shapeworks::QOptimize

Wraps Optimize as a QObject.

#include <QOptimize.h>

Inherits from QObject, shapeworks::Optimize

Public Signals

	Name
void	progress(int , QString )

Public Functions

	Name
	QOptimize(QObject * parent =nullptr)
virtual	~QOptimize()
virtual std::vector< std::vector< itk::Point< double > > >	GetLocalPoints() override Return the local points.
virtual std::vector< std::vector< itk::Point< double > > >	GetGlobalPoints() override Return the global points.
std::vector< Particles >	GetParticles()
virtual std::vector< std::vector< std::vector< double > > >	GetProcrustesTransforms() override
virtual void	UpdateExportablePoints() override

Protected Functions

	Name
virtual void	SetIterationCallback() override Set the iteration callback. Derived classes should override to set their own callback.
virtual void	IterateCallback(itk::Object * caller, const itk::EventObject & ) override

Additional inherited members

Public Types inherited from shapeworks::Optimize

	Name
using itk::Image< float, 3 >	ImageType
using VectorFunction::VectorType	VectorType
using Eigen::MatrixXd	MatrixType

Public Functions inherited from shapeworks::Optimize

	Name
	Optimize() Constructor.
virtual	~Optimize() Destructor.
bool	Run() Run the optimization.
bool	LoadParameterFile(std::string filename) Load a parameter file.
bool	SetUpOptimize(ProjectHandle project) Set up this Optimize object using a ShapeWorks project.
void	SetProject(std::shared_ptr< Project > project) Set the Project object.
void	SetIterationCallbackFunction(const std::function< void(void)> & f) Set an iteration callback function to be called after each iteration.
void	AbortOptimization() Abort optimization.
bool	GetAborted() Return if the optimization was aborted.
void	SetCutPlanes(std::vector< std::array< itk::Point< double >, 3 > > cut_planes) Set cutting planes.
void	SetVerbosity(int verbosity_level) Set the verbosity level (0-5)
void	SetDomainsPerShape(int domains_per_shape) Set the number of domains per shape.
int	GetDomainsPerShape() Return the number of domains per shape.
void	SetDomainType(shapeworks::DomainType type)
shapeworks::DomainType	GetDomainType()
void	SetNumberOfParticles(std::vector< int > number_of_particles) Set the numbers of particles (vector of numbers, one for each domain)
std::vector< int >	GetNumberOfParticles() Return the numbers of particles per domain.
void	SetTransformFile(std::string filename) Set the transform file.
std::string	GetTransformFile() Get the transform file.
void	SetPrefixTransformFile(std::string prefix_transform_file) Set the prefix transform file (TODO: details)
std::string	GetPrefixTransformFile() Get the prefix transform file.
void	SetOutputDir(std::string output_dir) Set the output directory.
void	SetOutputTransformFile(std::string output_transform_file) Set the output transform file.
void	SetOutputIndividualTransformFiles(bool value) Set whether individual transforms should be written.
void	SetUseMeshBasedAttributes(bool use_mesh_based_attributes) Set if mesh based attributes should be used.
bool	GetUseMeshBasedAttributes() Get if mesh based attributes are being used.
void	SetUseXYZ(std::vector< bool > use_xyz) Set if XYZ is used, one value per domain.
void	SetUseNormals(std::vector< bool > use_normals) Set if Normals are being used, one value per domain.
void	SetAttributesPerDomain(std::vector< int > attributes_per_domain) Set the attributes per domain.
std::vector< int >	GetAttributesPerDomain() Get attributes per domain.
void	SetDistributionDomainID(int distribution_domain_id) Set the distribution domain ID (TODO: details)
int	GetDistributionDomainID() Get the distribution domain ID.
void	SetOutputCuttingPlaneFile(std::string output_cutting_plane_file) Set the output cutting plane file.
void	SetUseCuttingPlanes(bool use_cutting_planes) Set if using cutting planes.
void	SetCuttingPlane(unsigned int i, const vnl_vector_fixed< double, 3 > & va, const vnl_vector_fixed< double, 3 > & vb, const vnl_vector_fixed< double, 3 > & vc) Set a given cutting plane for a shape.
void	SetMeshFFCMode(int mesh_ffc_mode) Set Mesh FFC Mode false/0 = mesh clipping mode, true/1 = mesh augmented lagrangian mode.
void	SetTimePtsPerSubject(int time_pts_per_subject) Set the number of time points per subject (TODO: details)
int	GetTimePtsPerSubject() Get the number of time points per subject (TODO: details)
void	SetOptimizationIterations(int optimization_iterations) Set the number of optimization iterations.
void	SetOptimizationIterationsCompleted(int optimization_iterations_completed) Set the number of optimization iterations already completed (TODO: details)
void	SetIterationsPerSplit(int iterations_per_split) Set the number of iterations per split.
