GenerateLinearShapeModel Class Reference

#include <AnatomyPlugin/include/ImFusion/AnatomyPlugin/GenerateLinearShapeModel.h>

Mean shape and linear shape model generation algorithm for anatomical structures using closed mesh representations. More...

Inheritance diagram for GenerateLinearShapeModel:

Detailed Description

Mean shape and linear shape model generation algorithm for anatomical structures using closed mesh representations.

This algorithm takes a set of input anatomical structure collections and (initial) mean shape and computes a linear shape model and updates the mean shape if requested.

The linear shape model is computed using PCA on the input shapes. The mean shape is updated iteratively in batches by optimizing the mean shape to minimize the distance to the input shapes. The mean shape defines the anatomical structures of interest.

Public Member Functions
	GenerateLinearShapeModel (AnatomicalStructureCollection *meanShape)
void	compute () override
	Execute the algorithm.
OwningDataList	takeOutput () override
	Return any new Data that was created by the Algorithm during the last call to compute().
Algorithm::Status	computeMeanShape ()
	Updates the mean shape from input directory using meanShape as reference.
std::unique_ptr< AnatomicalStructureCollection >	getMeanShape ()
Public Member Functions inherited from 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().
virtual bool	survivesDataDeletion (const Data *) const
	Indicates whether the algorithm can handle (partial) deletion of the specified data, by default this checks whether the data is in the input list.
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 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 Algorithm
static bool	createCompatible (const DataList &data, Algorithm **a=nullptr)
	Factory function to check algorithm compatibility with input data and optionally instantiate it.

Public Attributes
Parameter< int >	p_numInputs = {"numInputs", 20, this}
	Number of input shapes to generate the template.
Parameter< int >	p_numPCAValues = {"numPCAValues", 5, this}
Parameter< std::string >	p_inputDirectory = {"inputDirectory", "", this}
	Directory containing the input AnatomicalStructureCollections as .imf files to generate the mean shape from (if updateMeanShape is true) and to compute the linear shape model from.
Parameter< bool >	p_updateMeanShape = {"updateMeanShape", false, this}
	Update the mean shape from the input directory.
Parameter< int >	p_meanUpdateBatchSize = {"meanUpdateBatchSize", 5, this}
	Number of shapes to use for the mean shape computation at each iteration.
Parameter< int >	p_meanUpdateNumBatches = {"meanUpdateNumBatches", 100, this}
	Number of iterations to use for the mean shape computation.
Parameter< double >	p_meanUpdateStepSize = {"meanUpdateStepSize", 0.01, this}
	Step size for the mean shape computation in [0,1].
Public Attributes inherited from 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 Configurable
Signal	signalParametersChanged
	Emitted whenever one of the registered Parameters' or SubPropertys' signalValueChanged signal was emitted.

Additional Inherited Members
Public Types inherited from Algorithm
enum	Status {   Unknown = -1 , Success = 0 , Error = 1 , InvalidInput ,   IncompleteInput , OutOfMemoryHost , OutOfMemoryGPU , UnsupportedGPU ,   UnknownAction , AbortedByUser , User = 1000 }
	Status codes. More...
Protected Member Functions inherited from 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 Attributes inherited from 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 Configurable
std::vector< Param >	m_params
	List of all registered Parameter and SubProperty instances.

Member Function Documentation

compute()

void compute ( )

overridevirtual

Execute the algorithm.

Implements Algorithm.

takeOutput()

OwningDataList takeOutput ( )

overridevirtual

Return any new Data that was created by the Algorithm during the last call to compute().

The default implementation will return an empty list.

Note

Since ownership of the data is transferred, you can call this method only once between calls to compute().

Reimplemented from Algorithm.

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

• AnatomyPlugin/include/ImFusion/AnatomyPlugin/GenerateLinearShapeModel.h