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 |
| ?? | 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 | 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
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] | 3.6 Documentation Name [6] | |
|---|---|---|---|---|---|---|---|---|---|---|
| ACPC Transform | complete | yes and yes | yes and yes | 75% | 1 | Nicole Aucoin | same | |||
| Add Images | complete | yes and yes | yes and yes | 84.9% | 0 | Bill Lorensen | AddImages | |||
| 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 | |||
| BRAINSResample | no | yes and yes | yes and no | 76.7% | Unknown | Hans Johnson | n/a | |||
| BRAINSROIAuto | no | yes and no | yes and no | xx | Unknown | Hans Johnson | n/a | |||
| BRAINSVectorDemonWarping | no | yes and no | yes and no | xx | Unknown | Hans Johnson | n/a | |||
| Cast Image | complete | yes and yes | yes and yes | 24.1% | XX | Nicole Aucoin | Cast Image | |||
| CheckerBoard Filter | complete | yes and yes | yes and yes | 67.4% | xx | Bill Lorensen | CheckerBoard Filter | |||
| Create a DICOM Series | complete | yes and yes | yes and yes | 86.1% | xx | Bill Lorensen | Create a Dicom Series | |||
| Curvature Anisotropic Diffusion | complete | yes and yes | yes and yes | 64.3% | XX | Bill Lorensen | same | |||
| Deformable BSpline registration | complete | yes and yes | yes and yes | 82.3% | xx | Bill Lorensen | Fast Nonrigid BSpline Registration | |||
| Dicom to Nrrd Converter | 35.8% | xx | ?? | |n/a | ||||||
| Diffusion Tensor Estimation | complete | yes and no | yes and yes | 79.7% | 9 | CF Westin | same | |||
| Diffusion Tensor Scalar Measurements | no | yes and no | yes and yes | 56.2% | 5 | CF Westin | Diffusion Tensor Scalar Measurements | |||
| EMSegment BatchMake | TBF | TBF | author | |n/a | ||||||
| EMSegment Command-line | TBF | TBF | author | |n/a | ||||||
| EMSegment Simple | TBF | TBF | author | |n/a | ||||||
| Execution Model Tour | TBF | TBF | author | |n/a | ||||||
| Extract Skeleton | no | yes and no | no and yes | 0.0% | Unknown | Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward | n/a | |||
| Gaussian Blur BatchMake | TBF | TBF | author | |n/a | ||||||
| Gaussian Blur | complete | yes and no | yes and yes | 55.9% | 0 | Julien Jomier, Stephen Aylward | Gaussian Blur | |||
| Gradient Anisotropic Diffusion | complete | yes and yes | yes and yes | 63.4% | 0 | Bill Lorensen | GradientAnisotropicFilter | |||
| Grayscale Fill Hole | complete | yes and yes | yes and yes | 57.1% | 0 | Bill Lorensen | Grayscale Fill Hole | |||
| Grayscale Grind Peak | complete | yes and yes | yes and yes | 64.5% | 0 | Bill Lorensen | Grayscale Grind Peak | |||
| Grayscale Model Maker | TBF | TBF | author | |n/a | ||||||
| Histogram Matching | TBF | TBF | author | |n/a | ||||||
| Image Label Combine | TBF | TBF | author | |n/a | ||||||
| Joint Rician LMMSE Image Filter | TBF | TBF | author | |n/a | ||||||
| Labelmap Seeding | TBF | TBF | author | |n/a | ||||||
| Label Map Smoothing | TBF | TBF | author | |n/a | ||||||
| Linear registration | TBF | TBF | author | |n/a |
- ↑ 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
- ↑ http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6
Part B
| Score | Name[1] | Documentation | Help [2] | Acknowledgment [3] | Test coverage [4] | valgrind errors | Current Owner | Comments [5][6] | 3.6 Documentation Name [7] |
|---|---|---|---|---|---|---|---|---|---|
| 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 | |
| Mesh Contour Segmentation | complete | yes and yes | yes and yes | 5.1% | TBF | Peter Karasev | same | ||
| 5Coal | Model Maker | complete | yes and yes | yes and yes | 41% | 0 | Nicole Aucoin | same | |
| 6Hazard | 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 | |
| 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 | |
| Register Images MultiRes (Experimental) | complete | yes and yes | yes and yes | TBF | TBF | Casey Goodlett | no testing script found in Slicer3-build/bin | Robust Multiresolution Affine Registration | |
| Register Images | complete | yes and yes | yes and yes | TBF | 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% | TBF | 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 | |
| Rician LMMSE Image Filter | complete | yes and no | yes and yes | 20.5% | TBF | Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer | same | ||
| 3Bronze | Rigid registration | complete | yes and yes | yes and yes | 61% | 0 | Jim Miller | Fast Rigid Registration | |
| Robust Statistics Segmentation | complete | yes and yes | yes and yes | 82.3% | TBF | Yi Gao | RobustStatisticsSeg | ||
| ROISelect | complete | yes and no | yes and yes | TBF | TBF | Lauren O'Donnell | same | ||
| Simple DWI IO Test | no | yes and no | yes and yes | TBF | TBF | Raul San Jose | n/a | ||
| Simple IO Test | no | yes and no | yes and yes | TBF | TBF | Bill Lorensen | n/a | ||
| Simple region growing | complete | yes and no | yes and yes | TBF | TBF | Jim Miller, Harini Veeraraghavan | same | ||
| 2Silver | Subtract Images | complete | yes and yes | yes and yes | 76% | 0 | Harini Veeraraghavan | same | |
| 1Gold | Test GridTransform registration | no | yes and no | yes and yes | 100% | 0 | Yinglin Lee | n/a | |
| 4Clay | Threshold Image | complete | yes and yes | yes and yes | 59% | 0 | Nicole Aucoin | same | |
| Transform From Fiducials | complete | yes and yes | yes and yes | TBF | TBF | Casey Goodlett | same | ||
| Unbiased Non Local Means filter for DWI | complete | yes and no | yes and yes | 20.5% | TBF | Antonio Tristán Vega, Santiago Aja-Fernandez | 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
- ↑ 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.
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.
