diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp index 4e9c2430d8..7a58a8a5be 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp @@ -1,336 +1,336 @@ /*=================================================================== 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 __itkAddArtifactsToDwiImageFilter_txx #define __itkAddArtifactsToDwiImageFilter_txx #include #include #include #include "itkAddArtifactsToDwiImageFilter.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > AddArtifactsToDwiImageFilter< TPixelType > ::AddArtifactsToDwiImageFilter() : m_UseConstantRandSeed(false) { this->SetNumberOfRequiredInputs( 1 ); m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); m_RandGen->SetSeed(); } template< class TPixelType > void AddArtifactsToDwiImageFilter< TPixelType > ::GenerateData() { if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); m_StartTime = clock(); m_StatusText = "Starting simulation\n"; typename InputImageType::Pointer inputImage = static_cast< InputImageType* >( this->ProcessObject::GetInput(0) ); itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion(); typename itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage( inputImage ); duplicator->Update(); typename InputImageType::Pointer outputImage = duplicator->GetOutput(); // is input slize size even? int xMax=inputRegion.GetSize(0); int yMax=inputRegion.GetSize(1); if ( xMax%2 == 1 ) xMax += 1; if ( yMax%2 == 1 ) yMax += 1; // create slice object typename SliceType::Pointer slice = SliceType::New(); ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, xMax); sliceRegion.SetSize(1, yMax); slice->SetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->Allocate(); slice->FillBuffer(0.0); ImageRegion<2> upsampledSliceRegion; if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { upsampledSliceRegion.SetSize(0, xMax*2); upsampledSliceRegion.SetSize(1, yMax*2); } // frequency map slice typename SliceType::Pointer fMapSlice = NULL; if ( m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); fMapSlice->SetLargestPossibleRegion( sliceRegion ); fMapSlice->SetBufferedRegion( sliceRegion ); fMapSlice->SetRequestedRegion( sliceRegion ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } m_Parameters.m_SignalGen.m_SignalScale = 1; m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; if ( m_Parameters.m_SignalGen.m_Spikes>0 || m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() || m_Parameters.m_SignalGen.m_KspaceLineOffset>0.0 || m_Parameters.m_SignalGen.m_DoAddGibbsRinging || m_Parameters.m_SignalGen.m_EddyStrength>0 || m_Parameters.m_SignalGen.m_CroppingFactor<1.0) { ImageRegion<3> croppedRegion = inputRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)* m_Parameters.m_SignalGen.m_CroppingFactor); itk::Point shiftedOrigin = inputImage->GetOrigin(); shiftedOrigin[1] += (inputRegion.GetSize(1)-croppedRegion.GetSize(1))*inputImage->GetSpacing()[1]/2; outputImage = InputImageType::New(); outputImage->SetSpacing( inputImage->GetSpacing() ); outputImage->SetOrigin( shiftedOrigin ); outputImage->SetDirection( inputImage->GetDirection() ); outputImage->SetLargestPossibleRegion( croppedRegion ); outputImage->SetBufferedRegion( croppedRegion ); outputImage->SetRequestedRegion( croppedRegion ); outputImage->SetVectorLength( inputImage->GetVectorLength() ); outputImage->Allocate(); typename InputImageType::PixelType temp; temp.SetSize(inputImage->GetVectorLength()); temp.Fill(0.0); outputImage->FillBuffer(temp); int tempY=croppedRegion.GetSize(1); tempY += tempY%2; croppedRegion.SetSize(1, tempY); m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; if ( m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; if ( m_Parameters.m_SignalGen.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; if ( m_Parameters.m_SignalGen.m_Spikes>0) m_StatusText += "Simulating spikes\n"; if ( m_Parameters.m_SignalGen.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; if ( m_Parameters.m_SignalGen.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; std::vector< unsigned int > spikeVolume; for (unsigned int i=0; i< m_Parameters.m_SignalGen.m_Spikes; i++) spikeVolume.push_back(m_RandGen->GetIntegerVariate()%inputImage->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); FiberfoxParameters doubleParam = m_Parameters.CopyParameters(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(inputImage->GetVectorLength()*inputRegion.GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%inputImage->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } std::vector< SliceType::Pointer > compartmentSlices; // extract slice from channel g for (unsigned int y=0; yGetPixel(index3D)[g]; slice->SetPixel(index2D, pix2D); if (fMapSlice.IsNotNull()) fMapSlice->SetPixel(index2D, m_Parameters.m_SignalGen.m_FrequencyMap->GetPixel(index3D)); } if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(slice); resampler->SetOutputParametersFromImage(slice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(slice->GetSpacing()/2); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); typename SliceType::Pointer upslice = resampler->GetOutput(); compartmentSlices.push_back(upslice); if (fMapSlice.