shapeworks

User usage reporting (telemetry) More...

Namespaces

Name
shapeworks::mesh
shapeworks::particles
shapeworks::project

Classes

	Name
class	shapeworks::AnalysisTool
class	shapeworks::AnalysisUtils
class	shapeworks::Analyze High level analyze API.
class	shapeworks::AnalyzeCommandGroup
class	shapeworks::ColorMap
class	shapeworks::ColorMaps
class	shapeworks::Command
class	shapeworks::CompareSettings
class	shapeworks::CompareWidget
class	shapeworks::Constraint
class	shapeworks::Constraints
class	shapeworks::ContourDomain
class	shapeworks::CorrespondenceFunction Correspondence term.
class	shapeworks::CurvatureSamplingFunction Please note: This is the sampling function currently being used.
class	shapeworks::DataTool
class	shapeworks::DeepSSMJob Qt Wrapper for DeepSSM.
class	shapeworks::DeepSSMParameters
class	shapeworks::DeepSSMTool
class	shapeworks::DisentangledCorrespondenceFunction
class	shapeworks::DualVectorFunction
class	shapeworks::EigenUtils
class	shapeworks::ExcelProjectReader Excel file format reader for Project.
class	shapeworks::ExcelProjectWriter Excel file format writer for Project.
class	shapeworks::Executable
class	shapeworks::ExportImageDialog
class	shapeworks::ExportUtils Export utilities for Studio.
class	shapeworks::FreeFormConstraint
class	shapeworks::GenericContainer This class seems to be only a wrapper around std::vector implementing ITK DataObject (for smart pointer?)
class	shapeworks::GenericContainerArray This class appears to be an array of GenericContainers (e.g. std::vector) that implements the Observer interface. The array size tracks the number of domains in the system. E.g. one per domain.
class	shapeworks::GradientDescentOptimizer
class	shapeworks::Groom High level groom API.
class	shapeworks::GroomCommandGroup
class	shapeworks::GroomParameters
class	shapeworks::GroomTool
class	shapeworks::GroupPvalueJob
class	shapeworks::Image
class	shapeworks::ImageCommand
class	shapeworks::ImageDomain
class	shapeworks::ImageDomainWithCurvature
class	shapeworks::ImageDomainWithGradients
class	shapeworks::ImageDomainWithGradN
class	shapeworks::ImageLabel An extention of QLabel especially for scaled images.
class	shapeworks::ImageUtils Helper functions for image.
class	shapeworks::ImplicitSurfaceDomain
class	shapeworks::IndexRegion Indices into a 3d region of memory (can be negative, e.g., for the purpose of padding an image)
class	shapeworks::Job
class	shapeworks::JsonProjectReader JSON file format reader for Project.
class	shapeworks::JsonProjectWriter JSON file format writer for Project.
class	shapeworks::KeyboardShortcuts
class	shapeworks::LandmarkDefinition Landmark class containing properties of each landmark.
class	shapeworks::LandmarkItemDelegate
class	shapeworks::LandmarkTableModel
class	shapeworks::LandmarkWidget LandmarkWidget.
class	shapeworks::LegacyCorrespondenceFunction
class	shapeworks::LegacyShapeMatrix
class	shapeworks::Lightbox Display multiple Viewers in a tiled display.
class	shapeworks::LinearRegressionShapeMatrix
class	shapeworks::Logging ShapeWorks Logging Library.
class	shapeworks::LogWindow Log Window.
class	shapeworks::MatrixContainer
class	shapeworks::MeanCurvatureContainer
class	shapeworks::Mesh
class	shapeworks::MeshCache Thread safe cache for meshes index by shape.
class	shapeworks::MeshCommand
class	shapeworks::MeshDomain
class	shapeworks::MeshGenerator
struct	shapeworks::MeshGeoEntry
class	shapeworks::MeshGroup Representation of a group of meshes.
class	shapeworks::MeshManager Class to manage meshes.
class	shapeworks::MeshReader reads mesh (used only by one of the Mesh constructors)
class	shapeworks::MeshReconstructors
class	shapeworks::MeshSlice MeshSlice.
class	shapeworks::MeshUtils
class	shapeworks::MeshWarper
class	shapeworks::MeshWorker
class	shapeworks::MeshWorkItem Provides concurrent access to a list of shapes to work needing reconstruction.
class	shapeworks::MeshWorkQueue
class	shapeworks::MeshWrapper
class	shapeworks::MixedEffectsShapeMatrix
struct	shapeworks::MultiVariateNormalRandom
class	shapeworks::NetworkAnalysisJob
class	shapeworks::Observer This class is an observer interface for classes to monitor for changes to the optimizer (observer pattern)
class	shapeworks::OptimizationVisualizer
class	shapeworks::Optimize
class	shapeworks::OptimizeCommandGroup
class	shapeworks::OptimizeParameterFile
class	shapeworks::OptimizeParameters
class	shapeworks::OptimizeTool
class	shapeworks::PaintWidget
class	shapeworks::Parameters Parameter settings.
class	shapeworks::ParticleArea
class	shapeworks::ParticleAreaJob
class	shapeworks::ParticleAreaPanel
class	shapeworks::ParticleColors Supplies particle colors.
class	shapeworks::ParticleDomain
class	shapeworks::ParticleEvent
class	shapeworks::ParticleGaussianModeWriter
class	shapeworks::ParticleGoodBadAssessment Performs good/bad points assessment and reports the bad positions of the particle system.
class	shapeworks::ParticleNeighborhood
class	shapeworks::ParticleNormalEvaluation
class	shapeworks::ParticleNormalEvaluationJob
struct	shapeworks::ParticlePointIndexPair
class	shapeworks::ParticleRegionDomain
class	shapeworks::ParticleRegionNeighborhood
class	shapeworks::Particles Representation of correspondence points for a shape including multiple domains.
class	shapeworks::ParticleShapeStatistics
class	shapeworks::ParticleSurfaceNeighborhood
class	shapeworks::ParticleSystem A facade class managing interactions with a particle system.
class	shapeworks::ParticleSystemCommand
class	shapeworks::ParticleSystemEvaluation
class	shapeworks::PhysicalRegion physical bounds of a 3d region of space
class	shapeworks::PickResult
class	shapeworks::PlaneConstraint
class	shapeworks::PlaneWidget PlaneWidget.
class	shapeworks::PowerOfTwoPointTree
class	shapeworks::PowerOfTwoPointTreeNode
struct	shapeworks::powstruct
struct	shapeworks::powstruct< a, 0 >
class	shapeworks::PreferencesWindow Qt UI dialog to control preferences.
class	shapeworks::ProcrustesRegistration
class	shapeworks::Project Representation of a project.
class	shapeworks::ProjectCommandGroup
class	shapeworks::ProjectReader Base class for Project readers.
class	shapeworks::ProjectUtils
class	shapeworks::PythonWorker
class	shapeworks::QMeshWarper Wraps MeshWarper as a QObject.
class	shapeworks::QOptimize Wraps Optimize as a QObject.
struct	shapeworks::Reconstruction
class	shapeworks::ReconstructSurface
class	shapeworks::Sampler
class	shapeworks::SamplingFunction This function returns an estimate of the gradient of the entropy of a particle distribution with respect to change in position of a specific particle in that distribution.
class	shapeworks::Session Representation of a session.
class	shapeworks::Shape Representation of a single shape/patient/subject.
class	shapeworks::ShapeEvaluation
class	shapeworks::ShapeEvaluationJob
class	shapeworks::ShapeGradientMatrix Each column describes a shape. A shape may be composed of m_DomainsPerShape domains (default 1). ALL DOMAINS ARE NOT ASSUMED TO HAVE THE SAME NUMBER OF PARTICLES!
class	shapeworks::ShapeMatrix Each column describes a shape. A shape may be composed of m_DomainsPerShape domains (default 1). ALL DOMAINS ARE NOT ASSUMED TO HAVE THE SAME NUMBER OF PARTICLES!
class	shapeworks::ShapeScalarJob
class	shapeworks::ShapeScalarPanel
class	shapeworks::shapeworks_exception
class	shapeworks::ShapeworksCommand
class	shapeworks::ShapeWorksStudioApp Main ShapeWorksStudio window.
class	shapeworks::ShapeWorksUtils
class	shapeworks::ShapeworksWorker
struct	shapeworks::SharedCommandData
class	shapeworks::SliceView SliceView.
class	shapeworks::SplashScreen
class	shapeworks::StatsGroupLDAJob
class	shapeworks::StatusBarWidget StatusBarWidget.
class	shapeworks::StringUtils String utility functions.
class	shapeworks::StudioHandleWidget
class	shapeworks::StudioInteractorStyle
class	shapeworks::StudioMesh Representation of a single mesh.
class	shapeworks::StudioSliceInteractorStyle
class	shapeworks::StudioUtils Utilities for Studio.
class	shapeworks::StudioVtkOutputWindow Implementation of vtkOutputWindow to capture and display VTK error messages.
class	shapeworks::Style
class	shapeworks::Subject Representation of a single subject.
class	shapeworks::Telemetry
class	shapeworks::UpdateChecker Update Checker.
class	shapeworks::Variant Variant class to represent multiple types.
class	shapeworks::VectorFunction
class	shapeworks::VectorImage Gradient (vector) image.
class	shapeworks::Viewer 3D Viewer
class	shapeworks::Visualizer Controls display of objects in viewers.
class	shapeworks::WheelEventForwarder
class	shapeworks::Worker

