Public Types | Public Member Functions | Protected Member Functions | List of all members
mirtk::MetricDistortion Class Reference

#include <MetricDistortion.h>

Inheritance diagram for mirtk::MetricDistortion:
Inheritance graph
Collaboration diagram for mirtk::MetricDistortion:
Collaboration graph

Public Types

typedef Array< NodeDistances > DistancesArray
 Array of computed distances to neighboring nodes.
 
- Public Types inherited from mirtk::PointSetForce
typedef RegisteredPointSet::EdgeTable EdgeTable
 Adjacency matrix with edge IDs.
 
typedef Vector3D< double > GradientType
 Type of gradient w.r.t a single transformed data point.
 
typedef RegisteredPointSet::NodeNeighbors NodeNeighbors
 Table of n-connected node neighbors.
 
- Public Types inherited from mirtk::EnergyTerm
typedef ObjectFactory< enum EnergyMeasure, EnergyTermFactoryType
 Type of energy term factory.
 

Public Member Functions

void CopyAttributes (const MetricDistortion &)
 Copy attributes of this class from another instance.
 
virtual void Initialize ()
 Initialize internal force term once input and parameters have been set.
 
 MetricDistortion (const char *="", double=1.0)
 Constructor.
 
 MetricDistortion (const MetricDistortion &)
 Copy constructor.
 
 mirtkAttributeMacro (double, InitialArea)
 Area of initial surface mesh.
 
 mirtkAttributeMacro (Array< DistancesArray >, Distances)
 For each node, the initial and current distances to their neighboring nodes.
 
 mirtkPublicAttributeMacro (int, Radius)
 Radius of node neighborhood (i.e., maximum edge-connectivity)
 
MetricDistortionoperator= (const MetricDistortion &)
 Assignment operator.
 
virtual ParameterList Parameter () const
 Get parameter name/value pairs.
 
virtual void Reinitialize ()
 Reinitialize internal force term after change of input topology.
 
virtual void Update (bool)
 Update internal force data structures.
 
virtual ~MetricDistortion ()
 Destructor.
 
- Public Member Functions inherited from mirtk::SurfaceConstraint
virtual ~SurfaceConstraint ()
 Destructor.
 
- Public Member Functions inherited from mirtk::InternalForce
virtual ~InternalForce ()
 Destructor.
 
- Public Member Functions inherited from mirtk::PointSetForce
virtual void WriteDataSets (const char *, const char *, bool=true) const
 Write input of force term.
 
virtual void WriteGradient (const char *, const char *) const
 Write gradient of force term.
 
virtual ~PointSetForce ()
 Destructor.
 
- Public Member Functions inherited from mirtk::EnergyTerm
virtual enum EnergyMeasure EnergyMeasure () const =0
 Energy measure implemented by this term.
 
void Gradient (double *gradient, double step)
 
virtual void GradientStep (const double *gradient, double &min, double &max) const
 
double InitialValue ()
 Returns initial value of energy term.
 
void NormalizedGradient (double *gradient, double step)
 
string Prefix (const char *=NULL) const
 Prefix to be used for debug output files.
 
virtual void Print (Indent=0) const
 Print debug information.
 
virtual double RawValue (double) const
 
double RawValue ()
 
void ResetInitialValue ()
 Reset initial value of energy term.
 
void ResetValue ()
 Reset cached value of energy term.
 
virtual bool Upgrade ()
 Update energy term after convergence.
 
double Value ()
 Evaluate energy term.
 
virtual ~EnergyTerm ()
 Destructor.
 
- Public Member Functions inherited from mirtk::Configurable
string DefaultName () const
 
virtual bool Set (const char *, const char *)
 Set parameter value from string.
 
virtual ~Configurable ()
 Destructor.
 