void	SetUseShapeStatisticsInInit(bool use_shape_statistics_in_init) Set if shape statistics should be used in initialization.
void	SetProcrustesInterval(int procrustes_interval) Set the interval for running procrustes (0 to disable)
void	SetProcrustesScaling(bool procrustes_scaling) Set if procrustes scaling should be used.
void	SetProcrustesRotationTranslation(bool procrustes_rotation_translation) Set if procrustes rotation/translation should be used.
void	SetRelativeWeighting(double relative_weighting) Set the relative weighting (TODO: details)
void	SetInitialRelativeWeighting(double initial_relative_weighting) Set the initial relative weigting (TODO: details)
void	SetStartingRegularization(double starting_regularization) Set the starting regularization (TODO: details)
void	SetEndingRegularization(double ending_regularization) Set the ending regularization (TODO: details)
void	SetRecomputeRegularizationInterval(int recompute_regularization_interval) Set the interval for recomputing regularization (TODO: details)
void	SetSaveInitSplits(bool save_init_splits) Set if initialization splits should be saved or not.
void	SetCheckpointingInterval(int checkpointing_interval) Set the checkpointing interval.
void	SetKeepCheckpoints(int keep_checkpoints) Set if checkpoints should be kept (0=disable, 1=enable)
void	SetUseRegression(bool use_regression) Set if regression should be used (TODO: details)
void	SetUseMixedEffects(bool use_mixed_effects) Set if mixed effects should be used (TODO: details)
void	SetUseDisentangledSpatiotemporalSSM(bool use_disentangled_ssm_4d) Set if optimization should be done using disentangled spatiotemporal SSM method.
bool	GetUseDisentangledSpatiotemporalSSM() Returns true if optimization is to be done using disentangled spatiotemporal SSM method.
void	SetNormalAngle(double normal_angle) For good/bad analysis, set the normal angle to use (TODO: details)
void	SetPerformGoodBad(bool perform_good_bad) Set if good/bad analysis should be done (TODO: details)
void	SetLogEnergy(bool log_energy) Set the log energy (TODO: details)
void	AddImage(ImageType::Pointer image, std::string name ="") Set the shape input images.
void	AddMesh(vtkSmartPointer< vtkPolyData > poly_data)
void	AddContour(vtkSmartPointer< vtkPolyData > poly_data)
void	SetFilenames(const std::vector< std::string > & filenames) Set the shape filenames (TODO: details)
void	SetPointFiles(const std::vector< std::string > & point_files) Set starting point files (TODO: details)
void	SetInitialPoints(std::vector< std::vector< itk::Point< double > > > initial_points) Set initial particle positions (e.g. for fixed subjects)
int	GetNumShapes() Get number of shapes.
void	SetAttributeScales(const std::vector< double > & scales) Set attribute scales (TODO: details)
void	SetFieldAttributes(const std::vector< std::string > & field_attributes) Set the field attributes.
void	SetParticleFlags(std::vector< int > flags) Set Particle Flags (TODO: details)
void	SetFixedDomains(std::vector< int > flags) Set Domain Flags (TODO: details)
void	SetSharedBoundaryEnabled(bool enabled) Shared boundary settings.
void	SetSharedBoundaryWeight(double weight)
const std::vector< int > &	GetDomainFlags()
void	SetFileOutputEnabled(bool enabled) Set if file output is enabled.
std::vector< bool >	GetUseXYZ() Return if XYZ is used, per shape.
std::vector< bool >	GetUseNormals() Return if Normals are used, per shape.
void	SetNarrowBand(double v) Set the narrow band used to be +/- the given value as a multiple of the spacing.
double	GetNarrowBand() Return the narrow band to be used.
void	SetUseShapeStatisticsAfter(int num_particles) Set the number of particles when correspondence based multiscale takes over.
int	GetUseShapeStatisticsAfter() Return the number of particles when correspondence based multiscale takes over.
void	PrintParamInfo() Print parameter info to stdout.
std::shared_ptr< Sampler >	GetSampler() Return the Sampler.
MatrixContainer	GetParticleSystem() Return the particle system as a matrix.
void	SetPythonFile(std::string filename) Set the python file to run at startup.
void	SetGeodesicsEnabled(bool is_enabled) Set whether or not geodesics are enabled.
bool	GetGeodesicsEnabled() const
void	SetGeodesicsCacheSizeMultiplier(size_t n)
void	SetGeodesicsRemeshPercent(double percent) Set the remeshing percent for the mesh used for computing geodesics (0-100)
OptimizationVisualizer &	GetVisualizer()
void	SetShowVisualizer(bool show)
bool	GetShowVisualizer()
bool	GetMeshFFCMode()
vnl_vector_fixed< double, 3 >	TransformPoint(int domain, vnl_vector_fixed< double, 3 > input) transform a point if necessary
void	UpdateProgress()
void	set_particle_format(std::string format)