Types

	Name
enum	DisplayMode
enum	Axis { invalid = -1, X, Y, Z} handy way to specify an axis
enum class char	ConstraintType
enum class int	CorrespondenceMode
enum class char	DomainType
enum	ArrayTransferOptions { COPY_ARRAY, SHARE_ARRAY, MOVE_ARRAY} ways of tranferring Arrays to Python, copy being the least efficient but most conservative
enum	LandmarkColumns
enum	LandmarkVisibility
enum class	MessageType
using std::map< MeshWorkItem, MeshHandle >	CacheMap
using std::list< MeshWorkItem >	CacheList
using std::shared_ptr< Shape >	ShapeHandle
using std::vector< ShapeHandle >	ShapeList
using std::shared_ptr< StudioMesh >	MeshHandle
using std::vector< MeshHandle >	MeshList
using itk::Index< 3 >	Coord Simple names for common types used in the framework.
using itk::Size< 3 >	Dims
using itk::Point< double, 3 >	Point3
using itk::Vector< double, 3 >	Vector3
using itk::Matrix< double, 4, 4 >	Matrix44
using itk::Matrix< double, 3, 3 >	Matrix33
using itk::Point< int, 3 >	IPoint3
using itk::Point< float, 3 >	FPoint3
using itk::CovariantVector< float, 3 >	Covariant
using Vector3	Vector
using Point3	Point
using Matrix33	Matrix
using vtkSmartPointer< vtkPlane >	Plane
using vtkSmartPointer< vtkDataArray >	Array
using Array	Field
using std::vector< Point3 >	PointArray
using itk::Transform< double, 3 >	GenericTransform All transforms can be accessed using a generic transform pointer.
using itk::IdentityTransform< double, 3 >	IdentityTransform
using GenericTransform::Pointer	TransformPtr
using itk::AffineTransform< double, 3 >	AffineTransform Affine transforms are used for many Image manipulation commands.
using AffineTransform::Pointer	AffineTransformPtr
using vtkSmartPointer< vtkTransform >	MeshTransform Mesh transforms.
using itk::ThinPlateSplineKernelTransform2< double, 3 >	ThinPlateSplineTransform Transforms that can be used for ReconstructSurface.
using itk::CompactlySupportedRBFSparseKernelTransform< double, 3 >	RBFSSparseTransform
using std::shared_ptr< Project >	ProjectHandle
template <typename T > using Eigen::Matrix< T, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor >	VnlMatrix
typedef QSharedPointer< Session >	SessionHandle
using vtkSmartPointer< vtkTransform >	TransformType TODO: replace this.
typedef QSharedPointer< Lightbox >	LightboxHandle
typedef QSharedPointer< Viewer >	ViewerHandle
typedef QVector< ViewerHandle >	ViewerList
typedef QSharedPointer< Visualizer >	VisualizerHandle

