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itkBloxCoreAtomPixel.txx
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itkBloxCoreAtomPixel.txx
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/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: itkBloxCoreAtomPixel.txx
Language: C++
Date: $Date$
Version: $Revision$
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_txx
#define __itkBloxCoreAtomPixel_txx
#include "itkBloxCoreAtomPixel.h"
namespace itk
{
template <unsigned int NDimensions>
BloxCoreAtomPixel<NDimensions>
::BloxCoreAtomPixel()
{
m_RawCMatrix.fill(0);
m_Eigenvalues.fill(0.0);
m_Eigenvectors.fill(0.0);
m_VotedCMatrix.fill(0);
m_VotedEigenvalues.fill(0.0);
m_VotedEigenvectors.fill(0.0);
m_MeanCoreAtomDiameter = 0;
m_ConstituencySize = 0;
m_WeightSum = 0;
m_MeanCoreAtomIntensity = 0.0;
m_LocationSums[0] = 0;
m_LocationSums[1] = 0;
m_LocationSums[2] = 0;
}
template <unsigned int NDimensions>
BloxCoreAtomPixel<NDimensions>
::~BloxCoreAtomPixel()
{
// The default destructor walks the pixel and deletes all bloxitems
}
//REMOVED: Boundary points dont know their intensities...profiles do!
template <unsigned int NDimensions>
void
BloxCoreAtomPixel<NDimensions>
::CalcMeanCoreAtomIntensity()
{
/*
double temp_intensity = 0.0;
int num_core_atoms = 0;
itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
for (bpiterator = this->begin(); bpiterator != this->end(); ++bpiterator)
{
// Get the pointer of the core atom
CoreAtomItemType* pCoreAtom = *bpiterator;
//get mean intensity for this core atom
temp_intensity = (pCoreAtom->GetBoundaryPointA()->GetValue()
+ pCoreAtom->GetBoundaryPointB()->GetValue())/2;
m_MeanCoreAtomIntensity += temp_intensity;
num_core_atoms++;
}
m_MeanCoreAtomIntensity /= num_core_atoms;
*/
}
template <unsigned int NDimensions>
void
BloxCoreAtomPixel<NDimensions>
::CalcWeightedCoreAtomLocation(double weight_factor, Self * votingPixel)
{
// The iterator for accessing linked list info
typename itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
PositionType center;
// Walk through all of the items in the voting pixel
for (bpiterator = votingPixel->begin(); bpiterator != votingPixel->end();
++bpiterator)
{
// Get the pointer of the core atom
CoreAtomItemType* pCoreAtom = *bpiterator;
// Get the center of the core atom
center = pCoreAtom->GetCenterPosition();
m_LocationSums[0] += (center[0]*weight_factor);
m_LocationSums[1] += (center[1]*weight_factor);
m_LocationSums[2] += (center[2]*weight_factor);
m_WeightSum += weight_factor;
}
}
template <unsigned int NDimensions>
double
BloxCoreAtomPixel<NDimensions>
::CalcMeanCoreAtomDiameter()
{
// Returns a mean of 0 if there are no core atoms present
if( this->empty() )
{
return 0;
}
unsigned long int numCoreAtoms = 0;
m_MeanCoreAtomDiameter = 0;
// The iterator for accessing linked list info
typename itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
// Walk through all of the items at the pixel
for (bpiterator = this->begin(); bpiterator != this->end(); ++bpiterator)
{
// Get the pointer of the core atom
CoreAtomItemType* pCoreAtom = *bpiterator;
m_MeanCoreAtomDiameter += pCoreAtom->GetDiameter();
numCoreAtoms++;
}
if(numCoreAtoms>0) // Check for /0 to be safe
{
m_MeanCoreAtomDiameter /= numCoreAtoms;
}
else
{
m_MeanCoreAtomDiameter = 0;
}
return m_MeanCoreAtomDiameter;
}
template <unsigned int NDimensions>
bool
BloxCoreAtomPixel<NDimensions>
