shapeworks

Classes

	Name
class	shapeworks::AnalysisTool
class	shapeworks::AnalysisUtils
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::DataTool
class	shapeworks::DeepSSMJob Qt Wrapper for DeepSSM.
class	shapeworks::DeepSSMParameters
class	shapeworks::DeepSSMTool
class	shapeworks::Executable
class	shapeworks::ExportImageDialog
class	shapeworks::ExportUtils Export utilities for Studio.
class	shapeworks::FreeFormConstraint FreeFormConstraint.
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::ImageLabel An extention of QLabel especially for scaled images.
class	shapeworks::ImageUtils Helper functions for image.
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::KeyboardShortcuts
class	shapeworks::LandmarkDefinition Landmark class containing properties of each landmark.
class	shapeworks::LandmarkItemDelegate
class	shapeworks::LandmarkTableModel
class	shapeworks::LandmarkWidget LandmarkWidget.
class	shapeworks::Lightbox Display multiple Viewers in a tiled display.
class	shapeworks::LogWindow Log Window.
class	shapeworks::MatrixContainer
class	shapeworks::Mesh
class	shapeworks::MeshCache
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	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
class	shapeworks::MeshWorkQueue
class	shapeworks::MeshWrapper
struct	shapeworks::MultiVariateNormalRandom
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::ParticleDomain
class	shapeworks::ParticleImageDomain
class	shapeworks::ParticleImageDomainWithCurvature
class	shapeworks::ParticleImageDomainWithGradients
class	shapeworks::ParticleImageDomainWithGradN
class	shapeworks::ParticleImplicitSurfaceDomain
class	shapeworks::ParticleNormalEvaluation
class	shapeworks::ParticleNormalEvaluationJob
class	shapeworks::ParticleProcrustesRegistration
class	shapeworks::ParticleRegionDomain
class	shapeworks::ParticleShapeStatistics
class	shapeworks::ParticleSystem
class	shapeworks::ParticleSystemCommand
class	shapeworks::PhysicalRegion physical bounds of a 3d region of space
class	shapeworks::PickResult
class	shapeworks::PlaneConstraint PlaneConstraint.
class	shapeworks::PlaneWidget PlaneWidget.
class	shapeworks::PreferencesWindow Qt UI dialog to control preferences.
class	shapeworks::Project Representation of a project.
class	shapeworks::ProjectUtils
class	shapeworks::PythonWorker
class	shapeworks::QGroom Qt Wrapper for Groom.
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::Session Representation of a session.
class	shapeworks::Shape Representation of a single shape/patient/subject.
class	shapeworks::ShapeEvaluation
class	shapeworks::ShapeEvaluationJob
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::SphereConstraint
class	shapeworks::SplashScreen
class	shapeworks::StatsGroupLDAJob
class	shapeworks::StatusBarWidget StatusBarWidget.
class	shapeworks::StringUtils String utility functions.
class	shapeworks::StudioHandleWidget
class	shapeworks::StudioInteractorStyle
class	shapeworks::StudioLog
class	shapeworks::StudioMesh Representation of a single mesh.
class	shapeworks::StudioParticles Representation of correspondence points for a shape including multiple domains.
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::TriMeshWrapper
class	shapeworks::Variant Variant class to represent multiple types.
class	shapeworks::VectorImage Gradient (vector) image.
class	shapeworks::Viewer 3D Viewer
class	shapeworks::Visualizer Controls display of objects in viewers.
class	shapeworks::VtkMeshWrapper
class	shapeworks::WheelEventForwarder
class	shapeworks::Worker

Types

	Name
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	DisplayMode
enum class	MessageType
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
using std::map< MeshWorkItem, MeshHandle >	CacheMap
using std::list< MeshWorkItem >	CacheList
typedef QSharedPointer< Session >	SessionHandle
using vtkSmartPointer< vtkTransform >	TransformType TODO: replace this.
using QSharedPointer< Shape >	ShapeHandle
using QVector< ShapeHandle >	ShapeList
using std::shared_ptr< StudioMesh >	MeshHandle
using std::vector< MeshHandle >	MeshList
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(Seed , ShapeworksCommand )
	COMMAND_DECLARE(OptimizeCommand , OptimizeCommandGroup )
	COMMAND_DECLARE(GroomCommand , GroomCommandGroup )
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}))
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
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)
std::string	display_mode_to_string(DisplayMode display_mode)
DisplayMode	string_to_display_mode(std::string str)

Attributes

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

Types Documentation

enum Axis

Enumerator	Value	Description
invalid	-1
X
Y
Z

handy way to specify an axis

enum ConstraintType

Enumerator	Value	Description
Sphere	'S'
CuttingPlane	'C'
FreeForm	'F'

enum CorrespondenceMode

Enumerator	Value	Description
MeanEnergy	0
EnsembleEntropy	1
EnsembleRegressionEntropy	3
EnsembleMixedEffectsEntropy	4
MeshBasedGeneralEntropy	5
MeshBasedGeneralMeanEnergy	6

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 DisplayMode

Enumerator	Value	Description
Original	0
Groomed	1
Reconstructed	2

enum MessageType

Enumerator	Value	Description
normal
warning
error
debug

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>;

using CacheMap

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

using CacheList

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

typedef SessionHandle

typedef QSharedPointer<Session> shapeworks::SessionHandle;

using TransformType

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

TODO: replace this.

using ShapeHandle

using shapeworks::ShapeHandle = typedef QSharedPointer<Shape>;

using ShapeList

using shapeworks::ShapeList = typedef QVector<ShapeHandle>;

using MeshHandle

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

using MeshList

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

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(
    Seed ,
    ShapeworksCommand 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    OptimizeCommand ,
    OptimizeCommandGroup 
)

function COMMAND_DECLARE

COMMAND_DECLARE(
    GroomCommand ,
    GroomCommandGroup 
)

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 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 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.

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
)

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 2022-07-23 at 17:50:03 -0600