Functions

	Name
	COMMAND_DECLARE(ReadImage , ImageCommand )
	COMMAND_DECLARE(WriteImage , ImageCommand )
	COMMAND_DECLARE(ImageInfo , ImageCommand )
	COMMAND_DECLARE(Antialias , ImageCommand )
	COMMAND_DECLARE(ResampleImage , ImageCommand )
	COMMAND_DECLARE(ResizeImage , ImageCommand )
	COMMAND_DECLARE(RecenterImage , ImageCommand )
	COMMAND_DECLARE(PadImage , ImageCommand )
	COMMAND_DECLARE(TranslateImage , ImageCommand )
	COMMAND_DECLARE(ScaleImage , ImageCommand )
	COMMAND_DECLARE(Rotate , ImageCommand )
	COMMAND_DECLARE(ExtractLabel , ImageCommand )
	COMMAND_DECLARE(CloseHoles , ImageCommand )
	COMMAND_DECLARE(Binarize , ImageCommand )
	COMMAND_DECLARE(ComputeDT , ImageCommand )
	COMMAND_DECLARE(CurvatureFilter , ImageCommand )
	COMMAND_DECLARE(GradientFilter , ImageCommand )
	COMMAND_DECLARE(SigmoidFilter , ImageCommand )
	COMMAND_DECLARE(TPLevelSetFilter , ImageCommand )
	COMMAND_DECLARE(TopologyPreservingFilter , ImageCommand )
	COMMAND_DECLARE(IntensityFilter , ImageCommand )
	COMMAND_DECLARE(Blur , ImageCommand )
	COMMAND_DECLARE(BoundingBoxImage , ImageCommand )
	COMMAND_DECLARE(ImageBounds , ImageCommand )
	COMMAND_DECLARE(CropImage , ImageCommand )
	COMMAND_DECLARE(ICPRigid , ImageCommand )
	COMMAND_DECLARE(ClipImage , ImageCommand )
	COMMAND_DECLARE(ReflectImage , ImageCommand )
	COMMAND_DECLARE(SetOrigin , ImageCommand )
	COMMAND_DECLARE(SetSpacing , ImageCommand )
	COMMAND_DECLARE(WarpImage , ImageCommand )
	COMMAND_DECLARE(CompareImage , ImageCommand )
	COMMAND_DECLARE(NegateImage , ImageCommand )
	COMMAND_DECLARE(AddImage , ImageCommand )
	COMMAND_DECLARE(SubtractImage , ImageCommand )
	COMMAND_DECLARE(MultiplyImage , ImageCommand )
	COMMAND_DECLARE(DivideImage , ImageCommand )
	COMMAND_DECLARE(ImageToMesh , ImageCommand )
	COMMAND_DECLARE(SetRegion , ImageCommand )
	COMMAND_DECLARE(Isolate , ImageCommand )
	COMMAND_DECLARE(ReadParticleSystem , ParticleSystemCommand )
	COMMAND_DECLARE(Compactness , ParticleSystemCommand )
	COMMAND_DECLARE(Generalization , ParticleSystemCommand )
	COMMAND_DECLARE(Specificity , ParticleSystemCommand )
	COMMAND_DECLARE(ReadMesh , MeshCommand )
	COMMAND_DECLARE(WriteMesh , MeshCommand )
	COMMAND_DECLARE(MeshInfo , MeshCommand )
	COMMAND_DECLARE(Coverage , MeshCommand )
	COMMAND_DECLARE(Smooth , MeshCommand )
	COMMAND_DECLARE(SmoothSinc , MeshCommand )
	COMMAND_DECLARE(Remesh , MeshCommand )
	COMMAND_DECLARE(RemeshPercent , MeshCommand )
	COMMAND_DECLARE(InvertNormals , MeshCommand )
	COMMAND_DECLARE(ReflectMesh , MeshCommand )
	COMMAND_DECLARE(TransformMesh , MeshCommand )
	COMMAND_DECLARE(FillHoles , MeshCommand )
	COMMAND_DECLARE(ProbeVolume , MeshCommand )
	COMMAND_DECLARE(ClipMesh , MeshCommand )
	COMMAND_DECLARE(TranslateMesh , MeshCommand )
	COMMAND_DECLARE(ScaleMesh , MeshCommand )
	COMMAND_DECLARE(BoundingBoxMesh , MeshCommand )
	COMMAND_DECLARE(MeshBounds , MeshCommand )
	COMMAND_DECLARE(Distance , MeshCommand )
	COMMAND_DECLARE(ComputeNormals , MeshCommand )
	COMMAND_DECLARE(SetField , MeshCommand )
	COMMAND_DECLARE(GetField , MeshCommand )
	COMMAND_DECLARE(SetFieldValue , MeshCommand )
	COMMAND_DECLARE(GetFieldValue , MeshCommand )
	COMMAND_DECLARE(FieldRange , MeshCommand )
	COMMAND_DECLARE(FieldMean , MeshCommand )
	COMMAND_DECLARE(FieldStd , MeshCommand )
	COMMAND_DECLARE(FieldNames , MeshCommand )
	COMMAND_DECLARE(FixElement , MeshCommand )
	COMMAND_DECLARE(ClipClosedSurface , MeshCommand )
	COMMAND_DECLARE(ClosestPoint , MeshCommand )
	COMMAND_DECLARE(GeodesicDistance , MeshCommand )
	COMMAND_DECLARE(GeodesicDistanceToLandmark , MeshCommand )
	COMMAND_DECLARE(MeanNormals , MeshCommand )
	COMMAND_DECLARE(Curvature , MeshCommand )
	COMMAND_DECLARE(MeshToImage , MeshCommand )
	COMMAND_DECLARE(MeshToDT , MeshCommand )
	COMMAND_DECLARE(CompareMesh , MeshCommand )
	COMMAND_DECLARE(WarpMesh , MeshCommand )
	COMMAND_DECLARE(ComputeThickness , MeshCommand )
	COMMAND_DECLARE(LandmarkGeodesics , MeshCommand )
	COMMAND_DECLARE(Seed , ShapeworksCommand )
	COMMAND_DECLARE(OptimizeCommand , OptimizeCommandGroup )
	COMMAND_DECLARE(GroomCommand , GroomCommandGroup )
	COMMAND_DECLARE(AnalyzeCommand , AnalyzeCommandGroup )
	COMMAND_DECLARE(ConvertProjectCommand , ProjectCommandGroup )
std::string	display_mode_to_string(DisplayMode display_mode)
DisplayMode	string_to_display_mode(std::string str)
std::ostream &	operator<<(std::ostream & os, const IndexRegion & region)
std::ostream &	operator<<(std::ostream & os, const PhysicalRegion & region)
Vector3	makeVector(std::array< double, 3 > && arr) Enables makeVector({1,2,3});, construction using an initializer list (likely an accidental omission in current ITK version)
PointArray	makePointArray(int size, Point3 value)
TransformPtr	createTransform(const Matrix33 & mat, const Vector3 & translate =makeVector({0, 0, 0}))
TransformPtr	convert_to_image_transform(vtkSmartPointer< vtkTransform > vtk_transform) Convert VTK to ITK transform.
Plane	makePlane(const Point & p, const Vector3 & n) Make a plane.
Plane	makePlane(const Point & p0, const Point & p1, const Point & p2)
Point	getOrigin(const Plane plane) Get origin and normal of plane.