Protected Functions inherited from shapeworks::Optimize

	Name
void	ComputeTotalIterations()
void	OptimizerStop()
void	ReadTransformFile()
void	ReadPrefixTransformFile(const std::string & s)
void	InitializeSampler()
double	GetMinNeighborhoodRadius()
void	AddSinglePoint()
void	Initialize()
void	RunOptimize()
void	ComputeEnergyAfterIteration()
void	SetCotanSigma()
void	WriteTransformFile(int iter =-1) const
void	WriteTransformFile(std::string iter_prefix) const
void	WriteTransformFiles(int iter =-1) const
void	WriteTransformFiles(std::string iter_prefix) const
void	WritePointFiles(int iter =-1)
void	WritePointFiles(std::string iter_prefix)
void	WritePointFilesWithFeatures(int iter =-1)
void	WritePointFilesWithFeatures(std::string iter_prefix)
void	WriteEnergyFiles()
void	WriteSplitFiles(std::string name)
void	WriteCuttingPlanePoints(int iter =-1)
void	WriteParameters(std::string output_dir ="")
void	ReportBadParticles()
int	SetParameters()
void	WriteModes()
void	PrintStartMessage(std::string str, unsigned int vlevel =0) const
void	PrintDoneMessage(unsigned int vlevel =0) const
void	UpdateProject()
std::string	GetCheckpointDir()