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(fMapSlice); resampler->SetOutputParametersFromImage(fMapSlice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(fMapSlice->GetSpacing()/2); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); fMapSlice = resampler->GetOutput(); } } else compartmentSlices.push_back(slice); // fourier transform slice typename ComplexSliceType::Pointer fSlice; itk::Size<2> outSize; outSize.SetElement(0, xMax); outSize.SetElement(1, croppedRegion.GetSize()[1]); typename itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(doubleParam); idft->SetCompartmentImages(compartmentSlices); idft->SetFrequencyMapSlice(fMapSlice); - idft->SetDiffusionGradientDirection( m_Parameters.GetGradientDirection(g)); + idft->SetDiffusionGradientDirection( m_Parameters.m_SignalGen.GetGradientDirection(g)); idft->SetZ((double)z-(double)inputRegion.GetSize(2)/2.0); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); fSlice = idft->GetOutput(); // inverse fourier transform slice typename SliceType::Pointer newSlice; typename itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { typename InputImageType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; typename InputImageType::PixelType pix3D = outputImage->GetPixel(index3D); typename SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; double signal = newSlice->GetPixel(index2D); if (signal>0) signal = floor(signal+0.5); else signal = ceil(signal-0.5); pix3D[g] = signal; outputImage->SetPixel(index3D, pix3D); } ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; } if ( m_Parameters.m_NoiseModel!=NULL) { m_StatusText += this->GetTime()+" > Adding noise\n"; m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; ImageRegionIterator it1 (outputImage, outputImage->GetLargestPossibleRegion()); boost::progress_display disp(outputImage->GetLargestPossibleRegion().GetNumberOfPixels()); while(!it1.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename InputImageType::PixelType signal = it1.Get(); m_Parameters.m_NoiseModel->AddNoise(signal); it1.Set(signal); ++it1; } m_StatusText += "\n\n"; } this->SetNthOutput(0, outputImage); m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); } template< class TPixelType > std::string AddArtifactsToDwiImageFilter< TPixelType >::GetTime() { unsigned long total = (double)(clock() - m_StartTime)/CLOCKS_PER_SEC; unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); return out; } } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index cf1803df39..d209a3b5df 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,1300 +1,1300 @@ /*=================================================================== 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. ===================================================================*/ #include "itkTractsToDWIImageFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk { template< class PixelType > TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter() : m_FiberBundle(NULL) , m_StatusText("") , m_UseConstantRandSeed(false) , m_RandGen(itk::Statistics::MersenneTwisterRandomVariateGenerator::New()) { m_RandGen->SetSeed(); } template< class PixelType > TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter() { } template< class PixelType > TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images ) { int numFiberCompartments = m_Parameters.m_FiberModelList.size(); // create slice object ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); Vector< double, 2 > sliceSpacing; sliceSpacing[0] = m_UpsampledSpacing[0]; sliceSpacing[1] = m_UpsampledSpacing[1]; // frequency map slice SliceType::Pointer fMapSlice = NULL; if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); fMapSlice->SetLargestPossibleRegion( region ); fMapSlice->SetBufferedRegion( region ); fMapSlice->SetRequestedRegion( region ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } DoubleDwiType::Pointer newImage = DoubleDwiType::New(); newImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing ); newImage->SetOrigin( m_Parameters.m_SignalGen.m_ImageOrigin ); newImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); newImage->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_ImageRegion ); newImage->SetBufferedRegion( m_Parameters.m_SignalGen.m_ImageRegion ); newImage->SetRequestedRegion( m_Parameters.m_SignalGen.m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); std::vector< unsigned int > spikeVolume; for (unsigned int i=0; iGetIntegerVariate()%images.at(0)->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (unsigned int i=0; i* signalModel; if (iSetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->SetSpacing(sliceSpacing); slice->Allocate(); slice->FillBuffer(0.0); // extract slice from channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]); if (fMapSlice.IsNotNull() && i==0) fMapSlice->SetPixel(index2D, m_Parameters.m_SignalGen.m_FrequencyMap->GetPixel(index3D)); } compartmentSlices.push_back(slice); t2Vector.push_back(signalModel->GetT2()); } if (this->GetAbortGenerateData()) return NULL; // create k-sapce (inverse fourier transform slices) itk::Size<2> outSize; outSize.SetElement(0, m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)); itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetT2(t2Vector); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(m_Parameters); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); - idft->SetDiffusionGradientDirection(m_Parameters.GetGradientDirection(g)); + idft->SetDiffusionGradientDirection(m_Parameters.m_SignalGen.GetGradientDirection(g)); idft->SetFrequencyMapSlice(fMapSlice); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; // fourier transform slice SliceType::Pointer newSlice; itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D); pix3D[g] = newSlice->GetPixel(index2D); newImage->SetPixel(index3D, pix3D); } ++disp; newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; return newImage; } template< class PixelType > void TractsToDWIImageFilter< PixelType >::GenerateData() { m_TimeProbe.Start(); m_StatusText = "Starting simulation\n"; // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); if (m_Parameters.m_FiberModelList.empty()) itkExceptionMacro("No diffusion model for fiber compartments defined!"); if (m_Parameters.m_NonFiberModelList.