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ImFusion C++ SDK 4.5.0
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ImFusion C++ SDK 4.5.0
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#include <CranialPlugin/include/ImFusion/Cranial/VesselSegmentationAlgorithm.h>
Algorithm for segmenting vessels in brain MR-T1C, ToF-MRA or CTA scans (from v4 onward). More...
Algorithm for segmenting vessels in brain MR-T1C, ToF-MRA or CTA scans (from v4 onward).
Warning: when using a version lower or equal than 3, the algorithm is expected to only work properly on MR-T1C scans. Initial model predictions can be refined with 3 possible refinement algorithms (all 3 can be used at the same time):
Public Member Functions | |
| VesselSegmentationAlgorithm (SharedImageSet &input, AnatomicalStructureCollection *asc=nullptr) | |
| Constructor. If asc is not null, segmentation results will be written to it. | |
| SharedImageSet & | input () const |
| void | setInputImage (SharedImageSet &newInput) |
| AnatomicalStructureCollection * | asc () const |
| const SharedImageSet * | vesselMap () const |
| Returns a non-owning pointer to the generated vessel map, or nullptr if the algorithm was not successful or if the output was already fetched via takeOutput(). | |
| Public Member Functions inherited from ImFusion::Algorithm | |
| Algorithm () | |
| Default constructor will registers a single "compute" action that calls compute() and returns status(). | |
| virtual void | setProgress (Progress *progress) |
| Sets a Progress interface the algorithm can use to notify observers about its computing progress. | |
| Progress * | progress () const |
| Returns the progress interface if set. | |
| virtual int | status () const |
| Indicates the status of the last call to compute(). | |
| const FactoryInfo & | factoryInfo () const |
| Returns the record describing how this Algorithm was instantiated by the AlgorithmFactory. | |
| void | setFactoryInfo (const FactoryInfo &value) |
| Sets the record describing how this Algorithm was instantiated by the AlgorithmFactory. | |
| Status | runAction (const std::string &id) |
| Run the action with name id if it exists. | |
| const std::vector< Action > & | actions () |
| Get a mapping from Action id to Action as registered in this algorithm. | |
| Public Member Functions inherited from ImFusion::Configurable | |
| virtual void | configureDefaults () |
| Retrieve the properties of this object, replaces values with their defaults and sets it again. | |
| void | registerParameter (ParameterBase *param) |
| Register the given Parameter or SubProperty, so that it will be configured during configure()/configuration(). | |
| void | unregisterParameter (const ParameterBase *param) |
| Remove the given Parameter or SubProperty from the list of registered parameters. | |
| Configurable (const Configurable &rhs) | |
| Configurable (Configurable &&rhs) noexcept | |
| Configurable & | operator= (const Configurable &) |
| Configurable & | operator= (Configurable &&) noexcept |
| Public Member Functions inherited from ImFusion::SignalReceiver | |
| SignalReceiver ()=default | |
| Default constructor. | |
| SignalReceiver (const SignalReceiver &other) | |
| Copy constructor, does not copy any existing signal connections from other. | |
| SignalReceiver & | operator= (SignalReceiver rhs) |
| Assignment operator, disconnects all existing connections, does not copy any existing signal connections from rhs. | |
| virtual | ~SignalReceiver () |
| Virtual destructor disconnects from all connected signals. | |
Public Attributes | |
| Parameter< std::string > | p_modelSet = {"modelSet", Models::Latest::ModelSetName, this} |
| Model set for all models (vessel segmentation and internal sub-models). | |
| Parameter< std::string > | p_modelSetVersion = {"modelSetVersion", Models::Latest::ModelSetVersion, this} |
| Model set version used for all models. | |
| Parameter< bool > | p_useBrainMask = {"useBrainMask", true, this} |
| If enabled, performs a brain segmentation to remove detections outside the brain. | |
| Parameter< bool > | p_keepLargestComponent = {"keepLargestComponent", false, this} |
| If enabled, removes all components but the largest one. | |
| Parameter< bool > | p_refinePredictions = {"refinePredictions", false, this} |
| If enabled, exposes the individual refinement method toggles (Hessian / graph / mesh). | |
| Parameter< bool > | p_hessianRefinement = {"hessianRefinement", false, this} |
| If enabled, augments the soft-probability map with multi-scale Hessian tubularity responses before binarisation, recovering small vessels missed by the model. | |
| Parameter< std::vector< double > > | p_hessianRefinementScales = {"hessianRefinementScales", std::vector<double>{1.}, this} |
| If hessianRefinement enabled, specifies the scales (in mm) at which the Hessian refinement is performed. | |
| Parameter< float > | p_hessianRefinementThreshold = {"hessianRefinementThreshold", -2.5, this} |
| If hessianRefinement is enabled, uses this threshold to detect additional vessels If at least 2 eigen values of the hessian are below that threshold, the structure is considered as tubular at the given location. | |
| Parameter< float > | p_vesselBinarizationThreshold = {"vesselBinarizationThreshold", 0.5f, this} |
| Threshold applied to the continuous vessel probability map (p(fg) plus additive Hessian responses) to produce the binary segmentation. | |
| Parameter< bool > | p_graphRefinement = {"graphRefinement", false, this} |
| If enabled, performs a round trip to and from graph centerline to smooth the predictions. | |
| Parameter< bool > | p_meshRefinement = {"meshRefinement", false, this} |
| If enabled, performs a round trip to and from mesh with an intermediate mesh processing (cleaning) step. | |
