shapeworks::Sampler
Public Classes
| Name | |
|---|---|
| struct | CuttingPlaneType |
| struct | SphereType |
Public Types
| Name | |
|---|---|
| using float | PixelType |
| using itk::Image< PixelType, Dimension > | ImageType |
| using ImageType::PointType | PointType |
| using MeanCurvatureContainer< PixelType, Dimension > | MeanCurvatureCacheType |
| using vnl_matrix_fixed< double, Dimension+1, Dimension+1 > | TransformType |
| using GradientDescentOptimizer | OptimizerType |
| using std::vector< std::vector< std::pair< Eigen::Vector3d, Eigen::Vector3d > > > | CuttingPlaneList |
Public Functions
Public Attributes
| Name | |
|---|---|
| constexpr unsigned int | Dimension |
Public Types Documentation
using PixelType
using shapeworks::Sampler::PixelType = float;
using ImageType
using shapeworks::Sampler::ImageType = itk::Image<PixelType, Dimension>;
using PointType
using shapeworks::Sampler::PointType = ImageType::PointType;
using MeanCurvatureCacheType
using shapeworks::Sampler::MeanCurvatureCacheType = MeanCurvatureContainer<PixelType, Dimension>;
using TransformType
using shapeworks::Sampler::TransformType = vnl_matrix_fixed<double, Dimension + 1, Dimension + 1>;
using OptimizerType
using shapeworks::Sampler::OptimizerType = GradientDescentOptimizer;
using CuttingPlaneList
using shapeworks::Sampler::CuttingPlaneList = std::vector<std::vector<std::pair<Eigen::Vector3d, Eigen::Vector3d> >>;
Public Functions Documentation
function Sampler
Sampler()
Constructor.
function ~Sampler
inline virtual ~Sampler()
Destructor.
function GetParticleSystem
inline ParticleSystem * GetParticleSystem()
Returns the particle system.
function GetParticleSystem
inline const ParticleSystem * GetParticleSystem() const
function GetGradientFunction
inline SamplingFunction * GetGradientFunction()
Returns a pointer to the gradient function used.
function GetCurvatureGradientFunction
inline CurvatureSamplingFunction * GetCurvatureGradientFunction()
function GetOptimizer
inline OptimizerType * GetOptimizer()
Return a pointer to the optimizer object.
function GetOptimizer
inline const OptimizerType * GetOptimizer() const
function SetPointsFile
inline void SetPointsFile(
unsigned int i,
const std::string & s
)
Optionally provide a filename for an initial point set.
function SetPointsFile
inline void SetPointsFile(
const std::string & s
)
function SetInitialPoints
inline void SetInitialPoints(
std::vector< std::vector< itk::Point< double > > > initial_points
)
Set initial particle positions (e.g. for fixed subjects)
function AddImage
void AddImage(
ImageType::Pointer image,
double narrow_band,
std::string name =""
)
function ApplyConstraintsToZeroCrossing
inline void ApplyConstraintsToZeroCrossing()
function AddMesh
void AddMesh(
std::shared_ptr< shapeworks::MeshWrapper > mesh,
double geodesic_remesh_percent =100
)
function AddContour
void AddContour(
vtkSmartPointer< vtkPolyData > poly_data
)
function SetFieldAttributes
void SetFieldAttributes(
const std::vector< std::string > & s
)
function SetDomainsPerShape
inline void SetDomainsPerShape(
int n
)
function SetCuttingPlane
void SetCuttingPlane(
unsigned int i,
const vnl_vector_fixed< double, Dimension > & va,
const vnl_vector_fixed< double, Dimension > & vb,
const vnl_vector_fixed< double, Dimension > & vc
)
Optionally supply a cutting plane that will be set as a particle optimization constraint in the image domains.
function AddFreeFormConstraint
void AddFreeFormConstraint(
int domain,
const FreeFormConstraint & ffc
)
function TransformCuttingPlanes
void TransformCuttingPlanes(
unsigned int i
)
Transform a cutting plane based on procrustes transformation
function AddSphere
void AddSphere(
unsigned int i,
vnl_vector_fixed< double, Dimension > & c,
double r
)
Optionally add spheres that may be used as constraints to the domain.
function SetAdaptivityMode
inline void SetAdaptivityMode(
int mode
)
This method sets the optimization function for the sampling. mode 0 = isotropic adaptivity mode 1 = no adaptivity
function GetAdaptivityMode
inline int GetAdaptivityMode() const
function SetCorrespondenceOn
inline void SetCorrespondenceOn()
function SetCorrespondenceOff
inline void SetCorrespondenceOff()
function SetSamplingOn
inline void SetSamplingOn()
function SetSamplingOff
inline void SetSamplingOff()
function GetCorrespondenceOn
inline bool GetCorrespondenceOn() const
function GetSamplingOn
inline bool GetSamplingOn() const
function SetCorrespondenceMode
void SetCorrespondenceMode(
shapeworks::CorrespondenceMode mode
)
This method sets the optimization function for correspondences between surfaces (domains).
