shapeworks::Shape

Representation of a single shape/patient/subject.

#include <Shape.h>

Public Classes

	Name
class	Point TODO: replace this wherever it is used.

Public Functions

	Name
	Shape()
	~Shape()
std::string	get_display_name()
MeshGroup	get_meshes(DisplayMode display_mode, bool wait =false)
void	set_annotations(std::vector< std::string > annotations, bool only_overwrite_blank =true)
std::vector< std::string >	get_annotations()
void	set_mesh_manager(std::shared_ptr< MeshManager > mesh_manager)
void	set_subject(std::shared_ptr< shapeworks::Subject > subject)
bool	is_subject() Is this shape a population subject (e.g. mean/pca constructions are not)
std::shared_ptr< shapeworks::Subject >	get_subject() Return the pointer to the subject object.
bool	is_fixed() Helper to ask if this shape is fixed or not.
bool	is_excluded() Helper to ask if this shape is excluded.
void	import_original_file(const std::string & filename) Import the original raw mesh or image file.
MeshGroup	get_original_meshes(bool wait =false) Retrieve the original meshes.
MeshGroup	get_groomed_meshes(bool wait =false) Retrieve the groomed meshes.
MeshGroup	get_reconstructed_meshes(bool wait =false) Retrieve the reconstructed meshes.
void	set_reconstructed_meshes(MeshGroup meshes) Set the reconstructed meshes.
void	reset_groomed_mesh() Reset the groomed mesh so that it will be re-created.
bool	import_global_point_files(std::vector< std::string > filenames) Import global correspondence point files.
bool	import_local_point_files(std::vector< std::string > filenames) Import local correspondence point files.
bool	import_landmarks_files(std::vector< std::string > filenames) Import landmarks files.
bool	store_landmarks() Store landmarks.
bool	import_constraints(std::vector< std::string > filenames) import constraints
bool	store_constraints() Store constraints.
void	set_particles(Particles particles) Set particles.
Particles	get_particles() Get particles.
void	set_particle_transform(vtkSmartPointer< vtkTransform > transform) Set the particle transform (alignment)
void	set_alignment_type(int alignment) Set the alignment type.
Eigen::VectorXd	get_global_correspondence_points() Get the global correspondence points.
std::vector< Eigen::VectorXd >	get_particles_for_display() Get the global correspondence points for display.
Eigen::VectorXd	get_local_correspondence_points() Get the local correspondence points.
void	clear_reconstructed_mesh()
int	get_id() Get the id of this shape.
void	set_id(int id) Set the id of this shape.
void	update_annotations() Update the name of this shape.
std::vector< std::string >	get_original_filenames()
std::vector< std::string >	get_original_filenames_with_path()
std::string	get_original_filename()
std::string	get_original_filename_with_path()
std::string	get_groomed_filename()
std::string	get_groomed_filename_with_path(int domain)
std::string	get_global_point_filename()
std::string	get_global_point_filename_with_path()
std::string	get_local_point_filename()
std::string	get_local_point_filename_with_path()
void	set_transform(vtkSmartPointer< vtkTransform > transform)
vtkSmartPointer< vtkTransform >	get_transform(int domain =0)
vtkSmartPointer< vtkTransform >	get_inverse_transform(int domain =0)
bool	has_alignment()
vtkSmartPointer< vtkTransform >	get_original_transform(int domain =0)
void	set_reconstruction_transforms(std::vector< vtkSmartPointer< vtkTransform > > transforms)
vtkSmartPointer< vtkTransform >	get_reconstruction_transform(int domain)
vtkSmartPointer< vtkTransform >	get_groomed_transform(int domain =0)
vtkSmartPointer< vtkTransform >	get_procrustes_transform(int domain =0)
std::vector< vtkSmartPointer< vtkTransform > >	get_procrustes_transforms()
vtkSmartPointer< vtkTransform >	get_alignment(int domain =0)
void	load_feature(DisplayMode display_mode, std::string feature)
std::shared_ptr< Image >	get_image_volume(std::string image_volume_name)
std::shared_ptr< Image >	get_segmentation()
std::string	get_segmentation_filename()
Eigen::VectorXd	get_point_features(std::string feature)
void	set_point_features(std::string feature, Eigen::VectorXd values)
void	load_feature_from_scalar_file(std::string filename, std::string feature_name)
void	set_override_feature(std::string feature)
std::string	get_override_feature()
Eigen::MatrixXd &	landmarks()
std::vector< Constraints > &	constraints()
Constraints &	get_constraints(int domain_id)
bool	has_planes()
std::vector< std::shared_ptr< MeshWrapper > >	get_groomed_mesh_wrappers()
void	recompute_original_surface()
void	ensure_segmentation() If a segmentation doesn't exist, create a blank canvas.

Public Functions Documentation

function Shape

Shape()

function ~Shape

~Shape()

function get_display_name

std::string get_display_name()

function get_meshes

MeshGroup get_meshes(
    DisplayMode display_mode,
    bool wait =false
)

function set_annotations

void set_annotations(
    std::vector< std::string > annotations,
    bool only_overwrite_blank =true
)

function get_annotations

std::vector< std::string > get_annotations()

function set_mesh_manager

void set_mesh_manager(
    std::shared_ptr< MeshManager > mesh_manager
)

function set_subject

void set_subject(
    std::shared_ptr< shapeworks::Subject > subject
)

function is_subject

bool is_subject()

Is this shape a population subject (e.g. mean/pca constructions are not)

function get_subject

std::shared_ptr< shapeworks::Subject > get_subject()

Return the pointer to the subject object.