Vector3	getNormal(const Plane plane)
MeshTransform	createMeshTransform(const vtkSmartPointer< vtkMatrix4x4 > & mat)
Point	toPoint(const Dims & d) For deliberate conversions between types.
Point	toPoint(const Coord & c)
Vector	toVector(const Dims & d)
Vector	toVector(const Point & p)
Vector	toVector(const itk::CovariantVector< double, 3 > & v)
Point	toPoint(const Vector & v)
Coord	toCoord(const Dims & d)
Dims	toDims(const Coord & c)
Dims	toDims(const Point & p)
Coord	toCoord(const Point & p)
template <typename P > P	negate(const P & p) Negation operator (ITK only has it for Vectors, but sometimes useful for Points)
Vector3	negate(const Vector3 & v) Negate function for Vector (requires makeVector)
template <typename P > P	invertValue(const P & p) Inversion function for all but Vector.
Vector3	invertValue(const Vector3 & v) Inversion function for Vector (requires makeVector)
Vector3	dotProduct(const Vector3 & a, const Vector3 & b) Vector dot and cross products.
Vector3	crossProduct(const Vector3 & a, const Vector3 & b)
double	length(const Vector3 & v)
Axis	toAxis(const std::string & str)
std::string	axisToString(Axis axis)
bool	axis_is_valid(const Vector3 & axis) Ensure an axis is valid.
bool	axis_is_valid(const Axis & axis)
double	degToRad(const double deg) convert degrees to radians
double	mean(const Field field) incrementally compute (single-component) mean of field
double	stddev(const Field field) compute (single-component) standard deviation of field
std::vector< double >	range(const Field field) compute (single-component) range of field
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename P ,typename =std::enable_if_t<std::is_same::value
template <typename T > bool	epsEqual(T a, T b, T epsilon)
template <typename P ,typename =std::enable_if_t<std::is_same::value
bool	epsEqual(double a, double b, double eps)
template <typename T > T	clamp(T value, T min, T max) Simple clamp operation until C++17.
std::ostream &	operator<<(std::ostream & os, const Image & img) stream insertion operators for Image
Image	operator*(const Image & img, const double x) override templates defined in [Shapeworks.h]
Image	operator/(const Image & img, const double x)
Image &	operator*=(Image & img, const double x)
Image &	operator/=(Image & img, const double x)
std::ostream &	operator<<(std::ostream & os, const Mesh & mesh) stream insertion operators for Mesh
	itkEventMacro(ParticleDomainAddEvent , ParticleEvent )
	itkEventMacro(ParticleTransformSetEvent , ParticleEvent )
	itkEventMacro(ParticlePrefixTransformSetEvent , ParticleEvent )
	itkEventMacro(ParticleNeighborhoodSetEvent , ParticleEvent )
	itkEventMacro(ParticlePositionSetEvent , ParticleEvent )
	itkEventMacro(ParticlePositionAddEvent , ParticleEvent )
	itkEventMacro(ParticlePositionRemoveEvent , ParticleEvent )
void	SaveReconstructions(std::vector< Reconstruction > & reconstructions, const std::vector< std::string > & srcPaths, const std::string & saveTo)
template <typename T > std::string	variant_to_string(T begin, T end)
void	printNumpyArrayInfo(const py::array & np_array) print buffer info for the given array (dims, format, strides, etc)
void	verifyOrderAndPacking(const py::array & np_array) verify py::array has expected order and is densely packed, throw if not
void	setOwnership(py::array & array, bool owns) sets the OWNDATA flag of the given array to owns
Image::ImageType::Pointer	wrapNumpyArr(py::array & np_array) helper function for Image.init and Image.assign
Array	pyToArr(py::array & np_array, bool take_ownership =true) converts py::array to vtkDataArray, optionally taking ownership of data
py::array	arrToPy(Array & array, ArrayTransferOptions xfer =COPY_ARRAY) convert a vtkDataArray (AOS assumed) to a py::array using specified means of transfer
Eigen::MatrixXd	itkTransformToEigen(TransformPtr itk_xform)
TransformPtr	eigen44ToItkTransform(const Eigen::Matrix< double, 4, 4 > & eigen_mat)
Eigen::Matrix< double, 4, 4, Eigen::RowMajor >	vtkTransformToEigen(MeshTransform vtk_xform)
MeshTransform	eigen44ToVtkTransform(const Eigen::Matrix< double, 4, 4, Eigen::RowMajor > & eigen_mat)
template <typename T ,unsigned NRows,unsigned NCols> Eigen::Matrix< T, NRows, NCols, Eigen::RowMajor >	itkToEigen(const itk::Matrix< T, NRows, NCols > & itk_mat) Conversion (by copy) of itk matrix to Eigen::Matrix.
template <typename T ,int NRows,int NCols> itk::Matrix< T, NRows, NCols >	eigenToItk(const Eigen::Matrix< T, NRows, NCols, Eigen::RowMajor > & eigen_mat) Conversion (by copy) of Eigen::Matrix to itk (i.e., vnl) matrix.
template <typename T > Eigen::Map< VnlMatrix< T > >	vnlToEigen(const vnl_matrix< T > & vnl_mat) Wrap vnl matrix data to Eigen Matrix.
template <int NRows,int NCols,typename T > Eigen::Map< Eigen::Matrix< T, NRows, NCols, Eigen::RowMajor > >	wrapDataWithEigen(T * data)
template <typename T > Eigen::Map< Eigen::Matrix< T, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor > >	wrapDataWithEigen(T * data, size_t nrows, size_t ncols) Wrap a data pointer of the specified size with Eigen::Matrix.
template <unsigned NRows,unsigned NCols,typename T > itk::Matrix< T, NRows, NCols >	wrapDataWithItk(T * data)

