============
Command List
============

.. contents:: Table of Contents
   :depth: 1
   :local:



.. _commandlist_DWIProcessing:

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


.. toctree::
   :maxdepth: 1
   :hidden:

   CorrectBValues
   DWIMultipleShellSplit
   DWINoiseGenerator
   DWIPreprocess
   DWISimulator
   DWISingleVoxelSimulator



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

   :doc:`CorrectBValues <CorrectBValues>`, "group similar b values into several shells."
   :doc:`DWIMultipleShellSplit <DWIMultipleShellSplit>`, "Split mutiple shell DWI data into several single shell    data."
   :doc:`DWINoiseGenerator <DWINoiseGenerator>`, "Add noise to a set of DWI data."
   :doc:`DWIPreprocess <DWIPreprocess>`, "Read DWI images, gradients, b values, and output the formal    normalized formalt in a configuration file."
   :doc:`DWISimulator <DWISimulator>`, "Simulate DWI data."
   :doc:`DWISingleVoxelSimulator <DWISingleVoxelSimulator>`, "Simulate DWI data with fixed single voxel    configuration."


.. _commandlist_DiffusionModels:

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


.. toctree::
   :maxdepth: 1
   :hidden:

   ComputeSHCoefficientsOfDWIFromSymmetricTensor
   MeanDiffusivityEstimator
   ODFNormalization
   SHCoefficientsFit
   SHCoefficientsPower
   SHCoefficientsRotate
   SHCoefficientsToGFA
   SHCoefficientsToSphericalFunctionSamples
   SPFToODF
   SPFToProfile
   SPFToScalarMap
   SphereTessellator
   SphericalPolarFourierImaging
   TensorFormatConverter



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

   :doc:`ComputeSHCoefficientsOfDWIFromSymmetricTensor <ComputeSHCoefficientsOfDWIFromSymmetricTensor>`, "Compute SH coefficients of DWI signal in DTI with symmetric    tensor (along z-axis). "
   :doc:`MeanDiffusivityEstimator <MeanDiffusivityEstimator>`, "Estimate Mean Diffusivity in each voxel. "
   :doc:`ODFNormalization <ODFNormalization>`, "Normalize ODF (VectorImage) represented by SH basis or    uniform spherical samples."
   :doc:`SHCoefficientsFit <SHCoefficientsFit>`, "Spherical Harmonics fit from spherical function samples."
   :doc:`SHCoefficientsPower <SHCoefficientsPower>`, "Power of a spherical function represented by SH basis."
   :doc:`SHCoefficientsRotate <SHCoefficientsRotate>`, "Spherical Harmonics Rotation. "
   :doc:`SHCoefficientsToGFA <SHCoefficientsToGFA>`, "calculate GFA from SH coefficients."
   :doc:`SHCoefficientsToSphericalFunctionSamples <SHCoefficientsToSphericalFunctionSamples>`, "conversion from SH coefficients to spherical function    samples."
   :doc:`SPFToODF <SPFToODF>`, "Convert SPF coefficients to ODFs (represented by SH basis    or discrete samples)."
   :doc:`SPFToProfile <SPFToProfile>`, "Convert SPF coefficients to DWI/EAP profile (represented by    SH basis or discrete samples)."
   :doc:`SPFToScalarMap <SPFToScalarMap>`, "Estimate scalar maps using SPFI. "
   :doc:`SphereTessellator <SphereTessellator>`, "Tessellation of a sphere via subdivision of basic    polyhedrons."
   :doc:`SphericalPolarFourierImaging <SphericalPolarFourierImaging>`, "Spherical Polar Fourier Imaging (SPFI): estimate SPF    coefficients from DWI signals. "
   :doc:`TensorFormatConverter <TensorFormatConverter>`, "Convert different tensor storage formats."


.. _commandlist_SamplingScheme:

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


.. toctree::
   :maxdepth: 1
   :hidden:

   OrientationStatistics
   SamplingSchemeDistance
   SamplingSchemeQSpace1OptEstimation
   SamplingSchemeQSpaceIMOCEstimation
   SamplingSchemeQSpaceIncrementalEstimation
   SamplingSchemeQSpaceRandomEstimation



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

   :doc:`OrientationStatistics <OrientationStatistics>`, "Get statistics information from a given orientation file.      Show the (min, max, mean, std) of the minimal angles of all samples.        Show electrostatic energy, spherical code cost function."
   :doc:`SamplingSchemeDistance <SamplingSchemeDistance>`, "Calculate the distance (maximum of the minimal angles)    between two single shell sampling schemes. "
   :doc:`SamplingSchemeQSpace1OptEstimation <SamplingSchemeQSpace1OptEstimation>`, "1-Opt estimation for single and multiple shell sampling    scheme "
   :doc:`SamplingSchemeQSpaceIMOCEstimation <SamplingSchemeQSpaceIMOCEstimation>`, "Single and multi-shell sampling scheme estimation using    Iterative Maximum Overlap Construction (IMOC)."
   :doc:`SamplingSchemeQSpaceIncrementalEstimation <SamplingSchemeQSpaceIncrementalEstimation>`, "Incrementatl estimation for single and multiple shell    sampling scheme. "
   :doc:`SamplingSchemeQSpaceRandomEstimation <SamplingSchemeQSpaceRandomEstimation>`, "Random generator for multi-shell schemes."