- Public Member Functions inherited from mirtk::Observable
void AddObserver (Observer &)
 Add observer.
 
void Broadcast (Event, const void *=NULL)
 Broadcast event to observers.
 
void ClearObservers ()
 Delete all observers.
 
void DeleteObserver (Observer &)
 Delete observer.
 
void NotifyObservers (Event, const void *=NULL)
 Notify all observers about given event if this object has changed.
 
int NumberOfObservers () const
 Number of current observers.
 
virtual ~Observable ()
 Destructor.
 
- Public Member Functions inherited from mirtk::Object
virtual const char * NameOfClass () const =0
 Get name of class, which this object is an instance of.
 
bool Parameter (const ParameterList &)
 Set parameters from name/value pairs.
 
virtual ~Object ()
 Destructor.
 

Protected Member Functions

virtual double Evaluate ()
 Compute penalty for current transformation estimate.
 
virtual void EvaluateGradient (double *, double, double)
 Compute internal force w.r.t. transformation parameters.
 
void Init ()
 
virtual bool SetWithoutPrefix (const char *, const char *)
 Set parameter value from string.
 
- Protected Member Functions inherited from mirtk::SurfaceConstraint
SurfaceConstraintoperator= (const SurfaceConstraint &)
 Assignment operator.
 
 SurfaceConstraint (const char *="", double=1.0)
 Constructor.
 
 SurfaceConstraint (const SurfaceConstraint &)
 Copy constructor.
 
- Protected Member Functions inherited from mirtk::InternalForce
vtkDataArray * ExternalMagnitude () const
 Get magnitude array of external force term.
 
 InternalForce (const char *="", double=1.0)
 Constructor.
 
 InternalForce (const InternalForce &)
 Copy constructor.
 
InternalForceoperator= (const InternalForce &)
 Assignment operator.
 
- Protected Member Functions inherited from mirtk::PointSetForce
void AddPointData (const char *name, vtkSmartPointer< vtkDataArray > &data, bool global=false)
 
vtkDataArray * AddPointData (const char *name, int c=1, int type=VTK_FLOAT, bool global=false)
 
void AllocateCount (int)
 Allocate _Count memory.
 
void AllocateGradient (int)
 Allocate memory for (non-parametric) gradient.
 
void CopyAttributes (const PointSetForce &)
 Copy attributes of this class from another instance.
 
vtkPointSet * DeformedPointSet () const
 Get point set on which this force is acting on.
 
vtkPolyData * DeformedSurface () const
 Get point set on which this force is acting on.
 
const EdgeTableEdges () const
 Get edge table of point set mesh.
 
vtkSmartPointer< vtkPoints > GetInitialPoints () const
 Get initial points, possibly pre-transformed by global transformation.
 
void Init ()
 Common (re-)initialization steps of this class only (non-virtual function!)
 
vtkDataArray * InitialStatus () const
 Get initial point status array.
 
 mirtkAggregateMacro (int, Count)
 
 mirtkAttributeMacro (int, GradientSize)
 Size of gradient vector.
 
 mirtkAttributeMacro (int, CountSize)
 Size of count vector.
 
 mirtkAttributeMacro (bool, InitialUpdate)
 Whether Update has not been called since initialization.
 
 mirtkComponentMacro (GradientType, Gradient)
 Negative node forces/gradient of external force term.
 
 mirtkPublicAggregateMacro (RegisteredPointSet, PointSet)
 Transformed point set.
 
 mirtkPublicAttributeMacro (int, GradientAveraging)
 Number of gradient averaging iterations.
 
 mirtkPublicAttributeMacro (bool, AverageSignedGradients)
 
 mirtkPublicAttributeMacro (bool, AverageGradientMagnitude)
 Whether to only average the magnitude of the gradient vectors.
 
 mirtkReadOnlyAttributeMacro (bool, SurfaceForce)
 
 mirtkReadOnlyAttributeMacro (int, NumberOfPoints)
 Number of points.
 
const NodeNeighborsNeighbors (int=-1) const
 Get edge-connectivity table of point set node neighbors.
 
vtkDataArray * Normals () const
 Get point normals array.
 
