong Tao | same | ||||||||||||
| 2Silver | Diffusion Tensor Estimation | complete | yes and no | yes and yes | 79.7% | 9 | CF Westin | same | ||||||||||||
| 6Hazard | Diffusion Tensor Scalar Measurements | no | yes and no | yes and yes | 56.2% | 5 | CF Westin | Diffusion Tensor Scalar Measurements | ||||||||||||
| EMSegment BatchMake | complete | yes and yes | yes and yes | TBF | TBF | Stephen Aylward, Brad Davis, Julien Jomier, Julien Finet | Batch Processing not in 3.6 RC2? | EMSegmentBatch | ||||||||||||
| EMSegment Command-line | complete | yes and yes | yes and yes | TBF | TBF | Kilian Pohl | documentation link in xml/GUI needs revising | same | ||||||||||||
| EMSegment Simple | complete | yes and yes | yes and yes | TBF | TBF | Kilian Pohl | EMSegmenter | |||||||||||||
| 6Hazard | Execution Model Tour | no | yes and yes | yes and yes | 88.2% | 0 | Daniel Blezek, Bill Lorensen | No 3.6 documentation (3.4 only) | same | |||||||||||
| 6Hazard | Extract Skeleton | no | yes and no | no and yes | 0.0% | Unknown | Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward | same | ||||||||||||
| Gaussian Blur BatchMake | complete | yes and yes | yes and yes | TBF | TBF | Julien Jomier, Stephen Aylward | Batch Processing not in 3.6 RC2? | GaussianBlurBatch | ||||||||||||
| 4Clay | Gaussian Blur | complete | yes and no | yes and yes | 55.9% | 0 | Julien Jomier, Stephen Aylward | same | ||||||||||||
| 3Bronze | Gradient Anisotropic Diffusion | complete | yes and yes | yes and yes | 63.4% | 0 | Bill Lorensen | GradientAnisotropicFilter | ||||||||||||
| 4Clay | Grayscale Fill Hole | complete | yes and yes | yes and yes | 57.1% | 0 | Bill Lorensen | same | ||||||||||||
| 3Bronze | Grayscale Grind Peak | complete | yes and yes | yes and yes | 64.5% | 0 | Bill Lorensen | same | ||||||||||||
| 1Gold | Grayscale Model Maker | complete | yes and yes | yes and yes | 82.1% | 0 | Bill Lorensen | same | ||||||||||||
| 3Bronze | Histogram Matching | complete | yes and yes | yes and yes | 65% | 0 | Bill Lorensen, Xiaodong Tao | same | ||||||||||||
| 5Coal | Image Label Combine | complete | yes and yes | yes and yes | 7.5% | 50 | Alex Yarmarkovich | same | ||||||||||||
| Joint Rician LMMSE Image Filter | complete | yes and yes | yes and yes | TBF | TBF | Antonio Tristán Vega, Santiago Aja-Fernandez | same | |||||||||||||
| Labelmap Seeding | complete | yes and yes | yes and yes | TBF | TBF | Raul San Jose Estepar | Label Seeding | |||||||||||||
| 6Hazard | Label Map Smoothing | no | yes and no | yes and yes | TBF | TBF | Dirk Padfield, Josh Cates, Ross Whitaker | same | ||||||||||||
| 6Hazard | Linear registration | no | yes and no | yes and yes | 66.7% | 45 | Daniel Blezek | sum of all errors from LinearRegistrationTest<n> tests | same |
- ↑ list produced with the script Slicer3/Scripts/generateListOfModules.sh
- ↑ 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
- ↑ https://www.slicer.org/wiki/Documentation-3.6
Part B
| Score | Name[1] | Documentation | Help [2] | Acknowledgment [3] | Test coverage [4] | valgrind errors | Current Owner | Comments [5][6] | - | 1Gold | Mask Image | complete | yes and yes | yes and yes | 82% | 0 | Nicole Aucoin | same | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4Clay | Median Filter | complete | yes and yes | yes and yes | 57% | 0 | Bill Lorensen | same | |||||||||||
| 1Gold | Merge Models | complete | yes and yes | yes and yes | 87% | 0 | Nicole Aucoin | same | |||||||||||
| 5Coal | Mesh Contour Segmentation | complete | yes and yes | yes and yes | 5.1% | 0 | Peter Karasev | same | |||||||||||
| 5Coal | Model Maker | complete | yes and yes | yes and yes | 41% | 0 | Nicole Aucoin | same | |||||||||||
| MRI Bias Field Correction | complete | yes and yes | yes and yes | 71% | TBF | Sylavin Jaume | same | ||||||||||||
| 5Coal | Multiple models example | no | yes and no | yes and yes | 2.5% | 50 | Bill Lorensen | n/a | |||||||||||
| 1Gold | Multiply Images | complete | yes and yes | yes and yes | 80% | 0 | Harini Veeraraghavan | same | |||||||||||
| 1Gold | N4ITK MRI Bias correction | complete | yes and yes | yes and yes | 84% | 0 | Andriy Fedorov | same | |||||||||||