.. _commandlist_Scripts:

Scripts
=======


.. toctree::
   :maxdepth: 1
   :hidden:

   CombineVTKPolyData.py
   ConvertGurobiSolToIndex.py
   VTKPolyData.py
   VTKPolyData_gui.py



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

   :doc:`CombineVTKPolyData.py <CombineVTKPolyData.py>`, "Combine several vtk files into one vtk file."
   :doc:`ConvertGurobiSolToIndex.py <ConvertGurobiSolToIndex.py>`, "Covert .sol file (by gurobi) to index file for subsampling gradients. It is used for subsampling gradients by Mixed Integer Linear Programming (MILP)"
   :doc:`VTKPolyData.py <VTKPolyData.py>`, "Render a list of VTK data  and (or) a nifti image, then view or save PNG or save WebGL. The code is modified from ITKExamples."
   :doc:`VTKPolyData_gui.py <VTKPolyData_gui.py>`, "GUI for VTKPolyData.py."


.. _commandlist_Utilities:

Utilities
=========


.. toctree::
   :maxdepth: 1
   :hidden:

   4DImageMath
   4DToVectorImageConverter
   ImageInfo
   PrintImage
   TextFileOperator
   VectorImageNormalization
   VectorTo4DImageConverter



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

   :doc:`4DImageMath <4DImageMath>`, "Perform math operators on 4D image (4D itk::Image or 3D    itk::VectorImage)."
   :doc:`4DToVectorImageConverter <4DToVectorImageConverter>`, "Convert a 4D image to a vector image. "
   :doc:`ImageInfo <ImageInfo>`, "Display image information."
   :doc:`PrintImage <PrintImage>`, "print image (4D image, tensors, SH    coefficients)."
   :doc:`TextFileOperator <TextFileOperator>`, "Operations for text files."
   :doc:`VectorImageNormalization <VectorImageNormalization>`, "Normalize each voxel in a VectorImage or    SparseVectorImage."
   :doc:`VectorTo4DImageConverter <VectorTo4DImageConverter>`, "Convert a vector image to a 4D image."


.. _commandlist_Visualization:

Visualization
=============


.. toctree::
   :maxdepth: 1
   :hidden:

   CombineVTKPolyData.py
   MeshFromDiscreteFiberODF
   MeshFromPeaks
   MeshFromSHCoefficients
   MeshFromSphericalFunctionTessellatedSamples
   MeshFromTensors
   MeshFromTracts
   OrientationsViewer
   RGBImageToVTKXMLImageConverter
   VTKPolyData.py
   VTKPolyData_gui.py
   VTKXMLImageToVectorImageConverter
   VectorImageToVTKXMLImageConverter
   vtkviewer



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

   :doc:`CombineVTKPolyData.py <CombineVTKPolyData.py>`, "Combine several vtk files into one vtk file."
   :doc:`MeshFromDiscreteFiberODF <MeshFromDiscreteFiberODF>`, "Create a mesh (a spherical profile of DWI/EAP/ODF) from    discrete fiber ODF for visualization."
   :doc:`MeshFromPeaks <MeshFromPeaks>`, "Create a mesh from peaks for visualization."
   :doc:`MeshFromSHCoefficients <MeshFromSHCoefficients>`, "Create a mesh from spherical harmonics coefficients for    visualization."
   :doc:`MeshFromSphericalFunctionTessellatedSamples <MeshFromSphericalFunctionTessellatedSamples>`, "Create a mesh from spherical samples using tessellation."
   :doc:`MeshFromTensors <MeshFromTensors>`, "Create a mesh from tensors for visualization."
   :doc:`MeshFromTracts <MeshFromTracts>`, "Create a mesh from fiber tracts for visualization."
   :doc:`OrientationsViewer <OrientationsViewer>`, "Single and multi-shell orientations viewer."
   :doc:`RGBImageToVTKXMLImageConverter <RGBImageToVTKXMLImageConverter>`, "Convert an ITK image to a VTK XML image."
   :doc:`VTKPolyData.py <VTKPolyData.py>`, "Render a list of VTK data  and (or) a nifti image, then view or save PNG or save WebGL. The code is modified from ITKExamples."
   :doc:`VTKPolyData_gui.py <VTKPolyData_gui.py>`, "GUI for VTKPolyData.py."
   :doc:`VTKXMLImageToVectorImageConverter <VTKXMLImageToVectorImageConverter>`, "Convert a VTK XML image to an ITK image."
   :doc:`VectorImageToVTKXMLImageConverter <VectorImageToVTKXMLImageConverter>`, "Convert an ITK image to a VTK XML image."
   :doc:`vtkviewer <vtkviewer>`, "visualize vtk files."