Attributes

	Name
const auto	Pi pi that doesn't depend on deprecated or non-std lib defines

Detailed Description

User usage reporting (telemetry)

This class posts anonymous usage reporting statistics for usage tracking and software improvement purposes

Types Documentation

enum DisplayMode

Enumerator	Value	Description
Original	0
Groomed	1
Reconstructed	2

enum Axis

Enumerator	Value	Description
invalid	-1
X
Y
Z

handy way to specify an axis

enum ConstraintType

Enumerator	Value	Description
CuttingPlane	'C'
FreeForm	'F'

enum CorrespondenceMode

Enumerator	Value	Description
MeanEnergy	0
EnsembleEntropy	1
EnsembleRegressionEntropy	3
EnsembleMixedEffectsEntropy	4
MeshBasedGeneralEntropy	5
MeshBasedGeneralMeanEnergy	6
DisentagledEnsembleEntropy	7
DisentangledEnsembleMeanEnergy	8

enum DomainType

Enumerator	Value	Description
Image	'I'
Mesh	'M'
Contour	'C'

enum ArrayTransferOptions

Enumerator	Value	Description
COPY_ARRAY
SHARE_ARRAY
MOVE_ARRAY

ways of tranferring Arrays to Python, copy being the least efficient but most conservative

enum LandmarkColumns

Enumerator	Value	Description
VISIBLE_E
COLOR_E
NAME_E
POSITION_E
SET_BUTTON_E
COMMENT_E
END_E

enum LandmarkVisibility

Enumerator	Value	Description
ALL_VISIBLE_E
NONE_VISIBLE_E
SOME_VISIBLE_E

enum MessageType

Enumerator	Value	Description
normal
warning
error
debug

using CacheMap

using shapeworks::CacheMap = typedef std::map<MeshWorkItem, MeshHandle>;

using CacheList

using shapeworks::CacheList = typedef std::list<MeshWorkItem>;

using ShapeHandle

using shapeworks::ShapeHandle = typedef std::shared_ptr<Shape>;

using ShapeList

using shapeworks::ShapeList = typedef std::vector<ShapeHandle>;

using MeshHandle

using shapeworks::MeshHandle = typedef std::shared_ptr<StudioMesh>;

using MeshList

using shapeworks::MeshList = typedef std::vector<MeshHandle>;

using Coord

using shapeworks::Coord = typedef itk::Index<3>;

