Slicer3:Transition Testing

This page will describe the current status of testing classes of slicer2.

Modules to test

The Piority one modules are:

• Base
• vtkTensorUtil (mathieu)
• vtkDTMRI (mathieu)
• vtkEMAtlasBrainClassifier (Katie)
• vtkEMLocalSegment (Katie)
• vtkFreeSurferReaders (Nicole)

Within each of those modules, each class has a priority rank from 0 (non important) to 5 (very important)

And then the status specify if the task is not done (default), partial, or completed

Base

Nicole will look at the base classes to determine which ones need tests.

Potential candidates classes

Test Name	Priority	Status	Description	Dependencies
	1	If kept, need rewrite because of the use of static var (cleanup not done properly)	See vtkPolyBoolean	vtkBoolTess
	0	This is a simple macro, could be merged in one place		vtkCellTriMacro
	1	A vtk version would be good - does it exist (endoscopy package)? Comment:Use of vtkShortArray explicitely, use of vtkStructuredPoints, Write function instead of pipeline to writer...	vtkPolyDataToImageStencil/vtkImageStencil	vtkDataSetToLabelMap
	3	Minor diff with current VTK implementation (uses vtkOBBTree internally) Change will not be merged in VTK since result is slower and produce error Generic Warning: In /home/mathieu/Dashboards/MyTests/ParaView/VTK/Common/vtkMath.cxx, line 717 vtkMath::Jacobi: Error extracting eigenfunctions	Hardware picking (backbuffer) would be better	vtkFastCellPicker
	1	not compatible with VTK 5 ?? - can be removed	VTK 5.x has shaders, nicer to use in this context	vtkFog
	1	not used? - can be removed	ITK has FastMarching with input a list of points (level set)	vtkImageBandedDistanceMap
	5	Would be good to keep or find ITK way Well written, clear	Separate population (~Otsu), stays in slicer	vtkImageBimodalAnalysis
	5	Needed for Editor Well written, clear (only short type supported)	Stays in Slicer	vtkImageConnectivity
	3	Could be replaced by vtk clases very slicer specific, should be rewritten with vtkImageData::DeepCopy	Stays in Slicer	vtkImageCopy
	3	Handy to keep	Compare to vtkImageCursor3D ??	vtkImageCrossHair2D
	3	Great if this were in vtk Need doc, remove FileName stuff, minor cleanup .. good to go !	Move to EMSegment (too specific)	vtkImageCurveRegion
	1	?	Move to EM	vtkImageDrawObjects
	1	Used for editor looks like vtkPolyDataToImageStencil+vtkImageStencil...	Stays in Slicer	vtkImageDrawROI
	1	Important for slicer2 editor compare to vtkImageContinuousErode3D	ITK has a fast erosion (ErodeMorphometric, single object)	vtkImageErode
	1	Important for slicer2 editor	Nice to merge with vtkImageDrawROI	vtkImageFillROI
	0	Is there a vtk class for this? vtkWindowToImageFilter or vtkRenderLargeImage	vtkWindowToImage	vtkImageFrameSource
	1		Move to EM	vtkImageGraph
	1	Used in Editor	vtkImageMathematics can do that (SetOperationToReplaceCByK)	vtkImageLabelChange
		Needed for slice display		vtkImageLabelOutline
		Editor		vtkImageLabelVOI
	0	Is there a vtk replacement?	might not be needed if switching to ITK	vtkImageNeighborhoodFilter
	0	Replace with something from KWWidgets? why not vtkXYPlotActor?	Use instead: vtkKWHistogram	vtkImagePlot
	0	Move to MRML		vtkImageRealtimeScan
	1	Needed for editor	ITK has a notion of itkPaste...	vtkImageReplaceRegion
	0	Could be dropped (maybe speedups can go to vtk?) Well written, a few bugs in comments can be use to extent vtkLoookupTable...		vtkIndirectLookupTable
	1	Can easily be added into vtkMath done	Outer product, rest should be vnl (be carefull with numerical recipe...)	vtkMathUtils
	0	Better to use std formate if possible	vtkPolyDataWriter (to write set of points)	vtkPTSWriter
	1	Would be great functionality to move to vtk compare it to vtkImageMathematics/vtkImageLogic? ITK?		vtkPolyBoolean
	0	no need		vtkSlicer
	0	no need		vtkSlicerBaseWin32Header
	3	Used for measure - does vtk have something like this? Looks like a patch vtkMassPropertiesdone (04/28/06)	Should enhance vtkMassProperties	vtkSurfaceProps
	0	for the Twin module??		vtkXDisplayWindow