| Parameter< float > | p_meshRefinementCleanThreshold = {"meshRefinementCleanThreshold", 5, this} |
| If meshRefinement is enabled, defines the minimum connected component surface area (in mm^2) to be kept. | |
| Public Attributes inherited from ImFusion::Algorithm | |
| Signal | signalOutputChanged |
| Signal should be emitted by Algorithms when their output/result has changed. | |
| Signal | signalParametersChanged |
| Signal should be emitted by Algorithms when their parameter configuration has changed. | |
| Public Attributes inherited from ImFusion::Configurable | |
| Signal | signalParametersChanged |
| Emitted whenever one of the registered Parameters' or SubPropertys' signalValueChanged signal was emitted. | |
| void | configure (const Properties *p) override |
| Configure this object instance by de-serializing the given Properties. | |
| void | configuration (Properties *p) const override |
| Serialize the current object configuration into the given Properties object. | |
| void | compute () override |
| Execute the algorithm. | |
| bool | survivesDataDeletion (const Data *) const override |
| Indicates whether the algorithm can handle (partial) deletion of the specified data, by default this checks whether the data is in the input list. | |
| OwningDataList | takeOutput () override |
| Returns (1) the label map, (2) the AnatomicalStructureCollection if it has been created by the algorithm. | |
| static bool | createCompatible (const DataList &data, Algorithm **a=0) |
| Standard methods for the Algorithm interface. | |
Additional Inherited Members | |
| Public Types inherited from ImFusion::Algorithm | |
| enum | Status { Unknown = -1 , Success = 0 , Error = 1 , InvalidInput , IncompleteInput , OutOfMemoryHost , OutOfMemoryGPU , UnsupportedGPU , UnknownAction , AbortedByUser , User = 1000 } |
| Status codes. More... | |
| Static Public Member Functions inherited from ImFusion::Algorithm | |
| static bool | createCompatible (const DataList &data, Algorithm **a=nullptr) |
| Factory function to check algorithm compatibility with input data and optionally instantiate it. | |
| Protected Member Functions inherited from ImFusion::Algorithm | |
| void | loadDefaults () |
| void | registerAction (const std::string &id, const std::string &guiName, const std::function< Algorithm::Status(void)> &action) |
| Register an action to be run via runAction. | |
| template<typename D> | |
| void | registerAction (const std::string &id, const std::string &guiName, Algorithm::Status(D::*action)(void)) |
| Template version of runAction that can be used with a pointer to a member function. | |
| void | registerAction (const Action &action) |
| Register an action. | |
| Protected Member Functions inherited from ImFusion::SignalReceiver | |
| void | disconnectAll () |
| Disconnects all existing connections. | |
| Protected Attributes inherited from ImFusion::Algorithm | |
| std::string | m_name |
| Algorithm name. | |
| Progress * | m_progress = nullptr |
| Non-owing pointer to a progress interface. May be a nullptr. | |
| FactoryInfo | m_factoryInfo = {} |
| Record describing how this algorithm was instantiated by the AlgorithmFactory. | |
| int | m_status = Status::Unknown |
| Algorithm status after last call to compute(). | |
| std::vector< Action > | m_actions |
| Map of key given by the id of the action, of the available actions of this algorithm. | |
| Protected Attributes inherited from ImFusion::Configurable | |
| std::vector< Param > | m_params |
| List of all registered Parameter and SubProperty instances. | |
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overridevirtual |
Configure this object instance by de-serializing the given Properties.
The default implementation will do so automatically for all registered Parameter and SubProperty instances.
Reimplemented from ImFusion::Configurable.
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overridevirtual |
Serialize the current object configuration into the given Properties object.
The default implementation will do so automatically for all registered Parameter and SubProperty instances.
Reimplemented from ImFusion::Configurable.
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overridevirtual |
Execute the algorithm.
Implements ImFusion::Algorithm.
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overridevirtual |
Indicates whether the algorithm can handle (partial) deletion of the specified data, by default this checks whether the data is in the input list.
Reimplemented from ImFusion::Algorithm.
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overridevirtual |
Returns (1) the label map, (2) the AnatomicalStructureCollection if it has been created by the algorithm.
Reimplemented from ImFusion::Algorithm.
| Parameter<std::string> ImFusion::Cranial::VesselSegmentationAlgorithm::p_modelSetVersion = {"modelSetVersion", Models::Latest::ModelSetVersion, this} |
Model set version used for all models.
Changing this resets any parameters defined in the selected version's metadata to their version-specific defaults.
| Parameter<bool> ImFusion::Cranial::VesselSegmentationAlgorithm::p_refinePredictions = {"refinePredictions", false, this} |
If enabled, exposes the individual refinement method toggles (Hessian / graph / mesh).
At least one refinement method must also be enabled for any refinement to take effect.
| Parameter<float> ImFusion::Cranial::VesselSegmentationAlgorithm::p_vesselBinarizationThreshold = {"vesselBinarizationThreshold", 0.5f, this} |
Threshold applied to the continuous vessel probability map (p(fg) plus additive Hessian responses) to produce the binary segmentation.
Lower values yield more liberal (oversegmented) results, which can be useful when erasing is easier than drawing vessels.