::DoCoreAtomEigenanalysis()
{
// Don't attemp Eigenanalysis on an empty blox
if( this->empty() )
{
return false;
}
// The iterator for accessing linked list info
typename itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
// The number of items stored in the pixel
unsigned long int numItems = 0;
// Walk through all of the items at the pixel
for (bpiterator = this->begin(); bpiterator != this->end(); ++bpiterator)
{
// Get the pointer of the core atom
CoreAtomItemType* pCoreAtom = *bpiterator;
// Get the boundary points
BPItemType* pBPOne = pCoreAtom->GetBoundaryPointA();
BPItemType* pBPTwo = pCoreAtom->GetBoundaryPointB();
// Get the physical positions of the two boundary points
VectorType P1;
P1 = pBPOne->GetPhysicalPosition().GetVnlVector();
VectorType P2;
P2 = pBPTwo->GetPhysicalPosition().GetVnlVector();
// Figure out the "C" vector of the core atom
VectorType cVector = P2 - P1;
cVector.normalize();
// Now, add to m_RawCMatrix
for(unsigned int r = 0; r < NDimensions; r++) // row loop
{
for(unsigned int c = 0; c < NDimensions; c++) // column loop
{
m_RawCMatrix(r,c) += cVector[c]*cVector[r];
} // end column loop
} // end row loop
numItems++;
} // end walk all of the items in the pixel
// Divide through by the number of items
m_RawCMatrix /= numItems;
// Create an identity matrix of size n
vnl_matrix_fixed<double, NDimensions, NDimensions> identMatrix;
identMatrix.fill(0);
// Set the diagonal to 1
for(unsigned int n = 0; n < NDimensions; n++) // row loop
{
identMatrix(n,n) = 1.0;
} // end row loop
// Do eigen analysis
vnl_generalized_eigensystem* pEigenSys =
new vnl_generalized_eigensystem(m_RawCMatrix, identMatrix);
// Now, store the results
// First the eigenvectors
m_Eigenvectors = pEigenSys->V;
// Now the eigenvalues (stored as a vector to save space)
for(unsigned int i = 0; i < NDimensions; i++)
{
m_Eigenvalues[i] = pEigenSys->D(i,i);
}
delete pEigenSys;
return true;
}
template <unsigned int NDimensions>
typename BloxCoreAtomPixel<NDimensions>::PositionType
BloxCoreAtomPixel<NDimensions>
::GetVotedLocation()
{
m_VotedLocation[0] = m_LocationSums[0] / m_WeightSum;
m_VotedLocation[1] = m_LocationSums[1] / m_WeightSum;
m_VotedLocation[2] = m_LocationSums[2] / m_WeightSum;
return m_VotedLocation;
}
template <unsigned int NDimensions>
void
BloxCoreAtomPixel<NDimensions>
::CollectVote(MatrixType* pMatrix, double strength, double count)
{
m_VotedCMatrix += (*pMatrix)*strength;
m_ConstituencySize += count;
}
template <unsigned int NDimensions>
void
BloxCoreAtomPixel<NDimensions>
::NormalizeVotedCMatrix()
{
if(m_ConstituencySize != 0)
{
m_VotedCMatrix /= m_ConstituencySize;
}
}
template <unsigned int NDimensions>
void
BloxCoreAtomPixel<NDimensions>
::DoVotedEigenanalysis()
{
// Create an identity matrix of size n
vnl_matrix_fixed<double, NDimensions, NDimensions> identMatrix;
identMatrix.fill(0);
// Set the diagonal to 1
for(unsigned int n = 0; n < NDimensions; n++) // row loop
{
identMatrix(n,n) = 1.0;
} // end row loop
// Do eigen analysis
vnl_generalized_eigensystem* pEigenSys =
new vnl_generalized_eigensystem(m_VotedCMatrix, identMatrix);
// Now, store the results
// First the eigenvectors
m_VotedEigenvectors = pEigenSys->V;
// Now the eigenvalues (stored as a vector to save space)
for(unsigned int i = 0; i < NDimensions; i++)
{
m_VotedEigenvalues[i] = pEigenSys->D(i,i);
}
delete pEigenSys;
}
} // end namespace itk
#endif