Documentation/Labs/Surface Toolbox update

Overview

As part of the SALT project we would like to revamp some of the existing functionality in MeshMath into the SurfaceToolbox. We will be hiring a summer intern to work on this over a couple of months this summer.

Team

• JC Fillon-Robin
• Bea Paniagua
• Jared Vicory
• Andras Lasso
• Martin Styner
• Benjamin Wilson (Kitware Summer intern 2019)

Definitions

• KWMeshVisu: Legacy mesh viewer from the Styner Lab.
• Types of Mesh Operations:
  • Multiple Mesh (2+)
  • Single Mesh
  • MeshToVolume
  • MeshScalar to Mesh
  • MeshScalar to MeshScalar
  • MeshScalar Operation
  • Mutliple MeshScalar

Initial discussions

We will be potentially implementing individual CLIs for each functionality in MeshMath, and those will be plugged into the Surface Toolbox.

We would like to add a parameter node so if you save the scene and reload then all the node and parameter selections that you have made are not lost Enclose all functionality in C++ little CLIs that can be called from the python infrastructure, so they can be used from any modules Do the same thing for the functionality in MeshMath, creating independent CLIs and modules

Current MeshMath functionality

Name	Description	Type	Keep	Note
subtract	Subtract mesh from inputmesh, write a KWMeshVisu readable text file	PairWiseMesh		This functionality is currently available through ModelToModelDistance
magnitude	Magnitude of the input metaArray file (mvh/mva) and writes a KWMeshVisu readable file	?		It seems this is very specific to a certain application
scaleMVA	Scales the input metaArray file (mvh/mva) and writes a KWMeshVisu readable file	?		It seems this is very specific to a certain application
scaleMesh	Scales the input mesh file	SingleMesh		(Implemented)
avgMesh	Compute the average mesh from inputmesh file1, file2...	MultipleMesh		(Work in Progress)
ave	Compute the average vector field from file1, file2... generated with -substract	MultipleMesh / ScalarMesh Operator		Turn into a new MeshScalar operator. Given several Meshes with MeshScalars that are named the same way, it will allow averaging them and creating a new scalar map.
normave	Works as the \"-ave\" option, but the average vector are projected on the normal at each point	MultipleMesh / ScalarMesh Operator		Turn into a new MeshScalar operator. Given several Meshes with MeshScalars that are named the same way, it will allow averaging them and creating a new scalar map.
InvVect	Invert all the vectors created with the -substract option and write a KWMeshVisu readable file	MeshScalar Operation
magdir	Compute the signed magnitude of each of the vector from the vector field.(+ if in the normal direction, - otherwise)	SingleMesh		This functionality is currently available through ModelToModelDistance
magNormdir	Compute the signed magnitude of the normal projection of the vector field	SingleMesh		This functionality is currently available through ModelToModelDistance
applyVec	Deforme the mesh according to the vector field specified as input	SingleMesh		(Work in Progress)
meshValues	Find the points and cells in a mesh. The outputfile is a textfile with the values	SingleMesh		(Work in Progress) Export through CSV
avgGaussMesh	<Meshfile1> <Meshfile2> ... -gaussMeshPara <mean>,<stdev>,<val1>,<val2>,... Compute the gaussian average for mesh files. The first parameter is the average, then the standard deviation of the Gaussian model and the rest are the values associated with the files	MultipleMesh
avgGaussKWM	Compute the gaussian average for KWMeshVisu files. The first parameter is the average, then the standard deviation of the Gaussian model and the rest are the values associated with the files	MeshScalar Operation		See "ave"
alignMesh	Align all of the meshes to the inputmesh (== MeshFile0) using Procrustes alignment [-scalingOn]	MultipleMesh		Fix the scaling, give an option to export the scaling factors associated with the mesh (so it can be reverted via scaleMesh)
alignMeshICP	Align all of the meshes to the inputmesh (== MeshFile0) using IterativeClosestPoints (no correspondence required)	MultipleMesh
BadTriangle	Find the bad triangles in a Mesh. The <thresh value> is the value of the threshFactor to calculate the standard deviation for the bad triangles. The output is a KWMeshVisu text file with the values of the average of the triangles of the mesh	SingleMesh		Probably not keep since this is the same than "Clean" in the SurfaceToolbox
extraction	To extract an attribute.The Input is the Mesh, the extractFilename is the attribute image and the Output is a KWMeshVisu text file with the attribute extraction [-extractClosest]: extract closest attribute [-nn]: nearest neighbor interpolation (default: linear)	MeshToVolume
value	Extract the 5th column from a textfile and write a KWMeshVisu file with the values obtained	SingleMesh		(Work in Progress) Turn into "import from file" or something similar. This new operation would import a scalar field from a csv file into a mesh
subKWM	Difference between 2 KWMeshVisu files	MeshScalar Operation		See "ave"
MaxColor	Compare each point in every files, find a max for every points, keep 5% near the max, the other values will be 0	MeshScalar Operation		Transform this into a Threshold scalar map
dist_absolute	Absolute distance map between KWMeshVisu files	MeshScalar Operation		Transform this into something better, something that can operate over several scalar maps
dist_relative	Relative distance map between KWMeshVisu files (values between -1 & 1)	MeshScalar Operation		Transform this into something better, "normalize scalar map", and give the option to set up the range