Simple names for common types used in the framework.

using Dims

using shapeworks::Dims = typedef itk::Size<3>;

using Point3

using shapeworks::Point3 = typedef itk::Point<double, 3>;

using Vector3

using shapeworks::Vector3 = typedef itk::Vector<double, 3>;

using Matrix44

using shapeworks::Matrix44 = typedef itk::Matrix<double, 4, 4>;

using Matrix33

using shapeworks::Matrix33 = typedef itk::Matrix<double, 3, 3>;

using IPoint3

using shapeworks::IPoint3 = typedef itk::Point<int, 3>;

using FPoint3

using shapeworks::FPoint3 = typedef itk::Point<float, 3>;

using Covariant

using shapeworks::Covariant = typedef itk::CovariantVector<float, 3>;

using Vector

using shapeworks::Vector = typedef Vector3;

using Point

using shapeworks::Point = typedef Point3;

using Matrix

using shapeworks::Matrix = typedef Matrix33;

using Plane

using shapeworks::Plane = typedef vtkSmartPointer<vtkPlane>;

using Array

using shapeworks::Array = typedef vtkSmartPointer<vtkDataArray>;

using Field

using shapeworks::Field = typedef Array;

using PointArray

using shapeworks::PointArray = typedef std::vector<Point3>;

using GenericTransform

using shapeworks::GenericTransform = typedef itk::Transform<double, 3>;

All transforms can be accessed using a generic transform pointer.

using IdentityTransform

using shapeworks::IdentityTransform = typedef itk::IdentityTransform<double, 3>;

using TransformPtr

using shapeworks::TransformPtr = typedef GenericTransform::Pointer;

using AffineTransform

using shapeworks::AffineTransform = typedef itk::AffineTransform<double, 3>;

Affine transforms are used for many Image manipulation commands.

using AffineTransformPtr

using shapeworks::AffineTransformPtr = typedef AffineTransform::Pointer;

using MeshTransform

using shapeworks::MeshTransform = typedef vtkSmartPointer<vtkTransform>;

Mesh transforms.

using ThinPlateSplineTransform

using shapeworks::ThinPlateSplineTransform = typedef itk::ThinPlateSplineKernelTransform2<double, 3>;

Transforms that can be used for ReconstructSurface.

using RBFSSparseTransform

using shapeworks::RBFSSparseTransform = typedef itk::CompactlySupportedRBFSparseKernelTransform<double, 3>;

using ProjectHandle

using shapeworks::ProjectHandle = typedef std::shared_ptr<Project>;

using VnlMatrix

template <typename T >
using shapeworks::VnlMatrix = typedef Eigen::Matrix<T, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;

typedef SessionHandle

typedef QSharedPointer<Session> shapeworks::SessionHandle;

using TransformType

using shapeworks::TransformType = typedef vtkSmartPointer<vtkTransform>;

TODO: replace this.

typedef LightboxHandle

typedef QSharedPointer<Lightbox> shapeworks::LightboxHandle;

typedef ViewerHandle

typedef QSharedPointer<Viewer> shapeworks::ViewerHandle;

typedef ViewerList

typedef QVector<ViewerHandle> shapeworks::ViewerList;

typedef VisualizerHandle

typedef QSharedPointer<Visualizer> shapeworks::VisualizerHandle;

Functions Documentation

function COMMAND_DECLARE

COMMAND_DECLARE(
    ReadImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    WriteImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ImageInfo ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Antialias ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ResampleImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ResizeImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    RecenterImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    PadImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    TranslateImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ScaleImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Rotate ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ExtractLabel ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    CloseHoles ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Binarize ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ComputeDT ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    CurvatureFilter ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    GradientFilter ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SigmoidFilter ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    TPLevelSetFilter ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    TopologyPreservingFilter ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    IntensityFilter ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Blur ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    BoundingBoxImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ImageBounds ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    CropImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ICPRigid ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ClipImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ReflectImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SetOrigin ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SetSpacing ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    WarpImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    CompareImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    NegateImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    AddImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SubtractImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    MultiplyImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    DivideImage ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ImageToMesh ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SetRegion ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Isolate ,
    ImageCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ReadParticleSystem ,
    ParticleSystemCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Compactness ,
    ParticleSystemCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Generalization ,
    ParticleSystemCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Specificity ,
    ParticleSystemCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ReadMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    WriteMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    MeshInfo ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Coverage ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Smooth ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SmoothSinc ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Remesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    RemeshPercent ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    InvertNormals ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ReflectMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    TransformMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    FillHoles ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ProbeVolume ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ClipMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    TranslateMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ScaleMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    BoundingBoxMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    MeshBounds ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Distance ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ComputeNormals ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SetField ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    GetField ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    SetFieldValue ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    GetFieldValue ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    FieldRange ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    FieldMean ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    FieldStd ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    FieldNames ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    FixElement ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ClipClosedSurface ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ClosestPoint ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    GeodesicDistance ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    GeodesicDistanceToLandmark ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    MeanNormals ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Curvature ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    MeshToImage ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    MeshToDT ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    CompareMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    WarpMesh ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ComputeThickness ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    LandmarkGeodesics ,
    MeshCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    Seed ,
    ShapeworksCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    OptimizeCommand ,
    OptimizeCommandGroup 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    GroomCommand ,
    GroomCommandGroup 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    AnalyzeCommand ,
    AnalyzeCommandGroup 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    ConvertProjectCommand ,
    ProjectCommandGroup 
)

