Review and Refactor Matlab Code

[yujanshrestha]

The overarching goal of this ticket is to gauge how easy it will be to work with the Matlab code and identify risky areas that could affect the assessment deliverable. A good way to do this is to read through and refactor the code for readability and testability.

• Identify good points to break up a large matlab script into smaller scripts in a pipeline. Each step in the pipeline will read and write files. The Python port will mirror this structure so we can easily ensure numerical equivalence at each step.
• Refactor the samseg Matlab code into smaller functions to improve readability.

Ideally the above should be done in order. First identify good splice points, then refactor.

[yujanshrestha]

Let's not sink too much time into getting a fully functioning development environment until we meeting with Nick and the team. Lets focus our efforts for this week on getting more familiar with the code + samseg paper so we can be as confident as possible for our assessment deliverable.

[orwonthe]

These matlab files need conversion to python:

• kvlColorCodeProbabilityImages.m
• kvlMergeAlphas.m
• kvlReadCompressionLookupTable.m
• run_samseg.m
• samseg_registerAtlas.m
• samsegment.m

These matlab runners need equivalent python or c++ runners:

• kvlClear.h

• kvlCreateImage.h

• kvlCreateTransform.h

• kvlEvaluateMeshPosition.h

• kvlGetAlphasInMeshNodes.h

• kvlGetCostAndGradientCalculator.h

  'MutualInformation' 'Affine'
  'AtlasMeshToIntensityImage' 'Sliding'*

• kvlGetOptimizer.h

   'L-BFGS'

• kvlGetTransformMatrix.h

• kvlRasterizeAtlasMesh.h

• kvlReadMesh.h ???

• kvlReadMeshCollection.h

• kvlScaleMesh.h

• kvlSetAlphasInMeshNodes.h

• kvlSetMeshNodePositions.h

• kvlSmoothImageBuffer.h

• kvlSmoothMesh.h

• kvlStepOptimizer.h

• kvlWriteImage.h

These kvl functions may need wrapping to be called from python:

• kvlAtlasMeshAlphaDrawer.h
• kvlAtlasMeshDeformationOptimizer.h
• kvlAtlasMeshDeformationLBFGSOptimizer.h
• kvlAtlasMeshCollection.h
• kvlAtlasMeshSmoother.h
• kvlAtlasMeshMultiAlphaDrawer.h
• kvlAtlasMeshPositionCostAndGradientCalculator.h
• kvlCroppedImageReader.h
• kvlImageConverter.h
• kvlMutualInformationCostAndGradientCalculator.h

These ITK inclusions may need wrapping:

• include "itkCastImageFilter.h"

• include "itkDefaultStaticMeshTraits.h"

• include "itkDefaultDynamicMeshTraits.h"

• include "itkMesh.h"

• include "itkImage.h"

• include "itkImageFileWriter.h"

• include "itkImageRegionIterator.h"

• include

• include "itkMGHImageIO.h"

• include "itkVector.h"

These VNL inclusions may need wrapping:

• include "vnl/vnl_matrix_fixed.h"

• include "vnl/vnl_inverse.h"

• include "vnl/vnl_det.h"