diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp index a488ead82b..0e4aa5191b 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp @@ -1,240 +1,238 @@ /*=================================================================== 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. ===================================================================*/ #ifndef __itkKspaceImageFilter_txx #define __itkKspaceImageFilter_txx #include #include #include #include "itkKspaceImageFilter.h" #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > KspaceImageFilter< TPixelType > ::KspaceImageFilter() : m_tLine(1) , m_kOffset(0) , m_FrequencyMap(NULL) , m_SimulateRelaxation(true) , m_SimulateEddyCurrents(false) , m_Tau(70) , m_EddyGradientMagnitude(30) , m_IsBaseline(true) , m_SignalScale(1) , m_Spikes(0) , m_SpikeAmplitude(1) { m_DiffusionGradientDirection.Fill(0.0); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::BeforeThreadedGenerateData() { typename OutputImageType::Pointer outputImage = OutputImageType::New(); outputImage->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); outputImage->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); outputImage->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); itk::ImageRegion<2> region; region.SetSize(0, m_OutSize[0]); region.SetSize(1, m_OutSize[1]); outputImage->SetLargestPossibleRegion( region ); outputImage->SetBufferedRegion( region ); outputImage->SetRequestedRegion( region ); outputImage->Allocate(); m_TEMPIMAGE = InputImageType::New(); m_TEMPIMAGE->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); m_TEMPIMAGE->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); m_TEMPIMAGE->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); m_TEMPIMAGE->SetLargestPossibleRegion( region ); m_TEMPIMAGE->SetBufferedRegion( region ); m_TEMPIMAGE->SetRequestedRegion( region ); m_TEMPIMAGE->Allocate(); m_SimulateDistortions = true; if (m_FrequencyMap.IsNull()) { m_SimulateDistortions = false; m_FrequencyMap = InputImageType::New(); m_FrequencyMap->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); m_FrequencyMap->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); m_FrequencyMap->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); m_FrequencyMap->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_FrequencyMap->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_FrequencyMap->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_FrequencyMap->Allocate(); m_FrequencyMap->FillBuffer(0); } double gamma = 42576000; // Gyromagnetic ratio in Hz/T if (m_DiffusionGradientDirection.GetNorm()>0.001) { - m_DiffusionGradientDirection.Normalize(); m_EddyGradientMagnitude /= 1000; // eddy gradient magnitude in T/m + m_DiffusionGradientDirection.Normalize(); m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_EddyGradientMagnitude * gamma; m_IsBaseline = false; } - else - m_EddyGradientMagnitude = gamma*m_EddyGradientMagnitude/1000; this->SetNthOutput(0, outputImage); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId) { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); typedef ImageRegionConstIterator< InputImageType > InputIteratorType; double kxMax = outputImage->GetLargestPossibleRegion().GetSize(0); double kyMax = outputImage->GetLargestPossibleRegion().GetSize(1); double numPix = kxMax*kyMax; double dt = m_tLine/kxMax; double fromMaxEcho = - m_tLine*kyMax/2; double in_szx = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); double in_szy = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); int xOffset = in_szx-kxMax; int yOffset = in_szy-kyMax; vcl_complex spike(0,0); while( !oit.IsAtEnd() ) { itk::Index< 2 > kIdx; kIdx[0] = oit.GetIndex()[0]; kIdx[1] = oit.GetIndex()[1]; double t = fromMaxEcho + ((double)kIdx[1]*kxMax+(double)kIdx[0])*dt; // dephasing time // rearrange slice if( kIdx[0] < kxMax/2 ) kIdx[0] = kIdx[0] + kxMax/2; else kIdx[0] = kIdx[0] - kxMax/2; if( kIdx[1] < kyMax/2 ) kIdx[1] = kIdx[1] + kyMax/2; else kIdx[1] = kIdx[1] - kyMax/2; // calculate eddy current decay factors double eddyDecay = 0; if (m_SimulateEddyCurrents) eddyDecay = exp(-(m_TE/2 + t)/m_Tau) * t/1000; // calcualte signal relaxation factors std::vector< double > relaxFactor; if (m_SimulateRelaxation) for (int i=0; i=kxMax/2) kx += xOffset; if (ky>=kyMax/2) ky += yOffset; vcl_complex s(0,0); InputIteratorType it(m_CompartmentImages.at(0), m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { double x = it.GetIndex()[0]-in_szx/2; double y = it.GetIndex()[1]-in_szy/2; vcl_complex f(0, 0); // sum compartment signals and simulate relaxation for (int i=0; i( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * relaxFactor.at(i) * m_SignalScale, 0); else f += std::complex( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * m_SignalScale ); // simulate eddy currents and other distortions double omega_t = 0; if ( m_SimulateEddyCurrents && !m_IsBaseline) { itk::Vector< double, 3 > pos; pos[0] = x; pos[1] = y; pos[2] = m_Z; pos = m_DirectionMatrix*pos/1000; // vector from image center to current position (in meter) omega_t += (m_DiffusionGradientDirection[0]*pos[0]+m_DiffusionGradientDirection[1]*pos[1]+m_DiffusionGradientDirection[2]*pos[2])*eddyDecay; } if (m_SimulateDistortions) omega_t += m_FrequencyMap->GetPixel(it.GetIndex())*t/1000; // actual DFT term s += f * exp( std::complex(0, 2 * M_PI * (kx*x/in_szx + ky*y/in_szy + omega_t )) ); ++it; } s /= numPix; if (m_Spikes>0 && sqrt(s.imag()*s.imag()+s.real()*s.real()) > sqrt(spike.imag()*spike.imag()+spike.real()*spike.real()) ) spike = s; // m_TEMPIMAGE->SetPixel(kIdx, sqrt(s.real()*s.real()+s.imag()*s.imag())); outputImage->SetPixel(kIdx, s); ++oit; } spike *= m_SpikeAmplitude; for (int i=0; i spikeIdx; spikeIdx[0] = rand()%(int)kxMax; spikeIdx[1] = rand()%(int)kyMax; outputImage->SetPixel(spikeIdx, spike); } // typedef itk::ImageFileWriter< InputImageType > WriterType; // typename WriterType::Pointer writer = WriterType::New(); // writer->SetFileName("/local/kspace.nrrd"); // writer->SetInput(m_TEMPIMAGE); // writer->Update(); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::AfterThreadedGenerateData() { } } #endif