function display_mode_to_string

std::string display_mode_to_string(
    DisplayMode display_mode
)

function string_to_display_mode

DisplayMode string_to_display_mode(
    std::string str
)

function operator<<

std::ostream & operator<<(
    std::ostream & os,
    const IndexRegion & region
)

function operator<<

std::ostream & operator<<(
    std::ostream & os,
    const PhysicalRegion & region
)

function makeVector

Vector3 makeVector(
    std::array< double, 3 > && arr
)

Enables makeVector({1,2,3});, construction using an initializer list (likely an accidental omission in current ITK version)

function makePointArray

PointArray makePointArray(
    int size,
    Point3 value
)

function createTransform

TransformPtr createTransform(
    const Matrix33 & mat,
    const Vector3 & translate =makeVector({0, 0, 0})
)

function convert_to_image_transform

TransformPtr convert_to_image_transform(
    vtkSmartPointer< vtkTransform > vtk_transform
)

Convert VTK to ITK transform.

function makePlane

Plane makePlane(
    const Point & p,
    const Vector3 & n
)

Make a plane.

function makePlane

Plane makePlane(
    const Point & p0,
    const Point & p1,
    const Point & p2
)

function getOrigin

Point getOrigin(
    const Plane plane
)

Get origin and normal of plane.

function getNormal

Vector3 getNormal(
    const Plane plane
)

function createMeshTransform

MeshTransform createMeshTransform(
    const vtkSmartPointer< vtkMatrix4x4 > & mat
)

function toPoint

Point toPoint(
    const Dims & d
)

For deliberate conversions between types.

function toPoint

Point toPoint(
    const Coord & c
)

function toVector

Vector toVector(
    const Dims & d
)

function toVector

Vector toVector(
    const Point & p
)

function toVector

Vector toVector(
    const itk::CovariantVector< double, 3 > & v
)

function toPoint

Point toPoint(
    const Vector & v
)

function toCoord

Coord toCoord(
    const Dims & d
)

function toDims

Dims toDims(
    const Coord & c
)

function toDims

Dims toDims(
    const Point & p
)

function toCoord

Coord toCoord(
    const Point & p
)

function negate

template <typename P >
P negate(
    const P & p
)

Negation operator (ITK only has it for Vectors, but sometimes useful for Points)

function negate

Vector3 negate(
    const Vector3 & v
)

Negate function for Vector (requires makeVector)

function invertValue

template <typename P >
P invertValue(
    const P & p
)

Inversion function for all but Vector.

function invertValue

Vector3 invertValue(
    const Vector3 & v
)

Inversion function for Vector (requires makeVector)

function dotProduct

Vector3 dotProduct(
    const Vector3 & a,
    const Vector3 & b
)

Vector dot and cross products.

function crossProduct

Vector3 crossProduct(
    const Vector3 & a,
    const Vector3 & b
)

function length

double length(
    const Vector3 & v
)

function toAxis

Axis toAxis(
    const std::string & str
)

function axisToString

std::string axisToString(
    Axis axis
)

function axis_is_valid

bool axis_is_valid(
    const Vector3 & axis
)

Ensure an axis is valid.

function axis_is_valid

bool axis_is_valid(
    const Axis & axis
)

function degToRad

double degToRad(
    const double deg
)

convert degrees to radians

function mean

double mean(
    const Field field
)

incrementally compute (single-component) mean of field

function stddev

double stddev(
    const Field field
)

compute (single-component) standard deviation of field

function range

std::vector< double > range(
    const Field field
)

compute (single-component) range of field

function operator+

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P operator+(
    const P & p,
    const P & q
)

function operator-

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P operator-(
    const P & p,
    const P & q
)

function operator*

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Vector, P>::value ||                                                  std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P operator*(
    const P & p,
    const P & q
)

function operator/

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Vector, P>::value ||                                                  std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P operator/(
    const P & p,
    const P & q
)

function operator+=

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P & operator+=(
    P & p,
    const P & q
)

function operator-=

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P & operator-=(
    P & p,
    const P & q
)

function operator*

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P operator*(
    const P & p,
    const double x
)

function operator/

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P operator/(
    const P & p,
    const double x
)

function operator*=

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P & operator*=(
    P & p,
    const double x
)

function operator/=

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
P & operator/=(
    P & p,
    const double x
)

function epsEqual

template <typename T >
bool epsEqual(
    T a,
    T b,
    T epsilon
)

function epsEqual

template <typename P ,
typename  =std::enable_if_t<std::is_same<Image, P>::value ||                                                 std::is_same<Coord, P>::value ||                                                 std::is_same<Dims, P>::value ||                                                 std::is_same<Vector, P>::value ||                                                 std::is_same<Point, P>::value ||                                                 std::is_same<IPoint3, P>::value ||                                                 std::is_same<FPoint3, P>::value>>
bool epsEqual(
    const P & a,
    const P & b,
    const typename P::ValueType & eps
)

function epsEqual

bool epsEqual(
    double a,
    double b,
    double eps
)

function clamp

template <typename T >
T clamp(
    T value,
    T min,
    T max
)