| 1Gold | Orient Images | complete | yes and yes | yes and yes | 88% | 0 | Xiaodong Tao | same | |||||||||||
| 1Gold | Otsu Threshold Segmentation | complete | yes and no | yes and yes | 91% | 0 | Bill Lorensen | same | |||||||||||
| 1Gold | Otsu Threshold | complete | yes and no | yes and yes | 100% | 0 | Bill Lorensen | same | |||||||||||
| 1Gold | PolyData To Label Map | complete | yes and yes | yes and yes | 89% | 0 | Xiaodong Tao, Nicole Aucoin | same | |||||||||||
| 6Hazard | Register Images BatchMake | complete | yes and yes | yes and yes | TBF | TBF | Julien Finet, Stephen Aylward | no testing script found in Slicer3-build/bin | Register Images batch | ||||||||||
| 6Hazard | Register Images MultiRes (Experimental) | complete | yes and yes | yes and yes | 49.5% | TBF | Casey Goodlett | no testing script found in Slicer3-build/bin | Robust Multiresolution Affine Registration | ||||||||||
| 6Hazard | Register Images | complete | yes and yes | yes and yes | 0% | TBF | Casey Goodlett | no testing script found in Slicer3-build/bin | Expert Automated Registration | ||||||||||
| 5Coal | Resample DTI Volume | complete | yes and yes | yes and yes | 41% | 0 | Francois Budin | same | |||||||||||
| 5Coal | Resample Scalar/Vector/DWI Volume | complete | yes and yes | yes and yes | 43% | 0 | Francois Budin | same | |||||||||||
| Resample Scalar Volume BatchMake | complete | yes and yes | yes and yes | TBF | TBF | Julien Finet | no testing script found in Slicer3-build/bin | Resample Volume batch | |||||||||||
| 6Hazard | Rician LMMSE Image Filter | complete | yes and no | yes and yes | 20.5% | TBF | Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer | no testing script found in Slicer3-build/bin | same | ||||||||||
| 3Bronze | Rigid registration | complete | yes and yes | yes and yes | 61% | 0 | Jim Miller | Fast Rigid Registration | |||||||||||
| 6Hazard | Robust Statistics Segmentation | complete | yes and yes | yes and yes | 82.3% | TBF | Yi Gao | no testing script found in Slicer3-build/bin | RobustStatisticsSeg | ||||||||||
| 6Hazard | ROISelect | complete | yes and no | yes and yes | TBF | TBF | Lauren O'Donnell | no testing script found in Slicer3-build/bin | same | ||||||||||
| 6Hazard | Simple DWI IO Test | no | yes and no | yes and yes | TBF | TBF | Raul San Jose | no testing script found in Slicer3-build/bin | n/a | ||||||||||
| 6Hazard | Simple IO Test | no | yes and no | yes and yes | TBF | TBF | Bill Lorensen | no testing script found in Slicer3-build/bin | n/a | ||||||||||
| 6Hazard | Simple region growing | complete | yes and no | yes and yes | TBF | TBF | Jim Miller, Harini Veeraraghavan | no testing script found in Slicer3-build/bin | same | ||||||||||
| 2Silver | Subtract Images | complete | yes and yes | yes and yes | 76% | 0 | Harini Veeraraghavan | same | |||||||||||
| 6Hazard | Test GridTransform registration | no | yes and no | yes and yes | 100% | 0 | Yinglin Lee | same | |||||||||||
| 4Clay | Threshold Image | complete | yes and yes | yes and yes | 59% | 0 | Nicole Aucoin | same | |||||||||||
| 6Hazard | Transform From Fiducials | complete | yes and yes | yes and yes | TBF | TBF | Casey Goodlett | no testing script found in Slicer3-build/bin | same | ||||||||||
| 6Hazard | Unbiased Non Local Means filter for DWI | complete | yes and no | yes and yes | 20.5% | TBF | Antonio Tristán Vega, Santiago Aja-Fernandez | no testing script found in Slicer3-build/bin | same | ||||||||||
| 1Gold | Voting Binary Hole Filling | complete | yes and yes | yes and yes | 100% | 0 | Jim Miller | same |
- ↑ list produced with the script Slicer3/Scripts/generateListOfModules.sh
- ↑ 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
- ↑ Valgrind errors determined through use of runValgrindForOneModule.sh script in Slicer3-build/Scripts directory; dependent upon module testing script being found in Slicer-3-build/bin/ directory
- ↑ https://www.slicer.org/wiki/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.
More information:
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.