Protected Attributes inherited from shapeworks::Optimize

	Name
std::shared_ptr< Sampler >	m_sampler
ProcrustesRegistration::Pointer	m_procrustes
std::shared_ptr< ParticleGoodBadAssessment >	m_good_bad
unsigned int	m_verbosity_level
std::vector< std::vector< itk::Point< double > > >	m_local_points
std::vector< std::vector< itk::Point< double > > >	m_global_points
int	m_checkpoint_counter
int	m_procrustes_counter
bool	m_use_cutting_planes
bool	m_optimizing
bool	m_use_regression
bool	m_use_mixed_effects
bool	m_use_disentangled_ssm
unsigned int	m_domains_per_shape
shapeworks::DomainType	m_domain_type
std::vector< int >	m_number_of_particles
std::string	m_transform_file
std::string	m_prefix_transform_file
std::string	m_output_dir
std::string	m_output_transform_file
bool	m_output_transform_files
bool	m_mesh_based_attributes
std::vector< bool >	m_use_xyz
std::vector< bool >	m_use_normals
std::vector< int >	m_attributes_per_domain
int	m_distribution_domain_id
std::string	m_output_cutting_plane_file
bool	m_mesh_ffc_mode
unsigned int	m_timepts_per_subject
int	m_optimization_iterations
int	m_optimization_iterations_completed
int	m_iterations_per_split
bool	m_use_shape_statistics_in_init
unsigned int	m_procrustes_interval
bool	m_procrustes_scaling
bool	m_procrustes_rotation_translation
double	m_relative_weighting
double	m_initial_relative_weighting
double	m_starting_regularization
double	m_ending_regularization
int	m_recompute_regularization_interval
bool	m_save_init_splits
unsigned int	m_checkpointing_interval
int	m_keep_checkpoints
double	m_cotan_sigma_factor
std::vector< int >	m_particle_flags
std::vector< int >	m_domain_flags
double	m_narrow_band
bool	m_narrow_band_set
bool	m_fixed_domains_present
int	m_use_shape_statistics_after
std::string	m_python_filename
bool	m_geodesics_enabled
size_t	m_geodesic_cache_size_multiplier
double	m_geodesic_remesh_percent
double	m_spacing
std::vector< std::string >	m_filenames
int	m_num_shapes
std::vector< double >	m_energy_a
std::vector< double >	m_energy_b
std::vector< double >	m_total_energy
bool	m_log_energy
std::string	m_str_energy
std::vector< std::vector< int > >	m_bad_ids
double	m_normal_angle
bool	m_perform_good_bad
std::vector< int >	m_cutting_planes_per_input
std::vector< int >	m_spheres_per_input
bool	m_file_output_enabled
bool	m_aborted
std::vector< std::array< itk::Point< double >, 3 > >	m_cut_planes
int	m_total_iterations
int	m_iteration_count
int	m_split_number
int	current_particle_iterations_
int	total_particle_iterations_
std::function< void(void)>	iteration_callback_
bool	show_visualizer_
shapeworks::OptimizationVisualizer	visualizer_
std::string	particle_format_
std::shared_ptr< Project >	project_
std::chrono::system_clock::time_point	m_start_time
std::chrono::system_clock::time_point	m_last_update_time
std::chrono::system_clock::time_point	m_last_remaining_update_time
std::string	m_remaining_time_message

Public Signals Documentation

signal progress

void progress(
    int ,
    QString 
)

Public Functions Documentation

function QOptimize

QOptimize(
    QObject * parent =nullptr
)

function ~QOptimize

virtual ~QOptimize()

function GetLocalPoints

virtual std::vector< std::vector< itk::Point< double > > > GetLocalPoints() override

Return the local points.

Reimplements: shapeworks::Optimize::GetLocalPoints

function GetGlobalPoints

virtual std::vector< std::vector< itk::Point< double > > > GetGlobalPoints() override

Return the global points.

Reimplements: shapeworks::Optimize::GetGlobalPoints

function GetParticles

std::vector< Particles > GetParticles()

function GetProcrustesTransforms

virtual std::vector< std::vector< std::vector< double > > > GetProcrustesTransforms() override

Reimplements: shapeworks::Optimize::GetProcrustesTransforms

function UpdateExportablePoints

virtual void UpdateExportablePoints() override

Reimplements: shapeworks::Optimize::UpdateExportablePoints

Protected Functions Documentation

function SetIterationCallback

virtual void SetIterationCallback() override

Set the iteration callback. Derived classes should override to set their own callback.

Reimplements: shapeworks::Optimize::SetIterationCallback

function IterateCallback

virtual void IterateCallback(
    itk::Object * caller,
    const itk::EventObject & 
) override

Reimplements: shapeworks::Optimize::IterateCallback

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