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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: $RCSfile: itkBloxCoreAtomPixel.h,v $
Language: C++
Date: $Date: 2007-04-06 12:50:58 $
Version: $Revision: 1.24 $
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 __itkBloxCoreAtomPixel_h
#define __itkBloxCoreAtomPixel_h
#include "vnl/vnl_matrix_fixed.h"
#include "vnl/vnl_vector_fixed.h"
#include "vnl/algo/vnl_generalized_eigensystem.h"
#include "itkObject.h"
#include "itkBloxCoreAtomItem.h"
#include "itkBloxBoundaryPointItem.h"
#include "itkPoint.h"
#include "itkCovariantVector.h"
#include "itkBloxPixel.h"
namespace itk
{
/**
* \class BloxCoreAtomPixel
* \brief Holds a linked list of itk::BloxCoreAtomItem's
*
* \ingroup ImageObjects
* */
template <unsigned int NDimensions>
class ITK_EXPORT BloxCoreAtomPixel : public BloxPixel<
BloxCoreAtomItem<NDimensions> >
{
public:
/** Standard class typedefs. */
typedef BloxCoreAtomPixel Self;
typedef BloxPixel< BloxCoreAtomItem<NDimensions> > Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** The type of core atom item we process. */
typedef BloxCoreAtomItem<NDimensions> CoreAtomItemType;
/** The type of boundary point item we process. */
typedef BloxBoundaryPointItem<NDimensions> BPItemType;
/** The type used to store the position of the BoundaryPointItem. */
typedef Point<double, NDimensions> PositionType;
/** The type of vector used to store the gradient of the BoundaryPointItem. */
typedef CovariantVector<double, NDimensions> GradientType;
/** VNL type used in eigenanalysis. */
typedef vnl_vector_fixed<double, NDimensions> VectorType;
/** Vector type used to store eigenvalues. */
typedef vnl_vector_fixed<double, NDimensions> EigenvalueType;
/** Matrix type used to store eigenvectors. */
typedef vnl_matrix_fixed<double, NDimensions, NDimensions> EigenvectorType;
/** Generalized matrix type used for several different tasks. */
typedef vnl_matrix_fixed<double, NDimensions, NDimensions> MatrixType;
/** Calculate and store the mean of core atom diameters. */
double CalcMeanCoreAtomDiameter();
/** Perform eigenanalysis on the population of core atoms
* stored in this pixel. */
bool DoCoreAtomEigenanalysis();
/** Perform eigenanalysis on the voted CMatrix */
void DoVotedEigenanalysis();
/** Get statements */
double GetMeanCoreAtomDiameter() {return m_MeanCoreAtomDiameter;}
double GetMeanCoreAtomIntensity() {return m_MeanCoreAtomIntensity;}
EigenvalueType GetEigenvalues() {return m_Eigenvalues;}
EigenvalueType GetVotedEigenvalues() {return m_VotedEigenvalues;}
EigenvectorType GetEigenvectors() {return m_Eigenvectors;}
EigenvectorType GetVotedEigenvectors() {return m_VotedEigenvectors;}
PositionType GetLocationSums() {return m_LocationSums;}
double GetWeightSum() {return m_WeightSum;}
/** Get the raw CMatrix (prior to voting) */
MatrixType* GetRawCMatrixPointer() {return &m_RawCMatrix;}
/** Collect a vote and update m_VotedCMatrix */
void CollectVote(MatrixType* pMatrix, double strength, double count);
/** Re-normalizes the voted CMatrix after all votes are cast */
void NormalizeVotedCMatrix();
/** Calculate location of the pixel based on core atoms voting for
* it.
*/
void CalcWeightedCoreAtomLocation(double weight_factor, Self * votingPixel);
/** Calculate mean intensity os the pixel based on its core atoms. */
void CalcMeanCoreAtomIntensity();
/** Returns the calculated voted location */
PositionType GetVotedLocation();
BloxCoreAtomPixel();
~BloxCoreAtomPixel();
private:
/** Average (arithmetic mean) of core atom diameters stored in this pixel. */
double m_MeanCoreAtomDiameter;
/** The raw CMatrix - this is the matrix that we do eigen analysis on. */
MatrixType m_RawCMatrix;
/** The eigenvalues of the core atom population in this pixel
* These are stored in increasing order of value (not absolute value) from
* indices 0 to n, where n is the number of dimensions in the source image */
EigenvalueType m_Eigenvalues;
/** The eigenvectors of the core atom population in this pixel
* Each eigenvector is a column of this matrix */
EigenvectorType m_Eigenvectors;
/** The CMatrix that collects votes cast by other blox. */
MatrixType m_VotedCMatrix;
/** Same as above, but calculated from the voted CMatrix */
EigenvalueType m_VotedEigenvalues;
/** Same as above, but calculated from the voted CMatrix */
EigenvectorType m_VotedEigenvectors;
/** The number of core atoms in all of the blox's that have voted for
* this blox (its constituency) */
double m_ConstituencySize;
/** Used to compute the voted location of the core atom population */
PositionType m_LocationSums;
/** Used to compute the voted location of the core atom population */
PositionType m_VotedLocation;
/** Total weights used to compute voted location */
double m_WeightSum;
/** Total weights used to compute voted location */
double m_MeanCoreAtomIntensity;
};
} // end namespace itk
// Define instantiation macro for this template.
#define ITK_TEMPLATE_BloxCoreAtomPixel(_, EXPORT, x, y) namespace itk { \
_(1(class EXPORT BloxCoreAtomPixel< ITK_TEMPLATE_1 x >)) \
namespace Templates { typedef BloxCoreAtomPixel< ITK_TEMPLATE_1 x > \
BloxCoreAtomPixel##y; } \
}
#if ITK_TEMPLATE_EXPLICIT
# include "Templates/itkBloxCoreAtomPixel+-.h"
#endif
#if ITK_TEMPLATE_TXX
# include "itkBloxCoreAtomPixel.txx"
#endif
#endif
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