Simple clamp operation until C++17.

function operator<<

std::ostream & operator<<(
    std::ostream & os,
    const Image & img
)

stream insertion operators for Image

function operator*

Image operator*(
    const Image & img,
    const double x
)

override templates defined in [Shapeworks.h]

function operator/

Image operator/(
    const Image & img,
    const double x
)

function operator*=

Image & operator*=(
    Image & img,
    const double x
)

function operator/=

Image & operator/=(
    Image & img,
    const double x
)

function operator<<

std::ostream & operator<<(
    std::ostream & os,
    const Mesh & mesh
)

stream insertion operators for Mesh

function itkEventMacro

itkEventMacro(
    ParticleDomainAddEvent ,
    ParticleEvent 
)

function itkEventMacro

itkEventMacro(
    ParticleTransformSetEvent ,
    ParticleEvent 
)

function itkEventMacro

itkEventMacro(
    ParticlePrefixTransformSetEvent ,
    ParticleEvent 
)

function itkEventMacro

itkEventMacro(
    ParticleNeighborhoodSetEvent ,
    ParticleEvent 
)

function itkEventMacro

itkEventMacro(
    ParticlePositionSetEvent ,
    ParticleEvent 
)

function itkEventMacro

itkEventMacro(
    ParticlePositionAddEvent ,
    ParticleEvent 
)

function itkEventMacro

itkEventMacro(
    ParticlePositionRemoveEvent ,
    ParticleEvent 
)

function SaveReconstructions

void SaveReconstructions(
    std::vector< Reconstruction > & reconstructions,
    const std::vector< std::string > & srcPaths,
    const std::string & saveTo
)

function variant_to_string

template <typename T >
std::string variant_to_string(
    T begin,
    T end
)

function printNumpyArrayInfo

void printNumpyArrayInfo(
    const py::array & np_array
)

print buffer info for the given array (dims, format, strides, etc)

function verifyOrderAndPacking

void verifyOrderAndPacking(
    const py::array & np_array
)

verify py::array has expected order and is densely packed, throw if not

function setOwnership

void setOwnership(
    py::array & array,
    bool owns
)

sets the OWNDATA flag of the given array to owns

function wrapNumpyArr

Image::ImageType::Pointer wrapNumpyArr(
    py::array & np_array
)

helper function for Image.init and Image.assign

function pyToArr

Array pyToArr(
    py::array & np_array,
    bool take_ownership =true
)

converts py::array to vtkDataArray, optionally taking ownership of data

function arrToPy

py::array arrToPy(
    Array & array,
    ArrayTransferOptions xfer =COPY_ARRAY
)

convert a vtkDataArray (AOS assumed) to a py::array using specified means of transfer

function itkTransformToEigen

Eigen::MatrixXd itkTransformToEigen(
    TransformPtr itk_xform
)

function eigen44ToItkTransform

TransformPtr eigen44ToItkTransform(
    const Eigen::Matrix< double, 4, 4 > & eigen_mat
)

function vtkTransformToEigen

Eigen::Matrix< double, 4, 4, Eigen::RowMajor > vtkTransformToEigen(
    MeshTransform vtk_xform
)

function eigen44ToVtkTransform

MeshTransform eigen44ToVtkTransform(
    const Eigen::Matrix< double, 4, 4, Eigen::RowMajor > & eigen_mat
)

function itkToEigen

template <typename T ,
unsigned NRows,
unsigned NCols>
Eigen::Matrix< T, NRows, NCols, Eigen::RowMajor > itkToEigen(
    const itk::Matrix< T, NRows, NCols > & itk_mat
)

Conversion (by copy) of itk matrix to Eigen::Matrix.

function eigenToItk

template <typename T ,
int NRows,
int NCols>
itk::Matrix< T, NRows, NCols > eigenToItk(
    const Eigen::Matrix< T, NRows, NCols, Eigen::RowMajor > & eigen_mat
)

Conversion (by copy) of Eigen::Matrix to itk (i.e., vnl) matrix.

function vnlToEigen

template <typename T >
Eigen::Map< VnlMatrix< T > > vnlToEigen(
    const vnl_matrix< T > & vnl_mat
)

Wrap vnl matrix data to Eigen Matrix.

function wrapDataWithEigen

template <int NRows,
int NCols,
typename T >
Eigen::Map< Eigen::Matrix< T, NRows, NCols, Eigen::RowMajor > > wrapDataWithEigen(
    T * data
)

Wrap data pointer with Eigen::Matrix. Handy for efficiently going back and forth between Python numpy arrays. WARNING: if data goes out of scope (e.g., numpy array size changes), matrix will point to invalid location.

function wrapDataWithEigen

template <typename T >
Eigen::Map< Eigen::Matrix< T, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor > > wrapDataWithEigen(
    T * data,
    size_t nrows,
    size_t ncols
)

Wrap a data pointer of the specified size with Eigen::Matrix.

function wrapDataWithItk

template <unsigned NRows,
unsigned NCols,
typename T >
itk::Matrix< T, NRows, NCols > wrapDataWithItk(
    T * data
)

Wrap data pointer with itk::Matrix. Handy for efficiently going back and forth between Python numpy arrays. WARNING: This function actually just copies data.

Attributes Documentation

variable Pi

const auto Pi = std::atan(1.0) * 4.0;

pi that doesn't depend on deprecated or non-std lib defines

---

Updated on 2024-03-17 at 12:58:44 -0600