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); - int baselineIndex = m_Parameters.GetFirstBaselineIndex(); + int baselineIndex = m_Parameters.m_SignalGen.GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); if (!m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition) m_Parameters.m_SignalGen.m_DoAddGibbsRinging = false; if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); // initialize output dwi image ImageRegion<3> croppedRegion = m_Parameters.m_SignalGen.m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_SignalGen.m_CroppingFactor); itk::Point shiftedOrigin = m_Parameters.m_SignalGen.m_ImageOrigin; shiftedOrigin[1] += (m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing ); outImage->SetOrigin( shiftedOrigin ); outImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); outImage->SetLargestPossibleRegion( croppedRegion ); outImage->SetBufferedRegion( croppedRegion ); outImage->SetRequestedRegion( croppedRegion ); - outImage->SetVectorLength( m_Parameters.GetNumVolumes() ); + outImage->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() ); outImage->Allocate(); typename OutputImageType::PixelType temp; - temp.SetSize(m_Parameters.GetNumVolumes()); + temp.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); temp.Fill(0.0); outImage->FillBuffer(temp); // ADJUST GEOMETRY FOR FURTHER PROCESSING // is input slize size a power of two? unsigned int x=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0); unsigned int y=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1); ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0; m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, x+pad[0]); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, y+pad[1]); if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_SignalGen.m_FrequencyMap); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_SignalGen.m_FrequencyMap = zeroPadder->GetOutput(); } if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_SignalGen.m_MaskImage); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_SignalGen.m_MaskImage = zeroPadder->GetOutput(); } // Apply in-plane upsampling for Gibbs ringing artifact double upsampling = 1; if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) upsampling = 2; m_UpsampledSpacing = m_Parameters.m_SignalGen.m_ImageSpacing; m_UpsampledSpacing[0] /= upsampling; m_UpsampledSpacing[1] /= upsampling; m_UpsampledImageRegion = m_Parameters.m_SignalGen.m_ImageRegion; m_UpsampledImageRegion.SetSize(0, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[0]*upsampling); m_UpsampledImageRegion.SetSize(1, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[1]*upsampling); m_UpsampledOrigin = m_Parameters.m_SignalGen.m_ImageOrigin; m_UpsampledOrigin[0] -= m_Parameters.m_SignalGen.m_ImageSpacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; m_UpsampledOrigin[1] -= m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; m_UpsampledOrigin[2] -= m_Parameters.m_SignalGen.m_ImageSpacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; // generate double images to store the individual compartment signals m_CompartmentImages.clear(); int numFiberCompartments = m_Parameters.m_FiberModelList.size(); int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_UpsampledOrigin ); doubleDwi->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); - doubleDwi->SetVectorLength( m_Parameters.GetNumVolumes() ); + doubleDwi->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; - pix.SetSize(m_Parameters.GetNumVolumes()); + pix.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); m_CompartmentImages.push_back(doubleDwi); } // initialize output volume fraction images m_VolumeFractions.clear(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleImg->SetOrigin( m_UpsampledOrigin ); doubleImg->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleImg->SetBufferedRegion( m_UpsampledImageRegion ); doubleImg->SetRequestedRegion( m_UpsampledImageRegion ); doubleImg->Allocate(); doubleImg->FillBuffer(0); m_VolumeFractions.push_back(doubleImg); } // get volume fraction images ItkDoubleImgType::Pointer sumImage = ItkDoubleImgType::New(); bool foundVolumeFractionImage = false; for (int i=0; iGetVolumeFractionImage().IsNotNull()) { foundVolumeFractionImage = true; itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(zeroPadder->GetOutput()); sumImage->SetSpacing( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetSpacing() ); sumImage->SetOrigin( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetOrigin() ); sumImage->SetDirection( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetDirection() ); sumImage->SetLargestPossibleRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetBufferedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetRequestedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->Allocate(); sumImage->FillBuffer(0); break; } } if (!foundVolumeFractionImage) { sumImage->SetSpacing( m_UpsampledSpacing ); sumImage->SetOrigin( m_UpsampledOrigin ); sumImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); sumImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); sumImage->SetBufferedRegion( m_UpsampledImageRegion ); sumImage->SetRequestedRegion( m_UpsampledImageRegion ); sumImage->Allocate(); sumImage->FillBuffer(0.0); } for (int i=0; iGetVolumeFractionImage().IsNull()) { ItkDoubleImgType::Pointer doubleImg = ItkDoubleImgType::New(); doubleImg->SetSpacing( sumImage->GetSpacing() ); doubleImg->SetOrigin( sumImage->GetOrigin() ); doubleImg->SetDirection( sumImage->GetDirection() ); doubleImg->SetLargestPossibleRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetBufferedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetRequestedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->Allocate(); doubleImg->FillBuffer(1.0/numNonFiberCompartments); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(doubleImg); } ImageRegionIterator