---

Class being dropped

Test Name	Priority	Status	Description	Dependencies
	1	I don't think this is needed anymore - right	vtkEuclideanPlaneFit ?	vtkDistractorSource
	0	I dont think this is needed anymore Looks like vtkImageEuclideanDistance	old Oliver Cuisenaire class	vtkImageEuclideanDistanceTransformation
	0	Better to use a vtkPolyData	vtkPolyData	vtkPolygonList
	0	should be vtkPolyData	vtkPolyData	vtkStackOfPolygons

---

Class that might have a vtk replacement already

...with vtkImageReslice

Test Name	Priority	Status	Description	Dependencies
		could be ImageReslice		vtkImageCloseUp2D
		Could be a vtkImageReslice		vtkImageDouble2D
		Replace with vtkImageReslice		vtkImageReformat
		Replace with vtkImageReslice		vtkImageReformatIJK
		Should switch to vtkImageReslice		vtkImageResize
		vtkImageReslice		vtkImageZoom2D
		Why not use vtkImageReslice		vtkResliceImage

---

...with vtkImageAccumulate

Test Name	Priority	Status	Description	Dependencies
		Useful What is the diff with vtkImageAccumulate?	Simply pipe to a vtkImageCast	vtkImageAccumulateDiscrete
		Could be done with an accumulate		vtkImageMeasureVoxels
	3	Can move to vtkImageAccumulate. Done(04/27)	Need the NonZero option so can switch to vtkImageAccumulate or better switch to itk::Histogram	vtkImageStatistics

---

Test Name	Priority	Status	Description	Dependencies
		Why not reuse vtkDICOMImageReader?		vtkDCMLister
		Why not reuse vtkDICOMImageReader?		vtkDCMParser
		Why not reuse vtkDICOMImageReader?		vtkImageDICOMReader

---

...with vtkImageBlend

Test Name	Priority	Status	Description	Dependencies
	0	Will probably transition to vtkImageBlend	vtkImageBlend	vtkImageOverlay
	1	Done, VTK CVS has a completely rewritten from scratch vtkImageWeightedSum	Maybe could be vtkImageBlend? Need a patched vtkImageMathmatics (sa vtkImplicitSum)	vtkImageWeightedSum

---

Class specific for Slicer (Editor)

Test Name	Priority	Status	Description	Dependencies
		Important for slicer2 editor		vtkImageEditor
		Important for slicer2 editor		vtkImageEditorEffects

---

Class that will be moved to Module

Test Name	Priority	Status	Description	Dependencies
		Livewire -> Move to Module		vtkImageLiveWire
		Livewire -> Move to Module		vtkImageLiveWireEdgeWeits
		Livewire -> Move to Module		vtkImageLiveWireScale
		Livewire -> Move to Module		vtkImageLiveWireTester
		Move to a PhaseWire module		vtkImageDijkstra

---

MRML

Testing should be done by Alex.

vtkMrmlColorNode
vtkMrmlCrossSectionNode
vtkMrmlData
vtkMrmlDataTetraMe
vtkMrmlDataVolume
vtkMrmlDataVolumeReadWrite
vtkMrmlDataVolumeReadWriteStructuredPoints
vtkMrmlEndFiducialsNode
vtkMrmlEndHieraryNode
vtkMrmlEndModelGroupNode
vtkMrmlEndPaNode
vtkMrmlEndScenesNode
vtkMrmlEndTransformNode
vtkMrmlEndVolumeStateNode
vtkMrmlFiducialsNode
vtkMrmlHieraryNode
vtkMrmlLandmarkNode
vtkMrmlLocatorNode
vtkMrmlMatrixNode
vtkMrmlModelGroupNode
vtkMrmlModelNode
vtkMrmlModelRefNode
vtkMrmlModelStateNode
vtkMrmlNode
vtkMrmlOptionsNode
vtkMrmlPaNode
vtkMrmlPointNode
vtkMrmlSceneOptionsNode
vtkMrmlScenesNode
vtkMrmlSlicer
vtkMrmlTetraMeNode
vtkMrmlTransformNode
vtkMrmlTree
vtkMrmlVolumeNode
vtkMrmlVolumeReadWriteNode
vtkMrmlVolumeReadWriteStructuredPointsNode
vtkMrmlVolumeStateNode
vtkMrmlWindowLevelNode

