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 Member Functions | Protected Member Functions | Friends | List of all members
Seg3D::LayerFilter Class Referenceabstract
Inheritance diagram for Seg3D::LayerFilter:
Seg3D::LayerAbstractFilter Core::Runnable Filter::NrrdResampleFilter Filter::PadFilter Filter::SingleThresholdFilter Filter::ThresholdFilter Seg3D::AndFilterAlgo Seg3D::ArithmeticFilterAlgo Seg3D::CropAlgo Seg3D::DilateErodeFilterAlgo Seg3D::DilateFilterAlgo Seg3D::ErodeFilterAlgo Seg3D::ExtractDataLayerAlgo Seg3D::InvertFilterAlgo Seg3D::IterativeDilateErodeFilterAlgo Seg3D::IterativeDilateFilterAlgo Seg3D::IterativeErodeFilterAlgo Seg3D::ITKFilter Seg3D::MaskDataFilterAlgo Seg3D::NeighborhoodConnectedFilterAlgo Seg3D::NrrdFilter Seg3D::OrFilterAlgo Seg3D::PermuteAlgo Seg3D::RemoveFilterAlgo Seg3D::TransformAlgo Seg3D::XorFilterAlgo

Public Member Functions

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 ()
 
virtual std::string get_filter_name () const =0
 
virtual std::string get_layer_prefix () const =0
 
void report_error (const std::string &error)
 
Layer::filter_key_type get_key () const
 

Protected Member Functions

virtual void handle_abort ()
 
virtual void handle_stop ()
 
virtual void run_filter ()=0
 
virtual void run ()
 

Friends

class LayerFilterPrivate
 

Additional Inherited Members

- Static Public Member Functions inherited from Core::Runnable
static void Start (RunnableHandle runnable)
 

Member Function Documentation

void LayerFilter::abort_and_wait ( )
overridevirtual

ABORT_AND_WAIT: NOTE: When undoing asynchronous layer operations, one may need to wait until the filter can be aborted. If not the state of the program is unclear. Hence this function will ensure that the filter has finished processing and that all locks are cleared. NOTE: This function should be run on the application thread only

Implements Seg3D::LayerAbstractFilter.

bool LayerFilter::check_abort ( )
overridevirtual

CHECK_ABORT: Check the abort flag

Implements Seg3D::LayerAbstractFilter.

Reimplemented in Seg3D::PointSetFilterAlgo.

bool LayerFilter::check_stop ( )

CHECK_STOP: Check the stop flag

void LayerFilter::connect_abort ( const LayerHandle &  layer)

CONNECT_ABORT: Monitor the abort flag of a layer

void LayerFilter::connect_stop ( const LayerHandle &  layer)

CONNECT_STOP: Monitor the stop flag of a layer

bool LayerFilter::create_and_lock_data_layer ( const Core::GridTransform &  grid_trans,
LayerHandle  src_layer,
LayerHandle &  dst_layer 
)

CREATE_AND_LOCK_DATA_LAYER: Create a new data layer with the given grid transform, the layer is immediately locked as it does not contain any data and will be in the creating state. NOTE: This function can only be run from the application thread

bool LayerFilter::create_and_lock_data_layer_from_layer ( LayerHandle  src_layer,
LayerHandle &  dst_layer 
)

CREATE_AND_LOCK_DATA_LAYER_FROM_LAYER: Create a new data layer with the same dimensions as another layer, the layer is immediately locked as it does not contain any data and will be in the creating state. NOTE: This function can only be run from the application thread

bool LayerFilter::create_and_lock_mask_layer ( const Core::GridTransform &  grid_trans,
LayerHandle  src_layer,
LayerHandle &  dst_layer 
)

CREATE_AND_LOCK_MASK_LAYER: Create a new mask layer with the given grid transform, the layer is immediately locked as it does not contain any data and will be in the creating state. NOTE: This function can only be run from the application thread

bool LayerFilter::create_and_lock_mask_layer_from_layer ( LayerHandle  src_layer,
LayerHandle &  dst_layer 
)

CREATE_AND_LOCK_MASK_LAYER_FROM_LAYER: Create a new mask layer with the same dimensions as another layer, the layer is immediately locked as it does not contain any data and will be in the creating state. NOTE: This function can only be run from the application thread.

bool LayerFilter::create_and_lock_mask_layer_from_layer ( LayerHandle  src_layer,
LayerHandle &  dst_layer,
std::string  dst_name 
)

CREATE_AND_LOCK_MASK_LAYER_FROM_LAYER: Create a new mask layer with the same dimensions as another layer, the layer is immediately locked as it does not contain any data and will be in the creating state. This one can use specified name instead of src_layer name NOTE: This function can only be run from the application thread.

bool LayerFilter::create_cropped_large_volume_layer ( const Core::GridTransform &  crop_trans,
LayerHandle  src_layer,
LayerHandle &  dst_layer 
)