label	Separate every labels, find the mean...	MeshScalar Operation		This will be changed into a different module. The module will list all the scalar fields in the Mesh
color -val <number_of_label>,<value_label>	To change the value of labels to see the evolution with KWMeshVisu.	MeshScalar Operation		This will not be kept as it has legacy operations
first <textfile>	Convert a column file into a line file with a comma between each value.	Random		This will not be kept as it should not be here.
MC2Origin	Convert a column file into a line file with a comma between each value.	SingleMesh		(Work in Progress)
avg/median/min/max/per1/per99OneKWM	Obtain descriptive statistics from scalar fields in a single VTK mesh	SingleMesh / ScalarMesh Operation		Keep with modifications, arguments should be the scalar field name and the operation to perform. Might revisit later, most of this functionality is in MeshStatistics
FillHole	Fills up a hole in a open mesh.	SingleMesh		(Work in Progress) Slight change it should close all the open holes until there are no more
BordersOut	Outputs the borders of a mesh (if there)	SingleMesh		(Implemented)
isOpen	Gives back an integer defining whether the mesh is open or not	SingleMesh		Probably not keep, will revisit later
CleanMesh	Re-mesh the input mesh and gives back a new clean mesh without degenerated triangles	SingleMesh		Already in the surface toolbox
SmoothMesh	Gives back a Laplacian smoothed surface	SingleMesh		Already in the surface toolbox
FilterNormals	Changes homogeneously normals of the polygons in a mesh	SingleMesh		Already in the surface toolbox
StatsROI	Process a KWMeshVisu file, given a ROI Mask	MeshScalar operation		Already in Slicer through Pick and Pain and MeshStatistics
KWMToPolyData	Writes a KWM scalar field (N Dimensions) into a PolyData Field Data Scalar to visualize in Slicer	SingleMesh		(Work in Progress) Keep with modifications, the scalar field can be input in a csv, it does not need to be a KWM file
FSAscData	Extracts a curvature/thickness etc information from a FreeSurfer style scalar file and adds it as attribute to the vtk mesh for visualization. FS format is line-by-line, no header, with each line 'point-id vertex-x vertex-y vertex-z scalar-prop	SingleMesh		Needs to be replaced by a conversion tool that allows VTK/Slicer and GIFTI (the new surface standard that FS is using with their newest versions, connectome projects are using only GIFTI)
surfaceArea	Computes surface area in a txt file	SingleMesh		(Work in Progress) Keep with modifications, we should create an option to extract vtkMassProperties from a single Mesh including surface area and volume
variance/mean/attSTD	Compute variance across population of scalar fields	Multiple MeshScalar (multiple Mesh)		Keep with modifications, we should compute variance in a scalar field given the scalar field name and a collection of meshes
GetCurvatures	Gets an assorted set of curvature measurements:	SingleMesh		(Work in Progress) Keep with modifications, embed the attributes as scalar fields in the mesh
particleConsistency	Generates new particle files where fliped particles does not appear	MultipleMesh		ShapeWorks functionality, do not keep
GetDirectionFeatures	Generates three KWM loadable files that have directionality features with respect to X, Y and Z directions	SingleMesh		(Work in Progress)
closestPoint	Computes interpolated attribute file (output file) for second mesh using closest point interpolation between two input meshes	Multiple Mesh		Keep with modifications. Two meshes, one target and one source with the source having the scalar field that needs to be transferred into target
extractVertices	Extract points and write 3 different files listing respectively X, Y and Z values	SingleMesh		(Work in Progress) Keep with modifications. Provide a point and a scalar field and values for that point will be output
cart2bary	Project each point in <vtkPointFileIn> onto the <inputmesh> and then calculate the Barycentric coordinate of the projected point, output to <OutputFileName>	SingleMesh		Keep with modifications. (styner: I think this can be removed)
VTKtoLpts	Create a particle file out of a triangulated VTK mesh	SingleMesh		ShapeWorks functionality, do not keep
relaxPolygons	Mesh relaxation based in vtkWindowedSincPolyDataFilter	SingleMesh		(Implemented) Check with @lasso to see if this is already included into the Surface toolbox
decimateMesh	Mesh decimation, reducing the number of points. Target reduction is a value from 0..1 that indicates in what % vertices should be reduced	SingleMesh		Do not keep, already included into the Surface toolbox
listPointData	lists info about all the VTK point Data in the vtk file	SingleMesh		Probably keep, but functionality slightly overlaps with other functionality that will be improved when ported. Will revisit later.
pointDataOP	threshold or subtract data	SingleMesh		(Work in Progress)
translateMesh	translates a mesh for a given amount	SingleMesh		(Implemented)
lookupPointData	substitutes scalar values in a given scalar field based on an input lookup	SingleMesh		(Work in Progress)
volumePolyData	provides volume count for the PolyData through the std output. NOTE: Only in closed surfaces.	SingleMesh		(Work in Progress) Keep altogether with the surface area functionality described above (vtkMassProperties)

Path forward

Using vtkMRMLScriptedModuleNode

This node is particularly useful as it helps store parameters used for computation. See vtkMRMLScriptedModuleNode.h

The main idea is to have a parameter node selector allowing to choose between different set of parameters.

For an example of use in a scripted module. See Modules/Scripted/SegmentStatistics/SegmentStatistics.py

Testing data

TBD