function is_fixed

bool is_fixed()

Helper to ask if this shape is fixed or not.

function is_excluded

bool is_excluded()

Helper to ask if this shape is excluded.

function import_original_file

void import_original_file(
    const std::string & filename
)

Import the original raw mesh or image file.

function get_original_meshes

MeshGroup get_original_meshes(
    bool wait =false
)

Retrieve the original meshes.

function get_groomed_meshes

MeshGroup get_groomed_meshes(
    bool wait =false
)

Retrieve the groomed meshes.

function get_reconstructed_meshes

MeshGroup get_reconstructed_meshes(
    bool wait =false
)

Retrieve the reconstructed meshes.

function set_reconstructed_meshes

void set_reconstructed_meshes(
    MeshGroup meshes
)

Set the reconstructed meshes.

function reset_groomed_mesh

void reset_groomed_mesh()

Reset the groomed mesh so that it will be re-created.

function import_global_point_files

bool import_global_point_files(
    std::vector< std::string > filenames
)

Import global correspondence point files.

function import_local_point_files

bool import_local_point_files(
    std::vector< std::string > filenames
)

Import local correspondence point files.

function import_landmarks_files

bool import_landmarks_files(
    std::vector< std::string > filenames
)

Import landmarks files.

function store_landmarks

bool store_landmarks()

Store landmarks.

function import_constraints

bool import_constraints(
    std::vector< std::string > filenames
)

import constraints

function store_constraints

bool store_constraints()

Store constraints.

function set_particles

void set_particles(
    Particles particles
)

Set particles.

function get_particles

Particles get_particles()

Get particles.

function set_particle_transform

void set_particle_transform(
    vtkSmartPointer< vtkTransform > transform
)

Set the particle transform (alignment)

function set_alignment_type

void set_alignment_type(
    int alignment
)

Set the alignment type.

function get_global_correspondence_points

Eigen::VectorXd get_global_correspondence_points()

Get the global correspondence points.

function get_particles_for_display

std::vector< Eigen::VectorXd > get_particles_for_display()

Get the global correspondence points for display.

function get_local_correspondence_points

Eigen::VectorXd get_local_correspondence_points()

Get the local correspondence points.

function clear_reconstructed_mesh

void clear_reconstructed_mesh()

function get_id

int get_id()

Get the id of this shape.

function set_id

void set_id(
    int id
)

Set the id of this shape.

function update_annotations

void update_annotations()

Update the name of this shape.

function get_original_filenames

std::vector< std::string > get_original_filenames()

function get_original_filenames_with_path

std::vector< std::string > get_original_filenames_with_path()

function get_original_filename

std::string get_original_filename()

function get_original_filename_with_path

std::string get_original_filename_with_path()

function get_groomed_filename

std::string get_groomed_filename()

function get_groomed_filename_with_path

std::string get_groomed_filename_with_path(
    int domain
)

function get_global_point_filename

std::string get_global_point_filename()

function get_global_point_filename_with_path

std::string get_global_point_filename_with_path()

function get_local_point_filename

std::string get_local_point_filename()

function get_local_point_filename_with_path

std::string get_local_point_filename_with_path()

function set_transform

void set_transform(
    vtkSmartPointer< vtkTransform > transform
)

function get_transform

vtkSmartPointer< vtkTransform > get_transform(
    int domain =0
)

function get_inverse_transform

vtkSmartPointer< vtkTransform > get_inverse_transform(
    int domain =0
)

function has_alignment

bool has_alignment()

function get_original_transform

vtkSmartPointer< vtkTransform > get_original_transform(
    int domain =0
)

function set_reconstruction_transforms

void set_reconstruction_transforms(
    std::vector< vtkSmartPointer< vtkTransform > > transforms
)

function get_reconstruction_transform

vtkSmartPointer< vtkTransform > get_reconstruction_transform(
    int domain
)

function get_groomed_transform

vtkSmartPointer< vtkTransform > get_groomed_transform(
    int domain =0
)

function get_procrustes_transform

vtkSmartPointer< vtkTransform > get_procrustes_transform(
    int domain =0
)

function get_procrustes_transforms

std::vector< vtkSmartPointer< vtkTransform > > get_procrustes_transforms()

function get_alignment

vtkSmartPointer< vtkTransform > get_alignment(
    int domain =0
)

function load_feature

void load_feature(
    DisplayMode display_mode,
    std::string feature
)

function get_image_volume

std::shared_ptr< Image > get_image_volume(
    std::string image_volume_name
)

function get_segmentation

std::shared_ptr< Image > get_segmentation()

function get_segmentation_filename

inline std::string get_segmentation_filename()

function get_point_features

Eigen::VectorXd get_point_features(
    std::string feature
)

function set_point_features

void set_point_features(
    std::string feature,
    Eigen::VectorXd values
)

function load_feature_from_scalar_file

void load_feature_from_scalar_file(
    std::string filename,
    std::string feature_name
)

function set_override_feature

void set_override_feature(
    std::string feature
)

function get_override_feature

std::string get_override_feature()

function landmarks

Eigen::MatrixXd & landmarks()

function constraints

std::vector< Constraints > & constraints()

function get_constraints

Constraints & get_constraints(
    int domain_id
)

function has_planes

bool has_planes()

function get_groomed_mesh_wrappers

std::vector< std::shared_ptr< MeshWrapper > > get_groomed_mesh_wrappers()

function recompute_original_surface

void recompute_original_surface()

function ensure_segmentation

void ensure_segmentation()

If a segmentation doesn't exist, create a blank canvas.

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Updated on 2024-11-11 at 19:51:46 +0000