CREATE_CROPPED_LARGE_VOLUME_LAYER: Create a cropped version of the soure large volume layer. NOTE: This function can only be run from the application thread

void LayerFilter::create_undo_redo_and_provenance_record ( Core::ActionContextHandle  context,
Core::ActionHandle  action,
bool  split_prov = false 
)

CREATE_UNDO_REDO_AND_RPOVENANCE_RECORD: Create a provenance record and add it to the provenance database, and an undo record and add it to the undo stack.

bool LayerFilter::dispatch_delete_layer ( LayerHandle  layer)

DISPATCH_DELETE_LAYER: Schedule a layer to be deleted

bool LayerFilter::dispatch_insert_data_volume_into_layer ( LayerHandle  layer,
Core::DataVolumeHandle  data,
bool  update_histogram 
)

DISPATCH_INSERT_DATA_VOLUME_INTO_LAYER: Schedule a new data volume to be inserted into a layer

bool LayerFilter::dispatch_insert_mask_volume_into_layer ( LayerHandle  layer,
Core::MaskVolumeHandle  mask 
)

DISPATCH_INSERT_MASK_VOLUME_INTO_LAYER: Schedule a new mask volume to be inserted into a layer

bool LayerFilter::dispatch_unlock_layer ( LayerHandle  layer)

DISPATCH_UNLOCK_LAYER: Schedule a layer to be unlocked.

bool LayerFilter::find_layer ( const std::string &  layer_id,
LayerHandle &  layer 
)

FIND_LAYER: Find a layer in the layer manager with this id

virtual std::string Seg3D::LayerFilter::get_filter_name ( ) const
pure virtual

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

Implemented in Seg3D::DilateErodeFilterAlgo, Seg3D::IntensityCorrectionFilterAlgo, Seg3D::PointSetFilterAlgo, Seg3D::IterativeDilateErodeFilterAlgo, Seg3D::ConnectedComponentFilterAlgo, Seg3D::ErodeFilterAlgo, Seg3D::DilateFilterAlgo, Seg3D::FillHolesFilterAlgo, Seg3D::IterativeErodeFilterAlgo, Seg3D::IterativeDilateFilterAlgo, Seg3D::ActionSpeedlineAlgo, Seg3D::SmoothDilateErodeFilterAlgo, Seg3D::NeighborhoodConnectedFilterAlgo, Seg3D::MaskDataFilterAlgo, Seg3D::ThresholdSegmentationLSFilterAlgo, Seg3D::InvertFilterAlgo, Seg3D::XorFilterAlgo, Seg3D::RemoveFilterAlgo, Seg3D::AndFilterAlgo, Seg3D::OrFilterAlgo, Seg3D::SmoothErodeFilterAlgo, Seg3D::SmoothDilateFilterAlgo, Seg3D::ConnectedComponentSizeFilterAlgo, Seg3D::ConfidenceConnectedFilterAlgo, Seg3D::CurvatureAnisotropicDiffusionFilterAlgo, Seg3D::GradientAnisotropicDiffusionFilterAlgo, Seg3D::PointSetTransformAlgo, Seg3D::MeanFilterAlgo, Seg3D::MedianFilterAlgo, Seg3D::DiscreteGaussianFilterAlgo, Seg3D::OtsuThresholdFilterAlgo, Seg3D::CannyEdgeDetectionFilterAlgo, Seg3D::GradientMagnitudeFilterAlgo, Seg3D::DistanceFilterAlgo, Seg3D::HistogramEqualizationFilterAlgo, Filter::NrrdResampleFilter, Seg3D::ExtractDataLayerAlgo, Seg3D::CropAlgo, Filter::ThresholdFilter, Filter::SingleThresholdFilter, Seg3D::TransformAlgo, Seg3D::PermuteAlgo, Filter::ITKResampleFilter, Seg3D::ArithmeticFilterAlgo, and Filter::PadFilter.

Layer::filter_key_type LayerFilter::get_key ( ) const

GET_KEY: Get the unique filter key

virtual std::string Seg3D::LayerFilter::get_layer_prefix ( ) const
pure virtual

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.