PointSetForceoperator= (const PointSetForce &)
 Assignment operator.
 
vtkPointSet * OriginalPointSet () const
 Get point set on which this force is acting on.
 
vtkPolyData * OriginalSurface () const
 Get point set on which this force is acting on.
 
vtkPointData * PointData () const
 Get point data.
 
vtkDataArray * PointData (const char *name, bool optional=false) const
 
vtkPoints * Points () const
 Get points of point set on which this force is acting on.
 
 PointSetForce (const char *="", double=1.0)
 Constructor.
 
 PointSetForce (const PointSetForce &)
 Copy constructor.
 
void RemovePointData (const char *name)
 
SharedPtr< const EdgeTableSharedEdgeTable () const
 Get edge table of point set mesh.
 
vtkDataArray * Status () const
 Get point status array.
 
- Protected Member Functions inherited from mirtk::EnergyTerm
 EnergyTerm (const char *="", double=1.0)
 Constructor.
 
 EnergyTerm (const EnergyTerm &)
 Copy constructor.
 
EnergyTermoperator= (const EnergyTerm &)
 Assignment operator.
 
virtual bool SetWithPrefix (const char *, const char *)
 Set parameter value from string.
 
- Protected Member Functions inherited from mirtk::Configurable
 Configurable (const char *="")
 Constructor.
 
 Configurable (const Configurable &)
 Copy constructor.
 
string DefaultPrefix () const
 Get default object name prefix (if any)
 
bool HasName () const
 Whether this object has an explicit name.
 
bool HasPrefix () const
 Whether this object has either an explicit name or default prefix.
 
template<class T >
bool InsertWithPrefix (ParameterList &, string, T) const
 Insert parameter into name/value list with object name prefix.
 
bool InsertWithPrefix (ParameterList &, const ParameterList &) const
 Insert parameters into name/value list with object name prefix.
 
Configurableoperator= (const Configurable &)
 Assignment operator.
 
string ParameterNameWithoutPrefix (const char *) const
 Get name of parameter without object name prefix.
 
string ParameterNameWithPrefix (const string &) const
 Get name of parameter with default object name prefix.
 
string ParameterNameWithPrefix (const char *) const
 Get name of parameter with default object name prefix.
 
- Protected Member Functions inherited from mirtk::Observable
 Observable ()
 Default constructor.
 
 Observable (const Observable &)
 Copy constructor.
 
Observableoperator= (const Observable &)
 Assignment operator.
 
- Protected Member Functions inherited from mirtk::Object
template<typename... Args>
void Throw (ErrorType err, const char *func, Args... args) const
 

Additional Inherited Members

- Static Public Member Functions inherited from mirtk::InternalForce
static InternalForceNew (InternalForceTerm, const char *="", double=1.0)
 Instantiate new constraint representing specified internal forces.
 
- Static Public Member Functions inherited from mirtk::EnergyTerm
static FactoryTypeFactory ()
 Get global energy term factory instance.
 
static EnergyTermNew (EnergyMeasure, const char *="", double=1.0)
 Construct new energy term.
 
static EnergyTermTryNew (EnergyMeasure, const char *="", double=1.0)
 Construct new energy term or return nullptr if term not available.
 
- Static Public Member Functions inherited from mirtk::Object
static const char * NameOfType ()
 Get name of this class type.
 
- Static Protected Member Functions inherited from mirtk::Object
template<typename... Args>
static void ThrowStatic (ErrorType err, const char *cls, const char *func, Args... args)
 

Detailed Description

Metric distortion constraint

Fischl et al.. Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System. NeuroImage, 9(2), 195–207 (1999).

Additional to the formulation in the NeuroImage paper of Fischl et al., this implementation contains a slight modification found in the implementation of FreeSurfer's mris_inflate tool. The normal component of the force term is removed from the gradient vector.

Definition at line 42 of file MetricDistortion.h.

Member Function Documentation

§ Init()

void mirtk::MetricDistortion::Init ( )
protected

Common (re-)initialization steps of this internal force term

Note
Must be a non-virtual function!

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