it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { sumImage->SetPixel(it.GetIndex(), sumImage->GetPixel(it.GetIndex())+it.Get()); ++it; } } for (int i=0; i it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (sumImage->GetPixel(it.GetIndex())>0) it.Set(it.Get()/sumImage->GetPixel(it.GetIndex())); ++it; } } // resample mask image and frequency map to fit upsampled geometry if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull()) { // rescale mask image (otherwise there are problems with the resampling) itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_Parameters.m_SignalGen.m_MaskImage); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); // resample mask image itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); resampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_MaskImage); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_SignalGen.m_MaskImage = resampler->GetOutput(); itk::ImageFileWriter::Pointer w = itk::ImageFileWriter::New(); w->SetFileName("/local/mask_ups.nrrd"); w->SetInput(m_Parameters.m_SignalGen.m_MaskImage); w->Update(); } // resample frequency map if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(m_Parameters.m_SignalGen.m_FrequencyMap); resampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_SignalGen.m_FrequencyMap = resampler->GetOutput(); } } // no input tissue mask is set -> create default m_MaskImageSet = true; if (m_Parameters.m_SignalGen.m_MaskImage.IsNull()) { m_StatusText += "No tissue mask set\n"; MITK_INFO << "No tissue mask set"; m_Parameters.m_SignalGen.m_MaskImage = ItkUcharImgType::New(); m_Parameters.m_SignalGen.m_MaskImage->SetSpacing( m_UpsampledSpacing ); m_Parameters.m_SignalGen.m_MaskImage->SetOrigin( m_UpsampledOrigin ); m_Parameters.m_SignalGen.m_MaskImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); m_Parameters.m_SignalGen.m_MaskImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); m_Parameters.m_SignalGen.m_MaskImage->SetBufferedRegion( m_UpsampledImageRegion ); m_Parameters.m_SignalGen.m_MaskImage->SetRequestedRegion( m_UpsampledImageRegion ); m_Parameters.m_SignalGen.m_MaskImage->Allocate(); m_Parameters.m_SignalGen.m_MaskImage->FillBuffer(1); m_MaskImageSet = false; } else { m_StatusText += "Using tissue mask\n"; MITK_INFO << "Using tissue mask"; } m_Parameters.m_SignalGen.m_ImageRegion = croppedRegion; x=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0); y=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1); if ( x%2 == 1 ) m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, x+1); if ( y%2 == 1 ) m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, y+1); // resample fiber bundle for sufficient voxel coverage m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n"; double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); double volumeAccuracy = 10; m_FiberBundleWorkingCopy->ResampleFibers(minSpacing/volumeAccuracy); double mmRadius = m_Parameters.m_SignalGen.m_AxonRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/volumeAccuracy; double maxVolume = 0; m_VoxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; if (m_Parameters.m_SignalGen.m_DoAddMotion) { std::string fileName = "fiberfox_motion_0.log"; std::string filePath = mitk::IOUtil::GetTempPath(); if (m_Parameters.m_Misc.m_OutputPath.size()>0) filePath = m_Parameters.m_Misc.m_OutputPath; int c = 1; while (itksys::SystemTools::FileExists((filePath+fileName).c_str())) { fileName = "fiberfox_motion_"; fileName += boost::lexical_cast(c); fileName += ".log"; c++; } m_Logfile.open((filePath+fileName).c_str()); m_Logfile << "0 rotation: 0,0,0; translation: 0,0,0\n"; if (m_Parameters.m_SignalGen.m_DoRandomizeMotion) { m_StatusText += "Adding random motion artifacts:\n"; m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_Parameters.m_SignalGen.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_Parameters.m_SignalGen.m_Translation) + "mm\n"; } else { m_StatusText += "Adding linear motion artifacts:\n"; m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_Parameters.m_SignalGen.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: " + boost::lexical_cast(m_Parameters.m_SignalGen.m_Translation) + "mm\n"; } m_StatusText += "Motion logfile: " + (filePath+fileName) + "\n"; MITK_INFO << "Adding motion artifacts"; MITK_INFO << "Maximum rotation: " << m_Parameters.m_SignalGen.m_Rotation; MITK_INFO << "Maxmimum translation: " << m_Parameters.m_SignalGen.m_Translation; } maxVolume = 0; m_StatusText += "\n"+this->GetTime()+" > Generating " + boost::lexical_cast(numFiberCompartments+numNonFiberCompartments) + "-compartment diffusion-weighted signal.\n"; int numFibers = m_FiberBundle->GetNumFibers(); - boost::progress_display disp(numFibers*m_Parameters.GetNumVolumes()); + boost::progress_display disp(numFibers*m_Parameters.m_SignalGen.GetNumVolumes()); // get transform for motion artifacts m_FiberBundleTransformed = m_FiberBundleWorkingCopy; - m_Rotation = m_Parameters.m_SignalGen.m_Rotation/m_Parameters.GetNumVolumes(); - m_Translation = m_Parameters.m_SignalGen.m_Translation/m_Parameters.GetNumVolumes(); + m_Rotation = m_Parameters.m_SignalGen.m_Rotation/m_Parameters.m_SignalGen.GetNumVolumes(); + m_Translation = m_Parameters.m_SignalGen.m_Translation/m_Parameters.m_SignalGen.GetNumVolumes(); // creat image to hold transformed mask (motion artifact) m_MaskImage = ItkUcharImgType::New(); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage); duplicator->Update(); m_MaskImage = duplicator->GetOutput(); // second upsampling needed for motion artifacts ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; DoubleVectorType upsampledSpacing = m_UpsampledSpacing; upsampledSpacing[0] /= 4; upsampledSpacing[1] /= 4; upsampledSpacing[2] /= 4; upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4); upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4); upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4); itk::Point upsampledOrigin = m_UpsampledOrigin; upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2; upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2; upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2; m_UpsampledMaskImage = ItkUcharImgType::New(); itk::ResampleImageFilter::Pointer upsampler = itk::ResampleImageFilter::New(); upsampler->SetInput(m_Parameters.m_SignalGen.m_MaskImage); upsampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_MaskImage); upsampler->SetSize(upsampledImageRegion.GetSize()); upsampler->SetOutputSpacing(upsampledSpacing); upsampler->SetOutputOrigin(upsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); upsampler->SetInterpolator(nn_interpolator); upsampler->Update(); m_UpsampledMaskImage = upsampler->GetOutput(); unsigned long lastTick = 0; int signalModelSeed = m_RandGen->GetIntegerVariate(); switch (m_Parameters.m_SignalGen.m_DiffusionDirectionMode) { case(SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS): // use fiber tangent directions to determine diffusion direction { m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; - for (unsigned int g=0; gSetSeed(signalModelSeed); for (int i=0; iSetSeed(signalModelSeed); ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); intraAxonalVolumeImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); vtkPolyData* fiberPolyData = m_FiberBundleTransformed->GetFiberPolyData(); // generate fiber signal (if there are any fiber models present) if (!m_Parameters.m_FiberModelList.empty()) for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; for( int j=0; jGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } double* temp = points->GetPoint(j); itk::Point vertex = GetItkPoint(temp); itk::Vector v = GetItkVector(temp); itk::Vector dir(3); if (jGetPoint(j+1))-v; else dir = v-GetItkVector(points->GetPoint(j-1)); if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2]) continue; itk::Index<3> idx; itk::ContinuousIndex contIndex; m_MaskImage->TransformPhysicalPointToIndex(vertex, idx); m_MaskImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!m_MaskImage->GetLargestPossibleRegion().IsInside(idx) || m_MaskImage->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment for (int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = m_CompartmentImages.at(k)->GetPixel(idx); pix[g] += segmentVolume*m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g); m_CompartmentImages.at(k)->SetPixel(idx, pix); } // update fiber volume image double vol = intraAxonalVolumeImage->GetPixel(idx) + segmentVolume; intraAxonalVolumeImage->SetPixel(idx, vol); if (g==0 && vol>maxVolume) maxVolume = vol; } // progress report ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } // generate non-fiber signal ImageRegionIterator it3(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); double fact = 1; if (m_Parameters.m_SignalGen.m_AxonRadius<0.0001 || maxVolume>m_VoxelVolume) fact = m_VoxelVolume/maxVolume; while(!it3.IsAtEnd()) { if (it3.Get()>0) { DoubleDwiType::IndexType index = it3.GetIndex(); // adjust intra-axonal signal to abtain an only-fiber voxel if (fabs(fact-1.0)>0.0001) for (int i=0; iGetPixel(index); pix[g] *= fact; m_CompartmentImages.at(i)->SetPixel(index, pix); } // simulate other compartments SimulateNonFiberSignal(index, intraAxonalVolumeImage->GetPixel(index)*fact, g); } ++it3; } // move fibers SimulateMotion(g); } break; } case (SignalGenerationParameters::MAIN_FIBER_DIRECTIONS): // use main fiber directions to determine voxel-wise diffusion directions { typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; // calculate main fiber directions itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(m_FiberBundleTransformed); fOdfFilter->SetMaskImage(m_MaskImage); fOdfFilter->SetAngularThreshold(cos(m_Parameters.m_SignalGen.m_FiberSeparationThreshold*M_PI/180.0)); fOdfFilter->SetNormalizeVectors(false); fOdfFilter->SetUseWorkingCopy(true); fOdfFilter->SetSizeThreshold(0); fOdfFilter->SetMaxNumDirections(3); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); // allocate image storing intra-axonal volume fraction information ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); intraAxonalVolumeImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); // determine intra-axonal volume fraction using the tract density itk::TractDensityImageFilter< ItkDoubleImgType >::Pointer tdiFilter = itk::TractDensityImageFilter< ItkDoubleImgType >::New(); tdiFilter->SetFiberBundle(m_FiberBundleTransformed); tdiFilter->SetBinaryOutput(false); tdiFilter->SetOutputAbsoluteValues(false); tdiFilter->SetInputImage(intraAxonalVolumeImage); tdiFilter->SetUseImageGeometry(true); tdiFilter->Update(); intraAxonalVolumeImage = tdiFilter->GetOutput(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; - boost::progress_display disp(m_MaskImage->GetLargestPossibleRegion().GetNumberOfPixels()*m_Parameters.GetNumVolumes()); + boost::progress_display disp(m_MaskImage->GetLargestPossibleRegion().GetNumberOfPixels()*m_Parameters.m_SignalGen.GetNumVolumes()); - for (unsigned int g=0; gSetSeed(signalModelSeed); for (int i=0; iSetSeed(signalModelSeed); if (m_Parameters.m_SignalGen.m_DoAddMotion && g>0) // if fibers have moved we need a new TDI and new directions { fOdfFilter->SetFiberBundle(m_FiberBundleTransformed); fOdfFilter->SetMaskImage(m_MaskImage); fOdfFilter->Update(); directionImageContainer = fOdfFilter->GetDirectionImageContainer(); tdiFilter->SetFiberBundle(m_FiberBundleTransformed); tdiFilter->Update(); intraAxonalVolumeImage = tdiFilter->GetOutput(); } ImageRegionIterator< ItkUcharImgType > it(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } if (it.Get()>0) { // generate fiber signal for (int c=0; cGetPixel(it.GetIndex()); for (unsigned int i=0; iSize(); i++) { itk::Vector< double, 3> dir; dir.CastFrom(directionImageContainer->GetElement(i)->GetPixel(it.GetIndex())); double norm = dir.GetNorm(); if (norm>0.0001) { m_Parameters.m_FiberModelList.at(c)->SetFiberDirection(dir); pix[g] += m_Parameters.m_FiberModelList.at(c)->SimulateMeasurement(g)*norm; count++; } } if (count>0) pix[g] /= count; pix[g] *= intraAxonalVolumeImage->GetPixel(it.GetIndex())*m_VoxelVolume; m_CompartmentImages.at(c)->SetPixel(it.GetIndex(), pix); } // simulate other compartments SimulateNonFiberSignal(it.GetIndex(), intraAxonalVolumeImage->GetPixel(it.GetIndex())*m_VoxelVolume, g); } ++it; } SimulateMotion(g); } itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); wr->SetInput(fOdfFilter->GetNumDirectionsImage()); wr->SetFileName(mitk::IOUtil::GetTempPath()+"/NumDirections_MainFiberDirections.nrrd"); wr->Update(); break; } case (SignalGenerationParameters::RANDOM_DIRECTIONS): { ItkUcharImgType::Pointer numDirectionsImage = ItkUcharImgType::New(); numDirectionsImage->SetSpacing( m_UpsampledSpacing ); numDirectionsImage->SetOrigin( m_UpsampledOrigin ); numDirectionsImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); numDirectionsImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); numDirectionsImage->SetBufferedRegion( m_UpsampledImageRegion ); numDirectionsImage->SetRequestedRegion( m_UpsampledImageRegion ); numDirectionsImage->Allocate(); numDirectionsImage->FillBuffer(0); double sepAngle = cos(m_Parameters.m_SignalGen.m_FiberSeparationThreshold*M_PI/180.0); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; boost::progress_display disp(m_MaskImage->GetLargestPossibleRegion().GetNumberOfPixels()); ImageRegionIterator it(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } if (it.Get()>0) { int numFibs = m_RandGen->GetIntegerVariate(2)+1; DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); double volume = m_RandGen->GetVariateWithClosedRange(0.3); // double sum = 0; std::vector< double > fractions; for (int i=0; iGetVariateWithClosedRange(0.5)); // sum += fractions.at(i); } // for (int i=0; i > directions; for (int i=0; iGetVariateWithClosedRange(2)-1.0; fib[1] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib[2] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib.Normalize(); double min = 0; for (unsigned int d=0; dmin) min = angle; } if (minSetFiberDirection(fib); pix += m_Parameters.m_FiberModelList.at(0)->SimulateMeasurement()*fractions[i]; directions.push_back(fib); } else i--; } pix *= (1-volume); m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); // CSF/GM { pix += volume*m_Parameters.m_NonFiberModelList.at(0)->SimulateMeasurement(); } numDirectionsImage->SetPixel(it.GetIndex(), numFibs); } ++it; } itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); wr->SetInput(numDirectionsImage); wr->SetFileName(mitk::IOUtil::GetTempPath()+"/NumDirections_RandomDirections.nrrd"); wr->Update(); } } if (m_Logfile.is_open()) { m_Logfile << "DONE"; m_Logfile.close(); } m_StatusText += "\n\n"; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } DoubleDwiType::Pointer doubleOutImage; if ( m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition ) // do k-space stuff { m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; MITK_INFO << "Adjusting complex signal:"; if (m_Parameters.m_SignalGen.m_DoSimulateRelaxation) m_StatusText += "Simulating signal relaxation\n"; if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; if (m_Parameters.m_SignalGen.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; if (m_Parameters.m_SignalGen.m_Spikes>0) m_StatusText += "Simulating spikes\n"; if (m_Parameters.m_SignalGen.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; if (m_Parameters.m_SignalGen.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; doubleOutImage = DoKspaceStuff(m_CompartmentImages); m_Parameters.m_SignalGen.m_SignalScale = 1; // already scaled in DoKspaceStuff } else // don't do k-space stuff, just sum compartments { m_StatusText += this->GetTime()+" > Summing compartments\n"; MITK_INFO << "Summing compartments"; doubleOutImage = m_CompartmentImages.at(0); for (unsigned int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); adder->SetInput2(m_CompartmentImages.at(i)); adder->Update(); doubleOutImage = adder->GetOutput(); } } if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } m_StatusText += this->GetTime()+" > Finalizing image\n"; MITK_INFO << "Finalizing image"; if (m_Parameters.m_SignalGen.m_SignalScale>1) m_StatusText += " Scaling signal\n"; if (m_Parameters.m_NoiseModel!=NULL) m_StatusText += " Adding noise\n"; unsigned int window = 0; unsigned int min = itk::NumericTraits::max(); ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); - DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.GetNumVolumes()); + DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; lastTick = 0; while(!it4.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp2; unsigned long newTick = 50*disp2.count()/disp2.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename OutputImageType::IndexType index = it4.GetIndex(); signal = doubleOutImage->GetPixel(index)*m_Parameters.m_SignalGen.m_SignalScale; if (m_Parameters.m_NoiseModel!