KWStyle - itkBloxCoreAtomPixel.txx

Matrix View

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1		/*=========================================================================
2
3		Program:   Insight Segmentation & Registration Toolkit
4		Module:    $RCSfile: itkBloxCoreAtomPixel.txx.html,v $
5		Language:  C++
6		Date:      $Date: 2006/01/17 19:15:33 $
7		Version:   $Revision: 1.4 $
8
9		Copyright (c) Insight Software Consortium. All rights reserved.
10		See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
11
12		This software is distributed WITHOUT ANY WARRANTY; without even
13		the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14		PURPOSE.  See the above copyright notices for more information.
15
16		=========================================================================*/
17		#ifndef __itkBloxCoreAtomPixel_txx
18		#define __itkBloxCoreAtomPixel_txx
19
20		#include "itkBloxCoreAtomPixel.h"
21
22		namespace itk
23		{
24
25		template <unsigned int NDimensions>
26		BloxCoreAtomPixel<NDimensions>
27		::BloxCoreAtomPixel()
28		{
29		m_RawCMatrix.fill(0);
30		m_Eigenvalues.fill(0.0);
31		m_Eigenvectors.fill(0.0);
32
33		m_VotedCMatrix.fill(0);
34		m_VotedEigenvalues.fill(0.0);
35		m_VotedEigenvectors.fill(0.0);
36
37		m_MeanCoreAtomDiameter = 0;
38		m_ConstituencySize = 0;
39
40		m_WeightSum = 0;
41
42		m_MeanCoreAtomIntensity = 0.0;
43
44		m_LocationSums[0] = 0;
45		m_LocationSums[1] = 0;
46		m_LocationSums[2] = 0;
47		}
48
49		template <unsigned int NDimensions>
50		BloxCoreAtomPixel<NDimensions>
51		::~BloxCoreAtomPixel()
52		{
53		// The default destructor walks the pixel and deletes all bloxitems
54		}
55
56
57		//REMOVED: Boundary points dont know their intensities...profiles do!
58		template <unsigned int NDimensions>
59		void
60		BloxCoreAtomPixel<NDimensions>
61		::CalcMeanCoreAtomIntensity()
62		{
63
64	IND	/*
65		double temp_intensity = 0.0;
66		int num_core_atoms = 0;
67
68		itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
69
70		for (bpiterator = this->begin(); bpiterator != this->end(); ++bpiterator)
71		{
72		// Get the pointer of the core atom
73		CoreAtomItemType* pCoreAtom = *bpiterator;
74
75		//get mean intensity for this core atom
76	LEN	temp_intensity = (pCoreAtom->GetBoundaryPointA()->GetValue() + pCoreAtom->GetBoundaryPointB()->GetValue())/2
77
78		m_MeanCoreAtomIntensity += temp_intensity;
79		num_core_atoms++;
80		}
81		m_MeanCoreAtomIntensity /= num_core_atoms;
82	IND	*/
83		}
84
85		template <unsigned int NDimensions>
86		void
87		BloxCoreAtomPixel<NDimensions>
88		::CalcWeightedCoreAtomLocation(double weight_factor, Self * votingPixel)
89		{
90		// The iterator for accessing linked list info
91		typename itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
92
93		PositionType center;
94
95		// Walk through all of the items in the voting pixel
96	LEN	for (bpiterator = votingPixel->begin(); bpiterator != votingPixel->end(); ++bpiterator)
97		{
98		// Get the pointer of the core atom
99		CoreAtomItemType* pCoreAtom = *bpiterator;
100
101		// Get the center of the core atom
102		center = pCoreAtom->GetCenterPosition();
103
104		m_LocationSums[0] += (center[0]*weight_factor);
105		m_LocationSums[1] += (center[1]*weight_factor);
106		m_LocationSums[2] += (center[2]*weight_factor);
107
108		m_WeightSum += weight_factor;
109		}
110		}
111
112		template <unsigned int NDimensions>
113		double
114		BloxCoreAtomPixel<NDimensions>
115		::CalcMeanCoreAtomDiameter()
116		{
117		// Returns a mean of 0 if there are no core atoms present
118		if( this->empty() )
119		{
120		return 0;
121		}
122
123		unsigned long int numCoreAtoms = 0;
124		m_MeanCoreAtomDiameter = 0;
125
126		// The iterator for accessing linked list info
127		typename itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
128
129		// Walk through all of the items at the pixel
130		for (bpiterator = this->begin(); bpiterator != this->end(); ++bpiterator)
131		{
132		// Get the pointer of the core atom
133		CoreAtomItemType* pCoreAtom = *bpiterator;
134
135		m_MeanCoreAtomDiameter += pCoreAtom->GetDiameter();
136
137		numCoreAtoms++;
138		}
139
140		if(numCoreAtoms>0) // Check for /0 to be safe
141	IND	****m_MeanCoreAtomDiameter /= numCoreAtoms;
142		else
143	IND	****m_MeanCoreAtomDiameter = 0;
144
145		return m_MeanCoreAtomDiameter;
146		}
147
148		template <unsigned int NDimensions>
149		bool
150		BloxCoreAtomPixel<NDimensions>
151		::DoCoreAtomEigenanalysis()
152		{
153		// Don't attemp Eigenanalysis on an empty blox