vtkTensorUtil

Class Name	Priority	Status	Description	Dependencies
vtkBSplineInterpolateImageFunction	2	Partial (VTKTENSORUTIL.TestBSplineInterpolateImageFunction)	Interpolation of a image with a BSpline kernel. The class compute the interpolated value for a given specific location, then the image can be treated as an ImplicitFunction	Use in the PreciceStreamline process. This class is used by vtkPreciseHyperStreamline after being encapsulated in vtkTensorImplicitFunctionToFunctionSet
vtkImageGetTensorComponents	4		This class get each tensor component as a different vtkImageData	This class is used in the registration framework of the DTMRI module based on the framework provided by vtkAG module. One of the registration modalities is to register each tensor component as a input channel in the vtkAG multichannel tensor framework
vtkPreciseHyperPoint	2		This class is a helper class for the streamline method implemented by vtkPreciseHyperStreamline	vtkPreciseHyperStreamline
vtkSuperquadricTensorGlyph	5		Main class to perform glyph rendering	Directly invoke from the tcl script to set up the glyph rendering pipeline (DTMRIGlyphs.tcl)
vtkTensorMathematics	5		Main class to perform serveral scalar calculation from a tensor field	Directly invoke in DTMRICalculateScalars.tcl
vtkHyperPointandArray	4		Helper class to keep the state info of the streamline/tractography algorithm	Used by vtkHyperStreamlineDTMRI
vtkImageSetTensorComponents	4		Pack different image channels into a Tensor field.	Used in the registration framework.
vtkPreciseHyperStreamline	2		Streamer class to do tractography using the Higher Order Runge Kutta	This class relies on the BSpline Interpolation classes to have a precise interpolation of the tensor field, needed by the high order Runge Kutta
vtkTensorFlip	1		Helper class to flip a tensor field	I do not think is currently use in any pipeline process. However it is an interesting class to have just as a pure extension of vtkImageFlip
vtkVectorToOuterProductDualBasis	1		Class to compute the Dual basis of the outer product of a set of vectors	This helper class was originally used for the estimation of diffusion tensor using Dual basis. The Estimation class was update to rely on a simple SVD for the computation of the B-matrix. This class is going to suffer further changes in an attempt to use teem as a main tensor estimation engine.
vtkHyperStreamlineDTMRI	5		Main class to do DTI tractography in the Slicer. Overload part of the functionality of vtkHyperStreamline	Used by vtkSeedTracts.cxx in the DTMRI module.
vtkInteractiveTensorGlyph	5		Main class to do DTI glyph rendering in the Slicer (what is the diff with vtkSuperquadricTensorGlyph)	Direclty invoked in DTMRIGlyphs.tcl
vtkPreciseHyperStreamlinePoints	3		Helper class to keep the state info of PreciseHyperStreamline class	Used by vtkSeedTracts.cxx
vtkTensorImplicitFunctionToFunctionSet	3		Class to evaluate a tensor field at a given location	Used by vtkPreciseHyperStreamline when doing the integration
vtkHyperStreamlineTeem	2		Tractography class encapsulating teem tractography framework	Use by vtkSeedTracts. This class is still in alpha state.
vtkPreciseHyperArray	3		Helper class to keep PreciseHyperStreamline state	Used by vtkPreciseHyperStreamlinePoints
vtkSuperquadricSource2	5		Modification of the Superquadric class to implement the superquadric glyphs as published by Gordon (the two class should be merged)	Used by vtkSuperquadricTensorGlyph
vtkTensorMask	5		Mask a tensor field	Used in the visualization pipeline in the DTMRI module