Implemented in Seg3D::DilateErodeFilterAlgo, Seg3D::IntensityCorrectionFilterAlgo, Seg3D::PointSetFilterAlgo, Seg3D::IterativeDilateErodeFilterAlgo, Seg3D::ConnectedComponentFilterAlgo, Seg3D::ErodeFilterAlgo, Seg3D::DilateFilterAlgo, Seg3D::FillHolesFilterAlgo, Seg3D::IterativeErodeFilterAlgo, Seg3D::IterativeDilateFilterAlgo, Seg3D::ActionSpeedlineAlgo, Seg3D::SmoothDilateErodeFilterAlgo, Seg3D::NeighborhoodConnectedFilterAlgo, Seg3D::MaskDataFilterAlgo, Seg3D::ThresholdSegmentationLSFilterAlgo, Seg3D::InvertFilterAlgo, Seg3D::XorFilterAlgo, Seg3D::RemoveFilterAlgo, Seg3D::AndFilterAlgo, Seg3D::OrFilterAlgo, Seg3D::SmoothErodeFilterAlgo, Seg3D::SmoothDilateFilterAlgo, Seg3D::ConnectedComponentSizeFilterAlgo, Seg3D::ConfidenceConnectedFilterAlgo, Seg3D::CurvatureAnisotropicDiffusionFilterAlgo, Seg3D::GradientAnisotropicDiffusionFilterAlgo, Seg3D::PointSetTransformAlgo, Seg3D::MeanFilterAlgo, Seg3D::MedianFilterAlgo, Seg3D::DiscreteGaussianFilterAlgo, Seg3D::OtsuThresholdFilterAlgo, Seg3D::CannyEdgeDetectionFilterAlgo, Seg3D::GradientMagnitudeFilterAlgo, Seg3D::DistanceFilterAlgo, Seg3D::HistogramEqualizationFilterAlgo, Filter::NrrdResampleFilter, Seg3D::ExtractDataLayerAlgo, Seg3D::CropAlgo, Filter::ThresholdFilter, Filter::SingleThresholdFilter, Seg3D::TransformAlgo, Seg3D::PermuteAlgo, Filter::ITKResampleFilter, Seg3D::ArithmeticFilterAlgo, and Filter::PadFilter.

Core::NotifierHandle LayerFilter::get_notifier ( )

GET_NOTIFIER: Return a notifier that can be used to wait for the filter to finish.

SandboxID LayerFilter::get_sandbox ( )

GET_SANDBOX: Get the sandbox in which the filter is running.

void LayerFilter::handle_abort ( )
protectedvirtual

HANDLE_ABORT: A virtual function that can be overloaded

Reimplemented in Seg3D::ITKFilter.

void LayerFilter::handle_stop ( )
protectedvirtual

HANDLE_STOP: A virtual function that can be overloaded

Reimplemented in Seg3D::ITKFilter.

bool LayerFilter::lock_for_deletion ( LayerHandle  layer)

LOCK_FOR_DELETION: Lock a layer for processing and then for deletion, i.e. when we change the data contained in the data/mask of the layer. NOTE: This function can only be run from the application thread. NOTE: The BaseFilter class records which layers are locked and will schedule an unlock for each layer that was not unlocked by the time this class is destroyed.

bool LayerFilter::lock_for_processing ( LayerHandle  layer)

LOCK_FOR_PROCESSING: Lock a layer for processing, i.e. when we change the data contained in the data/mask of the layer. NOTE: This function can only be run from the application thread. NOTE: The BaseFilter class records which layers are locked and will schedule an unlock for each layer that was not unlocked by the time this class is destroyed.

bool LayerFilter::lock_for_use ( LayerHandle  layer)

LOCK_FOR_USE: Lock a layer for usage, i.e. we need the data/mask volume but we will not change the data. NOTE: This function can only be run from the application thread NOTE: The BaseFilter class records which layers are locked and will schedule an unlock for each layer that was not unlocked by the time this class is destroyed.

void LayerFilter::raise_abort ( )
overridevirtual

RAISE_ABORT: Raise the abort flag

Implements Seg3D::LayerAbstractFilter.

void LayerFilter::raise_stop ( )

RAISE_STOP: Raise the stop flag

void LayerFilter::report_error ( const std::string &  error)

REPORT_ERROR: Report an error to the user

void LayerFilter::run ( )
protectedvirtual

RUN: The function called by runnable

Implements Core::Runnable.

virtual void Seg3D::LayerFilter::run_filter ( )
protectedpure virtual

RUN_FILTER: run the filter

Implemented in Seg3D::NeighborhoodConnectedFilterAlgo, Seg3D::InvertFilterAlgo, Seg3D::DilateErodeFilterAlgo, Seg3D::IterativeDilateErodeFilterAlgo, Seg3D::ExtractDataLayerAlgo, Seg3D::DilateFilterAlgo, Seg3D::ErodeFilterAlgo, Seg3D::IterativeDilateFilterAlgo, Seg3D::IterativeErodeFilterAlgo, Filter::NrrdResampleFilter, Seg3D::HistogramEqualizationFilterAlgo, Seg3D::CropAlgo, Filter::ThresholdFilter, Filter::SingleThresholdFilter, Seg3D::TransformAlgo, Seg3D::PermuteAlgo, Seg3D::ArithmeticFilterAlgo, and Filter::PadFilter.

void LayerFilter::set_sandbox ( SandboxID  sandbox)

SET_SANDBOX: Set the sandbox in which the filter should be running.

bool LayerFilter::update_provenance_action_string ( Core::ActionHandle  action)

UPDATE_PROVENANCE_ACTION_STRING: For filters that can be stopped at certain iterations the provenance string needs to be updated with the number of iterations. This function allows to update it

The documentation for this class was generated from the following files:
Generated on Wed Jun 29 2016 22:44:31 for Seg3D by   doxygen 1.8.10