Seg3D::PointSetFilterAlgo Class Reference

Inheritance diagram for Seg3D::PointSetFilterAlgo:

Public Types
typedef itk::PointSet< float, DIMENSION_C >	point_set_type
typedef point_set_type::PointType	point_type
typedef point_set_type::PointsContainer	points_container_type
typedef itk::EuclideanDistancePointMetric< point_set_type, point_set_type >	metric_type
typedef metric_type::TransformType	transform_base_type
typedef transform_base_type::ParametersType	parameters_type
typedef transform_base_type::JacobianType	jacobian_type
typedef itk::Euler3DTransform< double >	transform_type
typedef itk::LevenbergMarquardtOptimizer	optimizer_type
typedef itk::PointSetToPointSetRegistrationMethod< point_set_type, point_set_type >	registration_type
typedef itk::LinearInterpolateImageFunction< TYPED_IMAGE_TYPE, double >	interpolator_type
typedef itk::ResampleImageFilter< TYPED_IMAGE_TYPE, TYPED_IMAGE_TYPE >	resample_filter_type
Public Types inherited from Seg3D::ITKFilter
typedef itk::Image< unsigned short, 3 >	USHORT_IMAGE_TYPE
typedef itk::Image< unsigned int, 3 >	UINT_IMAGE_TYPE
typedef itk::Image< float, 3 >	FLOAT_IMAGE_TYPE
typedef itk::Image< unsigned char, 3 >	UCHAR_IMAGE_TYPE
typedef Core::ITKImageDataT< float >	FLOAT_CONTAINER_TYPE
typedef Core::ITKImageDataT< unsigned int >	UINT_CONTAINER_TYPE
typedef Core::ITKImageDataT< unsigned short >	USHORT_CONTAINER_TYPE
typedef Core::ITKImageDataT< unsigned char >	UCHAR_CONTAINER_TYPE