function RegisterGeneralShapeMatrices
inline void RegisterGeneralShapeMatrices()
function SetAttributeScales
inline void SetAttributeScales(
const std::vector< double > & s
)
function SetXYZ
inline void SetXYZ(
unsigned int i,
bool flag
)
function SetNormals
inline void SetNormals(
int i,
bool flag
)
function SetAttributesPerDomain
void SetAttributesPerDomain(
const std::vector< int > s
)
function GetShapeMatrix
inline LegacyShapeMatrix * GetShapeMatrix()
function GetGeneralShapeMatrix
inline ShapeMatrix * GetGeneralShapeMatrix()
function GetGeneralShapeGradientMatrix
inline ShapeGradientMatrix * GetGeneralShapeGradientMatrix()
function GetLinkingFunction
inline DualVectorFunction * GetLinkingFunction()
function GetEnsembleEntropyFunction
inline LegacyCorrespondenceFunction * GetEnsembleEntropyFunction()
function GetDisentangledEnsembleEntropyFunction
inline DisentangledCorrespondenceFunction * GetDisentangledEnsembleEntropyFunction()
function GetEnsembleRegressionEntropyFunction
inline LegacyCorrespondenceFunction * GetEnsembleRegressionEntropyFunction()
function GetEnsembleMixedEffectsEntropyFunction
inline LegacyCorrespondenceFunction * GetEnsembleMixedEffectsEntropyFunction()
function GetMeshBasedGeneralEntropyGradientFunction
inline CorrespondenceFunction * GetMeshBasedGeneralEntropyGradientFunction()
function GetLinkingFunction
inline const DualVectorFunction * GetLinkingFunction() const
function GetEnsembleEntropyFunction
inline const LegacyCorrespondenceFunction * GetEnsembleEntropyFunction() const
function GetDisentangledEnsembleEntropyFunction
inline const DisentangledCorrespondenceFunction * GetDisentangledEnsembleEntropyFunction() const
function GetEnsembleRegressionEntropyFunction
inline const LegacyCorrespondenceFunction * GetEnsembleRegressionEntropyFunction() const
function GetEnsembleMixedEffectsEntropyFunction
inline const LegacyCorrespondenceFunction * GetEnsembleMixedEffectsEntropyFunction() const
function GetMeshBasedGeneralEntropyGradientFunction
inline const CorrespondenceFunction * GetMeshBasedGeneralEntropyGradientFunction() const
function SetTimeptsPerIndividual
inline void SetTimeptsPerIndividual(
int n
)
function GetCorrespondenceMode
inline shapeworks::CorrespondenceMode GetCorrespondenceMode() const
function SetTransformFile
inline void SetTransformFile(
const std::string & s
)
function SetTransformFile
inline void SetTransformFile(
const char * s
)
function SetPrefixTransformFile
inline void SetPrefixTransformFile(
const std::string & s
)
function SetPrefixTransformFile
inline void SetPrefixTransformFile(
const char * s
)
function SetPairwisePotentialType
inline void SetPairwisePotentialType(
int pairwise_potential_type
)
function GetPairwisePotentialType
inline int GetPairwisePotentialType()
function SetVerbosity
inline void SetVerbosity(
unsigned int val
)
function GetVerbosity
inline unsigned int GetVerbosity()
function GetMeanCurvatureCache
inline MeanCurvatureCacheType * GetMeanCurvatureCache()
function SetSharedBoundaryEnabled
inline void SetSharedBoundaryEnabled(
bool enabled
)
function SetSharedBoundaryWeight
inline void SetSharedBoundaryWeight(
double weight
)
function ReadTransforms
void ReadTransforms()
function ReadPointsFiles
void ReadPointsFiles()
function AllocateDataCaches
void AllocateDataCaches()
function AllocateDomainsAndNeighborhoods
void AllocateDomainsAndNeighborhoods()
function InitializeOptimizationFunctions
void InitializeOptimizationFunctions()
function initialize_initial_positions
void initialize_initial_positions()
function Initialize
inline void Initialize()
function ReInitialize
void ReInitialize()
function Execute
void Execute()
function ComputeCuttingPlanes
CuttingPlaneList ComputeCuttingPlanes()
function ComputePlaneNormal
Eigen::Vector3d ComputePlaneNormal(
const vnl_vector< double > & a,
const vnl_vector< double > & b,
const vnl_vector< double > & c
)
function GetFFCs
inline std::vector< FreeFormConstraint > GetFFCs()
function SetMeshFFCMode
inline void SetMeshFFCMode(
bool mesh_ffc_mode
)
Public Attributes Documentation
variable Dimension
static constexpr unsigned int Dimension = 3;
Updated on 2024-03-17 at 12:58:44 -0600