154		if( this->empty() )
155		{
156		return false;
157		}
158
159		// The iterator for accessing linked list info
160		typename itk::BloxCoreAtomPixel<NDimensions>::iterator bpiterator;
161
162		// The number of items stored in the pixel
163		unsigned long int numItems = 0;
164
165		// Walk through all of the items at the pixel
166		for (bpiterator = this->begin(); bpiterator != this->end(); ++bpiterator)
167		{
168		// Get the pointer of the core atom
169		CoreAtomItemType* pCoreAtom = *bpiterator;
170
171		// Get the boundary points
172		BPItemType* pBPOne = pCoreAtom->GetBoundaryPointA();
173		BPItemType* pBPTwo = pCoreAtom->GetBoundaryPointB();
174
175		// Get the physical positions of the two boundary points
176		VectorType P1;
177		P1 = pBPOne->GetPhysicalPosition().GetVnlVector();
178
179		VectorType P2;
180		P2 = pBPTwo->GetPhysicalPosition().GetVnlVector();
181
182		// Figure out the "C" vector of the core atom
183		VectorType cVector = P2 - P1;
184		cVector.normalize();
185
186		// Now, add to m_RawCMatrix
187		for(unsigned int r = 0; r < NDimensions; r++) // row loop
188		{
189		for(unsigned int c = 0; c < NDimensions; c++) // column loop
190		{
191		m_RawCMatrix(r,c) += cVector[c]*cVector[r];
192		} // end column loop
193		} // end row loop
194
195		numItems++;
196
197		} // end walk all of the items in the pixel
198
199		// Divide through by the number of items
200		m_RawCMatrix /= numItems;
201
202		// Create an identity matrix of size n
203		vnl_matrix_fixed<double, NDimensions, NDimensions> identMatrix;
204		identMatrix.fill(0);
205
206		// Set the diagonal to 1
207		for(unsigned int n = 0; n < NDimensions; n++) // row loop
208		{
209		identMatrix(n,n) = 1.0;
210		} // end row loop
211
212		// Do eigen analysis
213	LEN	vnl_generalized_eigensystem* pEigenSys = new vnl_generalized_eigensystem(m_RawCMatrix, identMatrix);
214
215		// Now, store the results
216
217		// First the eigenvectors
218		m_Eigenvectors = pEigenSys->V;
219
220		// Now the eigenvalues (stored as a vector to save space)
221		for(unsigned int i = 0; i < NDimensions; i++)
222		{
223		m_Eigenvalues[i] = pEigenSys->D(i,i);
224		}
225
226		delete pEigenSys;
227		return true;
228		}
229
230		template <unsigned int NDimensions>
231		typename BloxCoreAtomPixel<NDimensions>::PositionType
232		BloxCoreAtomPixel<NDimensions>
233		::GetVotedLocation()
234		{
235		m_VotedLocation[0] = m_LocationSums[0] / m_WeightSum;
236		m_VotedLocation[1] = m_LocationSums[1] / m_WeightSum;
237		m_VotedLocation[2] = m_LocationSums[2] / m_WeightSum;
238
239		return m_VotedLocation;
240		}
241
242		template <unsigned int NDimensions>
243		void
244		BloxCoreAtomPixel<NDimensions>
245		::CollectVote(MatrixType* pMatrix, double strength, double count)
246		{
247		m_VotedCMatrix += (*pMatrix)*strength;
248		m_ConstituencySize += count;
249		}
250
251		template <unsigned int NDimensions>
252		void
253		BloxCoreAtomPixel<NDimensions>
254		::NormalizeVotedCMatrix()
255		{
256		if(m_ConstituencySize != 0)
257	IND	****m_VotedCMatrix /= m_ConstituencySize;
258		}
259
260		template <unsigned int NDimensions>
261		void
262		BloxCoreAtomPixel<NDimensions>
263		::DoVotedEigenanalysis()
264		{
265		// Create an identity matrix of size n
266		vnl_matrix_fixed<double, NDimensions, NDimensions> identMatrix;
267		identMatrix.fill(0);
268
269		// Set the diagonal to 1
270		for(unsigned int n = 0; n < NDimensions; n++) // row loop
271		{
272		identMatrix(n,n) = 1.0;
273		} // end row loop
274
275		// Do eigen analysis
276	LEN	vnl_generalized_eigensystem* pEigenSys = new vnl_generalized_eigensystem(m_VotedCMatrix, identMatrix);
277
278		// Now, store the results
279
280		// First the eigenvectors
281		m_VotedEigenvectors = pEigenSys->V;
282
283		// Now the eigenvalues (stored as a vector to save space)
284		for(unsigned int i = 0; i < NDimensions; i++)
285		{
286		m_VotedEigenvalues[i] = pEigenSys->D(i,i);
287		}
288
289		delete pEigenSys;
290
291		//printf("VotedCMatrix\n");
292		for(int i = 0; i < 3; i++)
293		{
294	LEN	//printf("%f %f %f\n", m_VotedCMatrix(i,0), m_VotedCMatrix(i,1), m_VotedCMatrix(i,2) );
295		}
296		//printf("\n");
297
298		//printf("Voted eigenvectors\n");
299		for(int i = 0; i < 3; i++)
300		{
301	LEN	//printf("%f %f %f\n", m_VotedEigenvectors(i,0), m_VotedEigenvectors(i,1), m_VotedEigenvectors(i,2) );
302		}
303		//printf("\n");
304		}
305
306		} // end namespace itk
307
308		#endif
309

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