Public Member Functions
bool	check_abort ()
	while (!sample_ready)
	for (cii=fixed_iso_points_set.begin();cii!=fixed_iso_points_set.end();cii++)
fixed_point_set	SetPoints (fixed_point_container)
	CORE_LOG_MESSAGE (std::string("Number of fixed Points = ")+boost::lexical_cast< std::string >(fixed_points_num))
	for (cii=moving_iso_points_set.begin();cii!=moving_iso_points_set.end();cii++)
moving_point_set	SetPoints (moving_point_container)
	CORE_LOG_MESSAGE (std::string("Number of moving Points = ")+boost::lexical_cast< std::string >(moving_points_num))
optimizer	SetUseCostFunctionGradient (false)
this	forward_abort_to_filter (registration, this->dst_layer_)
optimizer_type::ScalesType	scales (transform->GetNumberOfParameters())
optimizer	SetScales (scales)
optimizer	SetNumberOfIterations (number_of_iterations)
optimizer	SetValueTolerance (value_tolerance)
optimizer	SetGradientTolerance (gradient_tolerance)
optimizer	SetEpsilonFunction (epsilon_function)
transform	SetIdentity ()
registration	SetInitialTransformParameters (transform->GetParameters())
registration	SetMetric (metric)
registration	SetOptimizer (optimizer)
registration	SetTransform (transform)
registration	SetFixedPointSet (fixed_point_set)
registration	SetMovingPointSet (moving_point_set)
this	forward_abort_to_filter (registration, this->dst_layer_)
this	observe_itk_iterations (optimizer, boost::bind( &PointSetFilterAlgo::update_iteration, this, _1, progress_unit))
this	limit_number_of_itk_threads (registration)
	catch (...)
	if (this->check_abort()) return
	CORE_LOG_MESSAGE (std::string("Solution = ")+solution)
	for (unsigned int i=0;i< final_parameters.size();++i)
final_transform	SetParameters (final_parameters)
this	get_itk_image_from_layer (this->mask_layer_, moving_image)
resampler	SetInput (moving_image->get_image())
final_transform	GetInverse (final_transform)
resampler	SetTransform (final_transform)
this	get_itk_image_from_layer (this->src_layer_, fixed_image)
resampler	SetSize (fixed_image->get_image() ->GetLargestPossibleRegion().GetSize())
resampler	SetOutputOrigin (fixed_image->get_image() ->GetOrigin())
resampler	SetOutputSpacing (fixed_image->get_image() ->GetSpacing())
resampler	SetOutputDirection (fixed_image->get_image() ->GetDirection())
resampler	SetDefaultPixelValue (0)
resampler	Update ()
	if (resampler->GetOutput()!=NULL)
virtual std::string	get_filter_name () const
virtual std::string	get_layer_prefix () const
Public Member Functions inherited from Seg3D::LayerFilter
virtual void	raise_abort () override
void	raise_stop ()
bool	check_stop ()
virtual void	abort_and_wait () override
void	connect_abort (const LayerHandle &layer)
void	connect_stop (const LayerHandle &layer)
Core::NotifierHandle	get_notifier ()
bool	find_layer (const std::string &layer_id, LayerHandle &layer)
bool	lock_for_use (LayerHandle layer)
bool	lock_for_processing (LayerHandle layer)
bool	lock_for_deletion (LayerHandle layer)
bool	create_and_lock_data_layer_from_layer (LayerHandle src_layer, LayerHandle &dst_layer)
bool	create_and_lock_data_layer (const Core::GridTransform &grid_trans, LayerHandle src_layer, LayerHandle &dst_layer)
bool	create_cropped_large_volume_layer (const Core::GridTransform &crop_trans, LayerHandle src_layer, LayerHandle &dst_layer)
bool	create_and_lock_mask_layer_from_layer (LayerHandle src_layer, LayerHandle &dst_layer)
bool	create_and_lock_mask_layer_from_layer (LayerHandle src_layer, LayerHandle &dst_layer, std::string dst_name)
bool	create_and_lock_mask_layer (const Core::GridTransform &grid_trans, LayerHandle src_layer, LayerHandle &dst_layer)
bool	dispatch_unlock_layer (LayerHandle layer)
bool	dispatch_delete_layer (LayerHandle layer)
bool	dispatch_insert_data_volume_into_layer (LayerHandle layer, Core::DataVolumeHandle data, bool update_histogram)
bool	dispatch_insert_mask_volume_into_layer (LayerHandle layer, Core::MaskVolumeHandle mask)
void	create_undo_redo_and_provenance_record (Core::ActionContextHandle context, Core::ActionHandle action, bool split_prov=false)
bool	update_provenance_action_string (Core::ActionHandle action)
void	set_sandbox (SandboxID sandbox)
SandboxID	get_sandbox ()
void	report_error (const std::string &error)
Layer::filter_key_type	get_key () const

Public Attributes
LayerHandle	src_layer_
LayerHandle	mask_layer_
LayerHandle	dst_layer_
int	iterations_
std::string	transform_state_id_
MaskLayerHandle	input_moving_layer
double	quality_factor = 1.0
Core::IsosurfaceHandle	fixed_iso
Core::IsosurfaceHandle	moving_iso
std::vector< Core::PointF >	fixed_iso_points_set
std::vector< Core::PointF >	moving_iso_points_set
bool	sample_ready = false
const unsigned int	DIMENSION_C = 3
point_set_type::Pointer	fixed_point_set = point_set_type::New()
point_set_type::Pointer	moving_point_set = point_set_type::New()
points_container_type::Pointer	fixed_point_container = points_container_type::New()
points_container_type::Pointer	moving_point_container = points_container_type::New()
unsigned int	point_id = 0
std::vector< Core::PointF >::const_iterator	cii
unsigned long	fixed_points_num = fixed_point_set->GetNumberOfPoints()
	point_id = 0
unsigned long	moving_points_num = moving_point_set->GetNumberOfPoints()
metric_type::Pointer	metric = metric_type::New()
transform_type::Pointer	transform = transform_type::New()
optimizer_type::Pointer	optimizer = optimizer_type::New()
registration_type::Pointer	registration = registration_type::New()
const double	TRANSLATION_SCALE_C = 1000.0
const double	ROTATION_SCALE_C = 1.0
	scales [0] = 1.0 / ROTATION_SCALE_C
unsigned long	number_of_iterations = this->iterations_
double	gradient_tolerance = 1e-5
double	value_tolerance = 1e-5
double	epsilon_function = 1e-6
double	progress_unit = 1.0 / number_of_iterations
this	progress_ = 0.0
	try
registration_type::ParametersType	final_parameters
std::string	solution
std::vector< double >	matrix_entries
transform_type::Pointer	final_transform = transform_type::New()
resample_filter_type::Pointer	resampler = resample_filter_type::New()
Core::ITKImageDataT< VALUE_TYPE >::Handle	moving_image
Core::ITKImageDataT< VALUE_TYPE >::Handle	fixed_image

