diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx index 5be3422111..407f13a6e3 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx @@ -1,253 +1,254 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ /*========================================================================= Program: Tensor ToolKit - TTK Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx $ Language: C++ Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $ Version: $Revision: 68 $ Copyright (c) INRIA 2010. All rights reserved. See LICENSE.txt 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 _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_ #define _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_ #endif #define _USE_MATH_DEFINES #include "itkElectrostaticRepulsionDiffusionGradientReductionFilter.h" #include #include #include #include namespace itk { template ElectrostaticRepulsionDiffusionGradientReductionFilter ::ElectrostaticRepulsionDiffusionGradientReductionFilter() { this->SetNumberOfRequiredInputs( 1 ); } template double ElectrostaticRepulsionDiffusionGradientReductionFilter ::Costs() { double costs = 2*M_PI; for (IndicesVector::iterator it = m_UsedGradientIndices.begin(); it!=m_UsedGradientIndices.end(); ++it) { for (IndicesVector::iterator it2 = m_UsedGradientIndices.begin(); it2!=m_UsedGradientIndices.end(); ++it2) if (it != it2) { vnl_vector_fixed v1 = m_OriginalGradientDirections->at(*it); vnl_vector_fixed v2 = m_OriginalGradientDirections->at(*it2); v1.normalize(); v2.normalize(); double temp = dot_product(v1,v2); if (temp>1) temp = 1; else if (temp<-1) temp = -1; double angle = acos(temp); if (angle1) temp = 1; else if (temp<-1) temp = -1; angle = acos(temp); if (angle void ElectrostaticRepulsionDiffusionGradientReductionFilter ::GenerateData() { unsigned int randSeed = time(NULL); if(m_InputBValueMap.empty() || m_NumGradientDirections.size()!=m_InputBValueMap.size()) return; if(m_InputBValueMap.find(0) != m_InputBValueMap.end()) { //delete b0 from input BValueMap m_InputBValueMap.erase(0); } - BValueMap manipulatedMap = m_OriginalBValueMap; + BValueMap manipulatedMap = m_InputBValueMap; + manipulatedMap[0] = m_OriginalBValueMap[0]; int shellCounter = 0; for(BValueMap::iterator it = m_InputBValueMap.begin(); it != m_InputBValueMap.end(); it++ ) { srand(randSeed); // initialize index vectors m_UsedGradientIndices.clear(); m_UnusedGradientIndices.clear(); if ( it->second.size() <= m_NumGradientDirections[shellCounter] ) { itkWarningMacro( << "current directions: " << it->second.size() << " wanted directions: " << m_NumGradientDirections[shellCounter]); m_NumGradientDirections[shellCounter] = it->second.size(); shellCounter++; continue; } MITK_INFO << "Shell number: " << shellCounter; int c=0; for (int i=0; isecond.size(); i++) { if (csecond.at(i)); else m_UnusedGradientIndices.push_back(it->second.at(i)); c++; } double minAngle = Costs(); double newMinAngle = 0; MITK_INFO << "minimum angle: " << 180*minAngle/M_PI; int stagnationCount = 0; int rejectionCount = 0; int maxRejections = m_NumGradientDirections[shellCounter] * 1000; if (maxRejections<10000) maxRejections = 10000; int iUsed = 0; if (m_UsedGradientIndices.size()>0) while ( stagnationCount<1000 && rejectionCount minAngle) // accept or reject proposal { MITK_INFO << "minimum angle: " << 180*newMinAngle/M_PI; if ( (newMinAngle-minAngle)<0.01 ) stagnationCount++; else stagnationCount = 0; minAngle = newMinAngle; rejectionCount = 0; } else { rejectionCount++; m_UsedGradientIndices.at(iUsed) = vUsed; m_UnusedGradientIndices.at(iUnUsed) = vUnUsed; } iUsed++; iUsed = iUsed % m_UsedGradientIndices.size(); } manipulatedMap[it->first] = m_UsedGradientIndices; shellCounter++; } int vecLength = 0 ; for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++) vecLength += it->second.size(); // initialize output image typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( this->GetInput()->GetSpacing() ); // Set the image spacing outImage->SetOrigin( this->GetInput()->GetOrigin() ); // Set the image origin outImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction outImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion()); outImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() ); outImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() ); outImage->SetVectorLength( vecLength ); // Set the vector length outImage->Allocate(); itk::ImageRegionIterator< OutputImageType > newIt(outImage, outImage->GetLargestPossibleRegion()); newIt.GoToBegin(); typename InputImageType::Pointer inImage = const_cast(this->GetInput(0)); itk::ImageRegionIterator< InputImageType > oldIt(inImage, inImage->GetLargestPossibleRegion()); oldIt.GoToBegin(); // initial new value of voxel OutputPixelType newVec; newVec.SetSize( vecLength ); newVec.AllocateElements( vecLength ); // generate new pixel values while(!newIt.IsAtEnd()) { // init new vector with zeros newVec.Fill(0.0); InputPixelType oldVec = oldIt.Get(); int index = 0; for(BValueMap::iterator it=manipulatedMap.begin(); it!=manipulatedMap.end(); it++) for(int j=0; jsecond.size(); j++) { newVec[index] = oldVec[it->second.at(j)]; index++; } newIt.Set(newVec); ++newIt; ++oldIt; } // set new gradient directions m_GradientDirections = GradientDirectionContainerType::New(); int index = 0; for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++) for(int j = 0; j < it->second.size(); j++) { m_GradientDirections->InsertElement(index, m_OriginalGradientDirections->at(it->second.at(j))); index++; } this->SetNumberOfRequiredOutputs (1); this->SetNthOutput (0, outImage); MITK_INFO << "...done"; } } // end of namespace