=NULL) m_Parameters.m_NoiseModel->AddNoise(signal); for (unsigned int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); - if ( (!m_Parameters.IsBaselineIndex(i) || signal.Size()==1) && signal[i]>window) + if ( (!m_Parameters.m_SignalGen.IsBaselineIndex(i) || signal.Size()==1) && signal[i]>window) window = signal[i]; - if ( (!m_Parameters.IsBaselineIndex(i) || signal.Size()==1) && signal[i]SetNthOutput(0, outImage); m_StatusText += "\n\n"; m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); m_TimeProbe.Stop(); } template< class PixelType > void TractsToDWIImageFilter< PixelType >::SimulateMotion(int g) { - if (m_Parameters.m_SignalGen.m_DoAddMotion && gGetDeepCopy(); m_Rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[0]*2)-m_Parameters.m_SignalGen.m_Rotation[0]; m_Rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[1]*2)-m_Parameters.m_SignalGen.m_Rotation[1]; m_Rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[2]*2)-m_Parameters.m_SignalGen.m_Rotation[2]; m_Translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[0]*2)-m_Parameters.m_SignalGen.m_Translation[0]; m_Translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[1]*2)-m_Parameters.m_SignalGen.m_Translation[1]; m_Translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[2]*2)-m_Parameters.m_SignalGen.m_Translation[2]; } // rotate mask image if (m_MaskImageSet) { ImageRegionIterator maskIt(m_UpsampledMaskImage, m_UpsampledMaskImage->GetLargestPossibleRegion()); m_MaskImage->FillBuffer(0); while(!maskIt.IsAtEnd()) { if (maskIt.Get()<=0) { ++maskIt; continue; } DoubleDwiType::IndexType index = maskIt.GetIndex(); itk::Point point; m_UpsampledMaskImage->TransformIndexToPhysicalPoint(index, point); if (m_Parameters.m_SignalGen.m_DoRandomizeMotion) point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), m_Rotation[0],m_Rotation[1],m_Rotation[2],m_Translation[0],m_Translation[1],m_Translation[2]); else point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), m_Rotation[0]*(g+1),m_Rotation[1]*(g+1),m_Rotation[2]*(g+1),m_Translation[0]*(g+1),m_Translation[1]*(g+1),m_Translation[2]*(g+1)); m_MaskImage->TransformPhysicalPointToIndex(point, index); if (m_MaskImage->GetLargestPossibleRegion().IsInside(index)) m_MaskImage->SetPixel(index,100); ++maskIt; } } // rotate fibers if (m_Logfile.is_open()) { m_Logfile << g+1 << " rotation: " << m_Rotation[0] << "," << m_Rotation[1] << "," << m_Rotation[2] << ";"; m_Logfile << " translation: " << m_Translation[0] << "," << m_Translation[1] << "," << m_Translation[2] << "\n"; } m_FiberBundleTransformed->TransformFibers(m_Rotation[0],m_Rotation[1],m_Rotation[2],m_Translation[0],m_Translation[1],m_Translation[2]); } } template< class PixelType > void TractsToDWIImageFilter< PixelType >::SimulateNonFiberSignal(ItkUcharImgType::IndexType index, double intraAxonalVolume, int g) { int numFiberCompartments = m_Parameters.m_FiberModelList.size(); int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size(); if (intraAxonalVolume>0.0001 && m_Parameters.m_SignalGen.m_DoDisablePartialVolume) // only fiber in voxel { DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index); if (g>=0) pix[g] *= m_VoxelVolume/intraAxonalVolume; else pix *= m_VoxelVolume/intraAxonalVolume; m_CompartmentImages.at(0)->SetPixel(index, pix); m_VolumeFractions.at(0)->SetPixel(index, 1); for (int i=1; iGetPixel(index); if (g>=0) pix[g] = 0.0; else pix.Fill(0.0); m_CompartmentImages.at(i)->SetPixel(index, pix); } } else { m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/m_VoxelVolume); itk::Point point; m_MaskImage->TransformIndexToPhysicalPoint(index, point); if (m_Parameters.m_SignalGen.m_DoAddMotion) { if (m_Parameters.m_SignalGen.m_DoRandomizeMotion && g>0) point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), -m_Rotation[0],-m_Rotation[1],-m_Rotation[2],-m_Translation[0],-m_Translation[1],-m_Translation[2]); else if (g>=0) point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), -m_Rotation[0]*g,-m_Rotation[1]*g,-m_Rotation[2]*g,-m_Translation[0]*g,-m_Translation[1]*g,-m_Translation[2]*g); } if (m_Parameters.m_SignalGen.m_DoDisablePartialVolume) { int maxVolumeIndex = 0; double maxWeight = 0; for (int i=0; i1) { DoubleDwiType::IndexType newIndex; m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) continue; weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); } if (weight>maxWeight) { maxWeight = weight; maxVolumeIndex = i; } } DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(maxVolumeIndex+numFiberCompartments); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); if (g>=0) pix[g] += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(g); else pix += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(); doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(maxVolumeIndex+numFiberCompartments)->SetPixel(index, 1); } else { double extraAxonalVolume = m_VoxelVolume-intraAxonalVolume; // non-fiber volume double interAxonalVolume = 0; if (numFiberCompartments>1) interAxonalVolume = extraAxonalVolume * intraAxonalVolume/m_VoxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f double other = extraAxonalVolume - interAxonalVolume; // rest of compartment double singleinter = interAxonalVolume/(numFiberCompartments-1); // adjust non-fiber and intra-axonal signal for (int i=1; iGetPixel(index); if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment { if (g>=0) pix[g] /= intraAxonalVolume; else pix /= intraAxonalVolume; } if (g>=0) pix[g] *= singleinter; else pix *= singleinter; m_CompartmentImages.at(i)->SetPixel(index, pix); m_VolumeFractions.at(i)->SetPixel(index, singleinter/m_VoxelVolume); } for (int i=0; i1) { DoubleDwiType::IndexType newIndex; m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) continue; weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); } DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(i+numFiberCompartments); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); if (g>=0) pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*weight; else pix += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement()*other*weight; doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, other/m_VoxelVolume*weight); } } } } template< class