Seg3D  2.4
Seg3D is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute.
Public Types | Public Member Functions | Public Attributes | List of all members
Seg3D::ActionSpeedlineAlgo Class Reference
Inheritance diagram for Seg3D::ActionSpeedlineAlgo:
Seg3D::ITKFilter Seg3D::LayerFilter Seg3D::LayerAbstractFilter Core::Runnable

Public Types

typedef itk::Image< int, VOL_DIM_C > MASK_IMAGE_TYPE
 
typedef itk::Image< int, SLICE_DIM_C > MASK_IMAGE_TYPE_2D
 
typedef itk::Image< VALUE_TYPE, SLICE_DIM_C > TYPED_IMAGE_TYPE_2D
 
typedef itk::LiveWireImageFunction< TYPED_IMAGE_TYPE_2D > LiveWireType
 
typedef LiveWireType::OutputType PATH_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

template<class TYPED_IMAGE_TYPE , class TYPED_IMAGE_TYPE_2D >
TYPED_IMAGE_TYPE_2D::Pointer extract_2D_image (typename TYPED_IMAGE_TYPE::Pointer image)
 
template<class TYPED_IMAGE_TYPE_2D >
TYPED_IMAGE_TYPE_2D::IndexType extract_2D_point (const Point &point)
 
template<class PATH_TYPE >
Point build_3D_point (typename PATH_TYPE::ContinuousIndexType slice_point)
 
 if (StateEngine::Instance() ->get_state(this->world_path_state_id_, state_var))
 
this world_paths_ delete_all_paths ()
 
this get_itk_image_from_layer (this->target_layer_, input_image)
 
livewire SetInputImage (input_image_2D)
 
livewire SetGradientMagnitudeWeight (this->grad_mag_weight_)
 
livewire SetZeroCrossingWeight (this->zero_cross_weight_)
 
livewire SetGradientDirectionWeight (this->grad_dir_weight_)
 
livewire SetUseImageSpacing (this->image_spacing_)
 
livewire SetUseFaceConnectedness (this->face_conn_)
 
 if (this->roi_mask_layer_id_!="<none>")
 
this world_paths_ set_start_point (this->vertices_[0])
 
this world_paths_ set_end_point (this->vertices_[end_index])
 
 for (size_t index=0;index< this->vertices_.size();++index)
 
 Application::PostEvent (boost::bind(&StateSpeedlinePath::set, world_path_state, this->world_paths_, ActionSource::NONE_E))
 
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
 
virtual bool check_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

std::string target_layer_id_
 
std::string output_mask_layer_id_
 
std::string roi_mask_layer_id_
 
int slice_type_
 
size_t slice_number_
 
std::vector< Pointvertices_
 
DataLayerHandle target_layer_
 
MaskLayerHandle roi_mask_layer_
 
MaskLayerHandle output_mask_layer_
 
double grad_mag_weight_
 
double zero_cross_weight_
 
double grad_dir_weight_
 
bool image_spacing_
 
bool face_conn_
 
std::string world_path_state_id_
 
StateSpeedlinePathHandle world_path_state
 
StateBaseHandle state_var
 
ITKImageDataT< int >::Handle roi_mask_image
 
ITKImageDataT< VALUE_TYPE >::Handle input_image
 
TYPED_IMAGE_TYPE_2D::Pointer input_image_2D
 
LiveWireType::Pointer livewire = LiveWireType::New()
 
const size_t num_of_vertices = this->vertices_.size()
 
const size_t end_index = num_of_vertices - 1
 

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

virtual std::string Seg3D::ActionSpeedlineAlgo::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::ActionSpeedlineAlgo::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

TYPED_IMAGE_TYPE_2D::Pointer Seg3D::ActionSpeedlineAlgo::input_image_2D
Initial value:
=
extract_2D_image< TYPED_IMAGE_TYPE, TYPED_IMAGE_TYPE_2D >( input_image->get_image() )

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