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
?? 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
  1. including link to website documentation
  2. including name of author and of supervisor

Application CLI Modules

Version of 04-29-2010

Slicer 3.6 QA table 2010 04 29

Version of 05-2010

Part A

Slicer 3.6 Quality Assurance
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
  1. list produced with the script Slicer3/Scripts/generateListOfModules.sh
  2. including link to website documentation
  3. including name of author and of supervisor
  4. in % for non-interactive part
  5. Test coverage percentage determined by: [# lines code covered / total # lines of code (covered and non-covered) *100] of relevant .cxx and .h files
  6. http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6

Part B

Slicer 3.6 Quality Assurance
Score Name[1] Documentation Help [2] Acknowledgment [3] Test coverage [4] valgrind errors Current Owner Comments [5] 3.6 Documentation Name [6]
Mask Image complete yes and yes yes and yes 82% TBF Nicole Aucoin same
Median Filter complete yes and yes yes and yes 57% TBF Bill Lorensen same
Merge Models complete yes and yes yes and yes 87% TBF Nicole Aucoin same
Mesh Contour Segmentation complete yes and yes yes and yes TBF TBF Peter Karasev same
Model Maker complete yes and yes yes and yes 41% TBF Nicole Aucoin same
MRI Bias Field Correction complete yes and yes yes and yes 71% TBF Sylavin Jaume same
Multiple models example no yes and no yes and yes 2.5% TBF Bill Lorensen n/a
Multiply Images complete yes and yes yes and yes 80% TBF Harini Veeraraghavan same
N4ITK MRI Bias correction complete yes and yes yes and yes TBF TBF Andriy Fedorov same
Orient Images complete yes and yes yes and yes 88% TBF Xiaodong Tao same
Otsu Threshold Segmentation complete yes and no yes and yes 91% TBF Bill Lorensen same
Otsu Threshold complete yes and no yes and yes 100% TBF Bill Lorensen same
PolyData To Label Map complete yes and yes yes and yes 89% TBF Xiaodong Tao, Nicole Aucoin same
Register Images BatchMake complete yes and yes yes and yes TBF TBF Julien Finet, Stephen Aylward Register Images batch
Register Images MultiRes (Experimental) complete yes and yes yes and yes TBF TBF Casey Goodlett Robust Multiresolution Affine Registration
Register Images complete yes and yes yes and yes TBF TBF Casey Goodlett Expert Automated Registration
Resample DTI Volume complete yes and yes yes and yes 100% TBF Francois Budin same
Resample Scalar/Vector/DWI Volume complete yes and yes yes and yes 43% TBF Francois Budin same
Resample Scalar Volume BatchMake complete yes and yes yes and yes TBF TBF Julien Finet Resample Volume batch
Rician LMMSE Image Filter complete yes and no yes and yes TBF TBF Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer same
Rigid registration complete yes and yes yes and yes 61% TBF Jim Miller Fast Rigid Registration
Robust Statistics Segmentation complete yes and yes yes and yes TBF 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
Subtract Images complete yes and yes yes and yes 76% TBF Harini Veeraraghavan same
Test GridTransform registration no yes and no yes and yes 100 TBF Yinglin Lee n/a
Threshold Image complete yes and yes yes and yes 59% TBF 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 TBF TBF Antonio Tristán Vega, Santiago Aja-Fernandez same
Voting Binary Hole Filling complete yes and yes yes and yes 100% TBF Jim Miller same
  1. list produced with the script Slicer3/Scripts/generateListOfModules.sh
  2. including link to website documentation
  3. including name of author and of supervisor
  4. in % for non-interactive part
  5. Test coverage percentage determined by: [# lines code covered / total # lines of code (covered and non-covered) *100] of relevant .cxx and .h files
  6. 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:

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.