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ImFusion C++ SDK 4.4.0
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ImFusion C++ SDK 4.4.0
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#include <CranialPlugin/include/ImFusion/Cranial/WholeBrainSegmentationAlgorithm.h>
Algorithm for segmenting all the brain structures in T1 MR volumes. More...
Algorithm for segmenting all the brain structures in T1 MR volumes.
Public Member Functions | |
| WholeBrainSegmentationAlgorithm (SharedImageSet &input, AnatomicalStructureCollection *asc=nullptr) | |
| Constructor. If asc is not null, segmentation results will be written to it. | |
| Public Member Functions inherited from ImFusion::Cranial::FastSurferSegmentationAlgorithm | |
| FastSurferSegmentationAlgorithm (SharedImageSet &input, AnatomicalStructureCollection *asc=nullptr) | |
| SharedImageSet & | input () const |
| Returns a reference to the input image used for segmentation. | |
| AnatomicalStructureCollection * | asc () const |
| Returns a pointer to the anatomical structure collection where results are stored. | |
| const SharedImageSet * | outputLabelMap () const |
| Returns a pointer to the generated label map (this might be null). | |
| const LabelDataComponent * | labelDataComponent () const |
| Generate the label configuration for all possible labels in the output. This may be a superset of the labels present in the output label map. | |
| void | compute () override |
| Standard methods for the Algorithm interface. | |
| OwningDataList | takeOutput () override |
| Returns (1) the label map image if flag is enabled, (2) the AnatomicalStructureCollection if it has been created by 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. | |
| 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 | configure (const Properties *p) |
| Configure this object instance by de-serializing the given Properties. | |
| virtual void | configuration (Properties *p) const |
| Serialize the current object configuration into the given Properties object. | |
| 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 |
Static Public Member Functions | |
| static bool | createCompatible (const DataList &data, Algorithm **a=0) |
| 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 | |
| std::string | outputStructureIdentifier () const override |
| Key of the anatomical structure collection under which the results will be written. | |
| std::unique_ptr< SharedImageSet > | splitImage (SharedImageSet &feature) override |
| This function transforms the pre-processed volume into a series of slices to be fed to the network. | |
| const std::vector< unsigned short > & | sagittalChannelsMapping () const override |
| Sagittal slices have a left/right ambiguity so most pairs of labels are collapsed to the same value. | |
| const std::vector< unsigned short > & | freesurferLabelsMapping () const override |
| Extra virtual functions to be implemented by derived algorithmsMapping between neural network output channels of the the axial/coronal outputs (indices) to standardized FreeSurfer anatomical indices (values) defined in CranialPluginKeys. | |
| virtual bool | shouldFlipAxialSlices () const |
| Models have different pre-processing and orientation so we need to control whether axial slices should be flipped. | |
| std::unique_ptr< SharedImageSet > | computeFastSurfer (const SharedImageSet &inputImage) |
| Different steps of the pipelineThis function takes as input the main image and returns an unsigned short label map where structures are represented by a standardized label. | |
| std::unique_ptr< SharedImageSet > | preprocess (const SharedImageSet &input) |
| std::unique_ptr< SharedImageSet > | predictImage (std::unique_ptr< SharedImageSet >, std::string) |
| std::unique_ptr< SharedImageSet > | argmax (std::unique_ptr< SharedImageSet > output) |
| std::unique_ptr< SharedImageSet > | recombineImages (SharedImageSet &predictionSlices, double spacing) |
| std::unique_ptr< SharedImageSet > | fusePredictions (std::pair< std::unique_ptr< SharedImageSet >, std::unique_ptr< SharedImageSet > > predictions, float weight, bool sagittalMap) |
| 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. | |
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... | |
| Public Attributes inherited from ImFusion::Cranial::FastSurferSegmentationAlgorithm | |
| Parameter< std::string > | p_modelPath = {"modelPath", "", this} |
| Path to the folder containing the three models (assumed to be called axial_net.yaml, coronal_net.yaml, sagittal_net.yaml). | |
| Parameter< int > | p_imageSize = {"imageSize", 256, this} |
| Size of the image that will be used internally as model input. | |
| Parameter< double > | p_imageSpacing = {"imageSpacing", 1.0, this} |
| Spacing of the image that will be used internally as model input. | |
| Parameter< bool > | p_runAxial = {"runAxial", true, this} |
| Run the model on the axial slices. | |
| Parameter< bool > | p_runCoronal = {"runCoronal", true, this} |
| Run the model on the coronal slices. | |
| Parameter< bool > | p_runSagittal = {"runSagittal", true, this} |
| Run the model on the sagittal slices. | |
| Parameter< bool > | p_keepLargestComponent = {"keepLargestComponent", true, this} |
| Post-process the result to discard all non-connected components. | |
| Parameter< bool > | p_resampleToInput = {"resampleToInput", false, this} |
| If enabled, make sure the output label map has the same resolution as the input image. | |
| Parameter< bool > | p_extractMeshes = {"extractMeshes", false, this} |
| If disabled, the algorithm will not extract meshes but instead only save the segmentation images and keypoints. | |
| Parameter< bool > | p_exportLabelMap = {"exportLabelMap", true, this} |
| If enabled, export the label map as a separate data. | |
| 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. | |
| Protected Attributes inherited from ImFusion::Cranial::FastSurferSegmentationAlgorithm | |
| SharedImageSet & | m_inputImage |
| std::unique_ptr< GenericASC > | m_ascOwned |
| AnatomicalStructureCollection * | m_asc = nullptr |
| std::unique_ptr< SharedImageSet > | m_outputLabelMap |
| mat4 | m_correctionMatrix = mat4::Identity() |
| 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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inlineoverrideprotectedvirtual |
Key of the anatomical structure collection under which the results will be written.
Implements ImFusion::Cranial::FastSurferSegmentationAlgorithm.
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overrideprotectedvirtual |
This function transforms the pre-processed volume into a series of slices to be fed to the network.
It is virtual because it might depend on the application.
Implements ImFusion::Cranial::FastSurferSegmentationAlgorithm.
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overrideprotectedvirtual |
Sagittal slices have a left/right ambiguity so most pairs of labels are collapsed to the same value.
This mapping brings original axial/coronal label channel indices to the subset of the sagittal label indices. For instance, {0,1,1} means that 0 is mapped to 0, but both labels 1 and 2 are mapped to the second channel of the sagittal label map. The expected size of the mapping is the number of labels in the axial/coronal output, and the number of different values in the mapping is the number of labels in the sagittal output.
Implements ImFusion::Cranial::FastSurferSegmentationAlgorithm.
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overrideprotectedvirtual |
Extra virtual functions to be implemented by derived algorithmsMapping between neural network output channels of the the axial/coronal outputs (indices) to standardized FreeSurfer anatomical indices (values) defined in CranialPluginKeys.
Implements ImFusion::Cranial::FastSurferSegmentationAlgorithm.