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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: itkDeformableMesh3DFilter.h,v $
Language: C++
Date: $Date: 2004-08-07 17:20:40 $
Version: $Revision: 1.26 $
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkDeformableMesh3DFilter_h
#define __itkDeformableMesh3DFilter_h
#include "itkMeshToMeshFilter.h"
#include "vnl/vnl_matrix_fixed.h"
#include "vnl/vnl_math.h"
#include "itkMesh.h"
#include "itkVector.h"
#include "itkTriangleCell.h"
#include "itkImage.h"
#include "itkImageRegionIterator.h"
#include <itkCovariantVector.h>
namespace itk
{
/** \class DeformableMesh3D
* \brief
*
* The DeformableMesh3DFilter is used to deform a mesh (deformable model)
* under a potential force in 2D or 3D.
* The potential force is derived from the gradient information in the
* medical image and it will make the model deform to fit to the boundary
* features.
* Inputs are:
* (1) A deformable triangular model (Mesh). Import using the SetInput method.
* (2) A gradient map that make the model deform to fit to the estimated boundary.
* the gradient should be based on the 2nd derive of the original image. So the
* nodes on the model surface will stop at the edge features in the original
* image.
*
* \ingroup MeshFilters
* \ingroup MeshSegmentation */
template <class TInputMesh, class TOutputMesh>
class ITK_EXPORT DeformableMesh3DFilter : public MeshToMeshFilter<TInputMesh, TOutputMesh>
{
public:
/** Standard "Self" typedef. */
typedef DeformableMesh3DFilter Self;
/** Standard "Superclass" typedef. */
typedef MeshToMeshFilter<TInputMesh, TOutputMesh> Superclass;
/** Smart pointer typedef support */
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method of creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(DeformableMesh3DFilter,MeshToMeshFilter);
/** Some typedefs. */
typedef TInputMesh InputMeshType;
typedef TOutputMesh OutputMeshType;
typedef typename InputMeshType::PointsContainerPointer
InputPointsContainerPointer;
typedef typename InputMeshType::PointsContainer::Iterator
InputPointsContainerIterator;
typedef typename InputMeshType::PointDataContainerPointer
InputPointDataContainerPointer;
typedef typename InputMeshType::PointDataContainer::Iterator
InputPointDataContainerIterator;
typedef typename InputMeshType::CellsContainerPointer
InputCellsContainerPointer;
typedef typename InputMeshType::CellsContainer::Iterator
InputCellsContainerIterator;
typedef typename InputMeshType::CellDataContainerPointer
InputCellDataContainerPointer;
typedef typename InputMeshType::CellDataContainer::Iterator
InputCellDataContainerIterator;
typedef typename OutputMeshType::PointsContainerPointer
OutputPointsContainerPointer;
typedef typename OutputMeshType::CellsContainer
OutputCellsContainer;
typedef typename OutputMeshType::CellsContainerPointer
OutputCellsContainerPointer;
typedef typename OutputMeshType::PointsContainer::Iterator
OutputPointsContainerIterator;
/** Other definitions. */
typedef typename InputMeshType::CellType CellType;
typedef typename InputMeshType::CellTraits CellTraits;
typedef typename InputMeshType::PointType InputPointType;
typedef typename InputMeshType::PixelType PixelType;
/** Image and Image iterator definition. */
typedef Image<unsigned char, 3> PotentialImageType;
typedef ImageRegionIterator<PotentialImageType> PotentialIterator;
typedef CovariantVector<PixelType, 3> GradientType;
typedef Image<GradientType, 3> GradientImageType;
typedef ImageRegionIterator<GradientImageType> GradientIterator;
typedef typename GradientImageType::SizeType ImageSizeType;
typedef typename GradientImageType::IndexType ImageIndexType;
typedef itk::CellInterface<PixelType, CellTraits> TCellInterface;
typedef itk::TriangleCell<TCellInterface> TriCell;
typedef CovariantVector<int, 3> int3DVector;
typedef CovariantVector<double, 2> double2DVector;
typedef CovariantVector<double, 3> double3DVector;
/* Mesh pointer definition. */
typedef typename InputMeshType::Pointer InputMeshPointer;
typedef typename OutputMeshType::Pointer OutputMeshPointer;
typedef typename GradientImageType::Pointer GradientImagePointer;
/* Stiffness Matrix Type definition */
typedef vnl_matrix_fixed<double, 4, 4> StiffnessMatrixType;
typedef StiffnessMatrixType * StiffnessMatrixRawPointer;
/** Routines. */
void SetStiffnessMatrix( StiffnessMatrixType *stiff, int i );
/** Set/Get routines. */
itkSetMacro(Gradient, GradientImagePointer);
itkGetMacro(Gradient, GradientImagePointer);
itkSetMacro(StepThreshold, int);
itkGetMacro(StepThreshold, int);
itkSetMacro(Stiffness, double2DVector);
itkGetMacro(Stiffness, double2DVector);
itkSetMacro(TimeStep, double);
itkGetMacro(TimeStep, double);
itkSetMacro(Scale, double3DVector);
itkSetMacro(PotentialMagnitude, PixelType);
itkSetMacro(GradientMagnitude, PixelType);
itkSetMacro(PotentialOn, unsigned short);
itkSetMacro(ObjectLabel, unsigned char);
itkGetMacro(Normals, InputMeshPointer);
protected:
DeformableMesh3DFilter();
~DeformableMesh3DFilter();
DeformableMesh3DFilter(const Self&) {}
void operator=(const Self&) {}
void PrintSelf(std::ostream& os, Indent indent) const;
virtual void GenerateData();
private:
/** Meshes for Forces,Displacement,Normals, etc. */
InputMeshPointer m_Forces;
InputMeshPointer m_Normals;
InputMeshPointer m_Displacements;
InputMeshPointer m_Derives;
InputMeshPointer m_Locations;
void Initialize();
void SetDefaultStiffnessMatrix();
void SetMeshStiffness();
void Advance(); // update data for next iteration
void ComputeDt(); // compute point positions
void ComputeOutput();
void GradientFit(); // fit the model with gradient information
void ComputeNormals();
void PotentialFit();
/** Three different kinds of stiffness matrix. */
StiffnessMatrixType m_StiffnessMatrix[10];
StiffnessMatrixRawPointer *m_K;
/** Parameters definitions. */
double2DVector m_Stiffness;
double m_TimeStep; /** Time step of each iteration */
double3DVector m_Scale;
int m_Step; /** Number of iterations */
int m_NumberOfNodes;
int m_NumberOfCells;
int m_ImageWidth; /** Image size */
int m_ImageHeight;
int m_ImageDepth;
int m_StepThreshold;/** This threshold decides when to stop the model. */
unsigned short m_ModelXUpLimit;
unsigned short m_ModelXDownLimit;
unsigned short m_ModelYUpLimit;
unsigned short m_ModelYDownLimit;
unsigned short m_ModelZUpLimit;
unsigned short m_ModelZDownLimit;
unsigned short m_PotentialOn;
unsigned char m_ObjectLabel;
PixelType m_GradientMagnitude;
PixelType m_PotentialMagnitude;
/** To compute force derived from gradient data. */
GradientImagePointer m_Gradient;
PotentialImageType::Pointer m_Potential;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkDeformableMesh3DFilter.txx"
#endif
#endif
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