Additional Inherited Members
Static Public Member Functions inherited from Core::Runnable
static void	Start (RunnableHandle runnable)
Protected Member Functions inherited from Seg3D::ITKFilter
template<class T >
bool	get_itk_image_from_layer (const LayerHandle &layer, typename Core::ITKImageDataT< T >::Handle &image, bool invert=false)
template<class T >
bool	get_itk_image_from_mask_layer (const LayerHandle &layer, typename Core::ITKImageDataT< T >::Handle &image, double label=1.0)
template<class T >
bool	insert_itk_image_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image)
template<class T >
bool	insert_itk_image_pointer_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image)
template<class T >
bool	insert_itk_positive_labels_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image, bool invert=false)
template<class T >
bool	insert_itk_positive_labels_pointer_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image, bool invert=false)
template<class T >
bool	insert_itk_label_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image, T label)
template<class T >
bool	insert_itk_label_pointer_into_mask_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image, T label)
template<class T >
bool	convert_and_insert_itk_image_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 > *itk_image, Core::DataType data_type)
template<class T >
bool	convert_and_insert_itk_image_pointer_into_layer (const LayerHandle &layer, typename itk::Image< T, 3 >::Pointer itk_image, Core::DataType data_type)
template<class T >
void	forward_abort_to_filter (T filter_pointer, LayerHandle layer)
template<class T >
void	observe_itk_progress (T filter_pointer, const LayerHandle &layer, float progress_start=0.0, float progress_amount=1.0)
template<class T >
void	observe_itk_iterations (T filter_pointer, boost::function< void(itk::Object *) > iteration_fcn)
template<class T >
void	limit_number_of_itk_threads (T filter_pointer)
virtual void	handle_abort ()
virtual void	handle_stop ()
Protected Member Functions inherited from Seg3D::LayerFilter
virtual void	run_filter ()=0
virtual void	run ()

Member Function Documentation

bool Seg3D::PointSetFilterAlgo::check_abort ( )

inlinevirtual

CHECK_ABORT: Check the abort flag

Reimplemented from Seg3D::LayerFilter.

virtual std::string Seg3D::PointSetFilterAlgo::get_filter_name ( ) const

inlinevirtual

GET_FILTER_NAME: This functions returns the name of the filter that is used in the error report.

Implements Seg3D::LayerFilter.

virtual std::string Seg3D::PointSetFilterAlgo::get_layer_prefix ( ) const

inlinevirtual

GET_LAYER_PREFIX: This function returns the name of the filter. The latter is prepended to the new layer name, when a new layer is generated.

Implements Seg3D::LayerFilter.

Member Data Documentation

registration_type::ParametersType Seg3D::PointSetFilterAlgo::final_parameters

Initial value:

= 
      registration->GetLastTransformParameters()

MaskLayerHandle Seg3D::PointSetFilterAlgo::input_moving_layer

Initial value:

= 
      boost::dynamic_pointer_cast<MaskLayer>( this->mask_layer_ )

std::string Seg3D::PointSetFilterAlgo::solution

Initial value:

= "[" + boost::lexical_cast<std::string>(final_parameters[0]) +
      "," + boost::lexical_cast<std::string>(final_parameters[1]) +"," +
      boost::lexical_cast<std::string>(final_parameters[2]) + "," + 
      boost::lexical_cast<std::string>(final_parameters[3]) + "," +
      boost::lexical_cast<std::string>(final_parameters[4]) + "," +
      boost::lexical_cast<std::string>(final_parameters[5]) + "]"

Seg3D::PointSetFilterAlgo::try

Initial value:

{ 
      registration->Update()

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The documentation for this class was generated from the following file:

• Application/Filters/Actions/ActionPointSetRegisterFilter.cc