====================
Matlab Function List
====================

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.. _matlabfunctions_Common:

Common
======


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   mexITKImageWrite
   mexITKImageRead



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   :header: Command, Description
   :widths: 20, 20

   :doc:`mexITKImageWrite <mexITKImageWrite>`, "write Matlab image matrix to any image format supported by ITK using itk::Image and itk::VectorImage."
   :doc:`mexITKImageRead <mexITKImageRead>`, "read images stored as any format recognized by ITK"


.. _matlabfunctions_DWIProcessing:

DWIProcessing
=============


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   mexReadDWIList



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   :header: Command, Description
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   :doc:`mexReadDWIList <mexReadDWIList>`, "read dwi images, gradient files, and b values"


.. _matlabfunctions_DiffusionModels:

DiffusionModels
===============


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   mexSphericalPolarFourierImaging
   mexGetSHBasisMatrix
   mexGetSamplesFromSPFCoefficients
   mexGetSPFBasisMatrix



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   :header: Command, Description
   :widths: 20, 20

   :doc:`mexSphericalPolarFourierImaging <mexSphericalPolarFourierImaging>`, "estimate continuous DWI signal and EAP represented by coefficients of given basis."
   :doc:`mexGetSHBasisMatrix <mexGetSHBasisMatrix>`, "get sh matrix based on given order and orientationMatrix"
   :doc:`mexGetSamplesFromSPFCoefficients <mexGetSamplesFromSPFCoefficients>`, "get DWI or EAP samples (orignal samples or the SH coefficients) from given SPF coefficients"
   :doc:`mexGetSPFBasisMatrix <mexGetSPFBasisMatrix>`, "get SPF basis matrix with given spherical and radial orders, orientationMatrix, bVector"


.. _matlabfunctions_SamplingScheme:

SamplingScheme
==============


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   CartesianToSpherical
   CoveringRadius
   CoveringRadiusUpperBound
   GetGradAllShells
   OptimalSamplingMultiShellCNLO
   OptimalSamplingMultiShellCNLO_singleRun
   OptimalSamplingMultiSubsetsFromDifferentSets
   OptimalSamplingMultiSubsetsFromSameSet
   OptimalSamplingSingleShellCNLO
   OptimalSamplingSingleSubset
   ReadDirections
   VisualizeMultiShellScheme
   WriteDirections
   mexReadGrad



.. csv-table::
   :header: Command, Description
   :widths: 20, 20

   :doc:`CartesianToSpherical <CartesianToSpherical>`, "Convert x,y,z to theta, phi, r."
   :doc:`CoveringRadius <CoveringRadius>`, "Calculate the covering radius of the given samples."
   :doc:`CoveringRadiusUpperBound <CoveringRadiusUpperBound>`, "calculate the upper bound () of the minimal distance for a given number of points.    Note: for N antipodal symmetric samples, use CoveringRadiusUpperBound(2*N)."
   :doc:`GetGradAllShells <GetGradAllShells>`, "Get Nx3 gradient table from gradients in all shells."
   :doc:`OptimalSamplingMultiShellCNLO <OptimalSamplingMultiShellCNLO>`, "update gradients from an initial gradient set, such that the updated gradients are evenly distributed."
   :doc:`OptimalSamplingMultiShellCNLO_singleRun <OptimalSamplingMultiShellCNLO_singleRun>`, "update gradients from an initial gradient set, such that the updated gradients are evenly distributed."
   :doc:`OptimalSamplingMultiSubsetsFromDifferentSets <OptimalSamplingMultiSubsetsFromDifferentSets>`, "get K subsets of gradients from corresponding K given gradient sets, such that  gradients in each subset are evenly distributed."
   :doc:`OptimalSamplingMultiSubsetsFromSameSet <OptimalSamplingMultiSubsetsFromSameSet>`, "get K subsets of gradients from one given gradient set, such that  gradients in each subset are evenly distributed."
   :doc:`OptimalSamplingSingleShellCNLO <OptimalSamplingSingleShellCNLO>`, "update gradients from an initial gradient set, such that the updated gradients are evenly distributed."
   :doc:`OptimalSamplingSingleSubset <OptimalSamplingSingleSubset>`, "get several subsets of gradients from a given gradient set, such that  gradients in each subset are evenly distributed."
   :doc:`ReadDirections <ReadDirections>`, "read direction file into a matrix"
   :doc:`VisualizeMultiShellScheme <VisualizeMultiShellScheme>`, "visualize single or multiple shell schemes"
   :doc:`WriteDirections <WriteDirections>`, "Write gradient table to a file"
   :doc:`mexReadGrad <mexReadGrad>`, "read gradient files into a matrix"


.. _matlabfunctions_Utils:

Utils
=====


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   CopyDefaultStructParams



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   :header: Command, Description
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   :doc:`CopyDefaultStructParams <CopyDefaultStructParams>`, "Copy default parameter struct into a given user parameter struct"