vtkDTMRI

Class Name	Priority	Status	Description	Dependencies
vtkClusterTracts	5	Controller-type object to do Spectral clustering. This class take a Collecition of streamline and perform clustering upon user requests (The class is not a process object) although it could be designed in that sense. The design idea was to encapsulate clustering pipeline with that relies on itk::SpectralClustering (NAMIC sandbox)	Depends on itkSpectralClustering and vtkTractShapeFeatures
vtkColorROIFromPolyLines	3
vtkColorROIFromTracts	3
vtkDisplayTracts	5	Controller-type object that implement the visualization pipeline for the tracts/streamlines.	This class is used/managed by vtkMultipleStreamlineController
vtkEstimateDiffusionTensor	2	New interface to perform tensor fitting. This class is intented to rely on teem for doing tensor model fitting. This class will replace vtkImageDiffusionTensor	currently not used
vtkImageDiffusionTensor	5	Tensor fitting class. This class currently perform the job of tensor estimation	Used in DTMRICalculateTensor.tcl
vtkImageExtractSlices	5	Class used to split a Volume with multiple DWI acquistions in different volumes. As of Today slicer stores DWI as a stacked of 3D volumes. As part of NRRD support this process is going to evolve such as DWI are seen as a multicomponent 3D volume (a more natural way of looking at DWI images	Used in DTMRICalculateTensor.tcl
vtkLSDIreconTensor	0	Depreceated class
vtkMrmlTractGroupNode
vtkMrmlTractsNode
vtkMultipleStreamlineController	5	Manager class for tractography. This class has pointers to the classes in charge of seeding, visualizing and storing streamlines.	Used as main hub for tractography
vtkODFGlyph	0	Class for Q-ball glyph rendering	This class required a custom Q-ball images type developed by D. Tuch.
vtkPruneStreamline
vtkROISelectTracts
vtkSaveTracts
vtkSeedTracts
vtkStochasticTracking	1	Class under development
vtkStreamlineConvolve
vtkTractShapeFeatures	5	Compute different similarity metrics between fibers used for the clustering	Used by vtkClusterTracts

vtkEMAtlasBrainClassifier

Katie will transition older tests into Dart framework.

Test Name	Priority	Status	Description	Dependencies
TestImageEMAtlas.tcl	3	TBD	big test	vtkEMLocalSegment

vtkEMLocalSegment

Katie will first transition older tests into Dart framework.

Test Name	Priority	Status	Description	Dependencies
TestImageEMLocalSegment.tcl	1	Done	local test	none
TestImageEMMarkov.tcl	2	In progress	markov test	none

vtkFreeSurferReaders

Small test surface files written in ascii using the Surface File Formats and then converted to binary using mris_convert.

Class Name	Priority	Status	Description	Dependencies	Test Code
vtkBVolumeReader	4	TBD	Test reading and rendering of binary short and float volumes	none
vtkCORReader	3	TBD	Test reading and rendering of COR volumes	none
vtkFSIO	5	Not necessary	Reads ints, shorts, and floats from compressed or uncompressed files	none
vtkFSLookupTable	2	Done	Test reading in surface file with overlay and rendering with colours	vtkFSSurfaceReader, vtkFSSurfaceScalarReader	Tcl/testFSLUT.tcl
vtkFSSurfaceAnnotationReader	2	TBD	Test reading in surface with labels	vtkFSSurfaceReader
vtkFSSurfaceReader	2	Done	Test reading in a simple surface file	none	Tcl/testOrig.tcl
vtkFSSurfaceScalarReader	2	Done	Test reading in surface with scalar	vtkFSSurfaceReader	Tcl/testCurv.tcl
vtkFSSurfaceWFileReader	3	Done	Test reading in W surface	vtkFSSurfaceReader	Tcl/testW.tcl
vtkGDFReader	4	TBD	Read in FreeSurfer group descriptor files	vtkBVolumeReader
vtkMGHReader	1	Done	Test MGZ file reading and rendering	none	Tcl/testMGZBrain.tcl
vtkMGHReader	2	in progress	Test reading in aseg and rendering with colours	none	Tcl/testMGZAseg.tcl

Nicole transitioning older tests into Dart framework.

Test Name	Priority	Status	Description	Dependencies
annotation.tcl	3	TBD	test annotation overlay	surface and scalar reader
bvolume.tcl	1	TBD	test B volume reading	none
bvolume_slice.tcl	2	TBD	test B volume rendering	none
scalar.tcl	3	TBD	test scalar reading	none
scalars.tcl	3	TBD	test scalars	none
slice.tcl	4	TBD	test slices	none
surf-quad.tcl	3	TBD	test	none
surf-tri.tcl	3	TBD	test	none