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shapeworks::ReconstructSurface

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Public Types

Name
using typename TransformType::Pointer TransformTypePtr
using typename TransformType::PointSetType PointSetType
using typename PointSetType::PointIdentifier PointIdType

Public Functions

Name
ReconstructSurface() =default
ReconstructSurface(const std::string & denseFile, const std::string & sparseFile, const std::string & goodPointsFile)
double computeAverageDistanceToNeighbors(vtkSmartPointer< vtkPoints > points, std::vector< int > particlesIndices)
void checkMapping(TransformTypePtr transform, vtkSmartPointer< vtkPoints > sourcePoints, vtkSmartPointer< vtkPoints > targetPoints)
void generateWarpedMeshes(TransformTypePtr transform, vtkSmartPointer< vtkPolyData > & outputMesh)
Mesh getMesh(PointArray localPoints)
vtkSmartPointer< vtkPoints > convertToImageCoordinates(vtkSmartPointer< vtkPoints > particles, const Vector & spacing, const Point3 & origin)
int computeMedianShape(std::vector< Eigen::MatrixXd > & shapeList)
void performKMeansClustering(std::vector< PointArray > worldPoints, int numberOfParticles, std::vector< int > & centroidIndices)
Eigen::MatrixXd computeParticlesNormals(vtkSmartPointer< vtkPoints > particles, Image dt)
vtkSmartPointer< vtkPolyData > getDenseMean(std::vector< PointArray > localPoints, std::vector< PointArray > worldPoints, std::vector< std::string > distance_transform)
void computeDenseMean(std::vector< PointArray > localPoints, std::vector< PointArray > worldPoints, std::vector< std::string > distanceTransform)
std::vector< PointArray > computeSparseMean(std::vector< PointArray > localPoints, Point3 commonCenter)
void writeMeanInfo()
void surface(const std::vector< std::string > localPointsFiles)
void samplesAlongPCAModes(const std::vector< std::string > worldPointsFiles)
void meanSurface(const std::vector< std::string > distanceTransformFiles, const std::vector< std::string > localPointsFiles, const std::vector< std::string > worldPointsFiles)
void setOutPrefix(std::string prefix)
void setOutPath(std::string path)
void setDoProcrustes(bool doProcrusts)
void setDoProcrustesScaling(bool doProcrustsScaling)
void setPairwiseNormalsDiffForGoodBad(bool pairwiseNormalsDiffForGoodBad)
void setMeanBeforeWarp(bool meanBeforeWarp)
void setEnableOutput(bool enableOutput)
void setModeIndex(int modeIndex)
void setNumOfModes(int numOfModes)
void setNumOfSamplesPerMode(int numOfSamplesPerMode)
void setNumOfParticles(int numOfParticles)
void setNumOfClusters(int numOfClusters)
void setMaxStdDev(float maxStdDev)
void setMaxVarianceCaptured(float maxVarianceCaptured)
void setMaxAngleDegrees(float maxAngleDegrees)

Detailed Description

template <class TransformType >
class shapeworks::ReconstructSurface;

Public Types Documentation

using TransformTypePtr

using shapeworks::ReconstructSurface< TransformType >::TransformTypePtr =  typename TransformType::Pointer;

using PointSetType

using shapeworks::ReconstructSurface< TransformType >::PointSetType =  typename TransformType::PointSetType;

using PointIdType

using shapeworks::ReconstructSurface< TransformType >::PointIdType =  typename PointSetType::PointIdentifier;

Public Functions Documentation

function ReconstructSurface

ReconstructSurface() =default

function ReconstructSurface

ReconstructSurface(
    const std::string & denseFile,
    const std::string & sparseFile,
    const std::string & goodPointsFile
)

function computeAverageDistanceToNeighbors

double computeAverageDistanceToNeighbors(
    vtkSmartPointer< vtkPoints > points,
    std::vector< int > particlesIndices
)

function checkMapping

void checkMapping(
    TransformTypePtr transform,
    vtkSmartPointer< vtkPoints > sourcePoints,
    vtkSmartPointer< vtkPoints > targetPoints
)

function generateWarpedMeshes

void generateWarpedMeshes(
    TransformTypePtr transform,
    vtkSmartPointer< vtkPolyData > & outputMesh
)

function getMesh

Mesh getMesh(
    PointArray localPoints
)

function convertToImageCoordinates

vtkSmartPointer< vtkPoints > convertToImageCoordinates(
    vtkSmartPointer< vtkPoints > particles,
    const Vector & spacing,
    const Point3 & origin
)

function computeMedianShape

int computeMedianShape(
    std::vector< Eigen::MatrixXd > & shapeList
)

function performKMeansClustering

void performKMeansClustering(
    std::vector< PointArray > worldPoints,
    int numberOfParticles,
    std::vector< int > & centroidIndices
)

function computeParticlesNormals

Eigen::MatrixXd computeParticlesNormals(
    vtkSmartPointer< vtkPoints > particles,
    Image dt
)

function getDenseMean

vtkSmartPointer< vtkPolyData > getDenseMean(
    std::vector< PointArray > localPoints,
    std::vector< PointArray > worldPoints,
    std::vector< std::string > distance_transform
)

function computeDenseMean

void computeDenseMean(
    std::vector< PointArray > localPoints,
    std::vector< PointArray > worldPoints,
    std::vector< std::string > distanceTransform
)

function computeSparseMean

std::vector< PointArray > computeSparseMean(
    std::vector< PointArray > localPoints,
    Point3 commonCenter
)

function writeMeanInfo

void writeMeanInfo()

function surface

void surface(
    const std::vector< std::string > localPointsFiles
)

function samplesAlongPCAModes

void samplesAlongPCAModes(
    const std::vector< std::string > worldPointsFiles
)

function meanSurface

void meanSurface(
    const std::vector< std::string > distanceTransformFiles,
    const std::vector< std::string > localPointsFiles,
    const std::vector< std::string > worldPointsFiles
)

function setOutPrefix

inline void setOutPrefix(
    std::string prefix
)

function setOutPath

inline void setOutPath(
    std::string path
)

function setDoProcrustes

inline void setDoProcrustes(
    bool doProcrusts
)

function setDoProcrustesScaling

inline void setDoProcrustesScaling(
    bool doProcrustsScaling
)

function setPairwiseNormalsDiffForGoodBad

inline void setPairwiseNormalsDiffForGoodBad(
    bool pairwiseNormalsDiffForGoodBad
)

function setMeanBeforeWarp

inline void setMeanBeforeWarp(
    bool meanBeforeWarp
)

function setEnableOutput

inline void setEnableOutput(
    bool enableOutput
)

function setModeIndex

inline void setModeIndex(
    int modeIndex
)

function setNumOfModes

inline void setNumOfModes(
    int numOfModes
)

function setNumOfSamplesPerMode

inline void setNumOfSamplesPerMode(
    int numOfSamplesPerMode
)

function setNumOfParticles

inline void setNumOfParticles(
    int numOfParticles
)

function setNumOfClusters

inline void setNumOfClusters(
    int numOfClusters
)

function setMaxStdDev

inline void setMaxStdDev(
    float maxStdDev
)

function setMaxVarianceCaptured

inline void setMaxVarianceCaptured(
    float maxVarianceCaptured
)

function setMaxAngleDegrees

inline void setMaxAngleDegrees(
    float maxAngleDegrees
)

Updated on 2024-07-12 at 20:10:35 +0000