PixelType > itk::Point TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > itk::Vector TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } template< class PixelType > double TractsToDWIImageFilter< PixelType >::RoundToNearest(double num) { return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5); } template< class PixelType > std::string TractsToDWIImageFilter< PixelType >::GetTime() { m_TimeProbe.Stop(); unsigned long total = RoundToNearest(m_TimeProbe.GetTotal()); unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); m_TimeProbe.Start(); return out; } } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index a12c14b88a..d831c82377 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,648 +1,722 @@ /*=================================================================== 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. ===================================================================*/ #include #include #include #include +#include +#include + #include #include #include #include #include #include template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::FiberfoxParameters() : m_NoiseModel(NULL) - , m_NumGradients(6) - , m_NumBaseline(1) { m_FiberGen.m_RealTimeFibers = true; m_FiberGen.m_AdvancedOptions = false; m_FiberGen.m_Distribution = 0; m_FiberGen.m_Variance = 100; m_FiberGen.m_FiberDensity = 100; m_FiberGen.m_Sampling = 1; m_FiberGen.m_Tension = 0; m_FiberGen.m_Continuity = 0; m_FiberGen.m_Bias = 0; m_FiberGen.m_ConstantRadius = false; m_FiberGen.m_Rotation[0] = 0; m_FiberGen.m_Rotation[1] = 0; m_FiberGen.m_Rotation[2] = 0; m_FiberGen.m_Translation[0] = 0; m_FiberGen.m_Translation[1] = 0; m_FiberGen.m_Translation[2] = 0; m_FiberGen.m_Scale[0] = 1; m_FiberGen.m_Scale[1] = 1; m_FiberGen.m_Scale[2] = 1; m_FiberGen.m_IncludeFiducials = true; m_SignalGen.m_ImageDirection.SetIdentity(); m_SignalGen.m_ImageOrigin.Fill(0.0); m_SignalGen.m_ImageRegion.SetSize(0, 11); m_SignalGen.m_ImageRegion.SetSize(1, 11); m_SignalGen.m_ImageRegion.SetSize(2, 3); m_SignalGen.m_ImageSpacing.Fill(2.0); m_SignalGen.m_Translation.Fill(0.0); m_SignalGen.m_Rotation.Fill(0.0); m_SignalGen.m_FrequencyMap = NULL; m_SignalGen.m_MaskImage = NULL; m_SignalGen.m_SignalScale = 100; m_SignalGen.m_tEcho = 100; m_SignalGen.m_tLine = 1; m_SignalGen.m_tInhom = 50; m_SignalGen.m_Bvalue = 1000; m_SignalGen.m_SimulateKspaceAcquisition = false; m_SignalGen.m_AxonRadius = 0; m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; m_SignalGen.m_FiberSeparationThreshold = 30; m_SignalGen.m_Spikes = 0; m_SignalGen.m_SpikeAmplitude = 1; m_SignalGen.m_KspaceLineOffset = 0; m_SignalGen.m_EddyStrength = 0; m_SignalGen.m_Tau = 70; m_SignalGen.m_CroppingFactor = 1; m_SignalGen.m_DoAddNoise = false; m_SignalGen.m_DoAddGhosts = false; m_SignalGen.m_DoAddAliasing = false; m_SignalGen.m_DoAddSpikes = false; m_SignalGen.m_DoAddEddyCurrents = false; m_SignalGen.m_DoAddGibbsRinging = false; m_SignalGen.m_DoSimulateRelaxation = true; m_SignalGen.m_DoAddDistortions = false; m_SignalGen.m_DoDisablePartialVolume = false; m_SignalGen.m_DoAddMotion = false; m_SignalGen.m_DoRandomizeMotion = true; + m_SignalGen.SetNumWeightedVolumes(6); m_Misc.m_ResultNode = mitk::DataNode::New(); m_Misc.m_ParentNode = NULL; m_Misc.m_SignalModelString = ""; m_Misc.m_ArtifactModelString = ""; m_Misc.m_OutputPath = ""; - - GenerateGradientHalfShell(); } template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::~FiberfoxParameters() { // if (m_NoiseModel!=NULL) // delete m_NoiseModel; } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::GenerateGradientHalfShell() +void mitk::SignalGenerationParameters::GenerateGradientHalfShell() { int NPoints = 2*m_NumGradients; m_GradientDirections.clear(); m_NumBaseline = NPoints/20; if (m_NumBaseline==0) m_NumBaseline=1; GradientType g; g.Fill(0.0); for (unsigned int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i -std::vector< int > mitk::FiberfoxParameters< ScalarType >::GetBaselineIndices() +std::vector< int > mitk::SignalGenerationParameters::GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) result.push_back(i); return result; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetFirstBaselineIndex() +unsigned int mitk::SignalGenerationParameters::GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) return i; return -1; } -template< class ScalarType > -bool mitk::FiberfoxParameters< ScalarType >::IsBaselineIndex(unsigned int idx) +bool mitk::SignalGenerationParameters::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumWeightedVolumes() +unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes() { return m_NumGradients; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumBaselineVolumes() +unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes() { return m_NumBaseline; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumVolumes() +unsigned int mitk::SignalGenerationParameters::GetNumVolumes() { return m_GradientDirections.size(); } -template< class ScalarType > -typename mitk::FiberfoxParameters< ScalarType >::GradientListType mitk::FiberfoxParameters< ScalarType >::GetGradientDirections() +typename mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections() { return m_GradientDirections; } -template< class ScalarType > -typename mitk::FiberfoxParameters< ScalarType >::GradientType mitk::FiberfoxParameters< ScalarType >::GetGradientDirection(unsigned int i) +mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::SetNumWeightedGradients(int numGradients) +void mitk::SignalGenerationParameters::SetNumWeightedVolumes(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(GradientListType gradientList) +void mitk::SignalGenerationParameters::SetGradienDirections(GradientListType gradientList) { m_GradientDirections = gradientList; m_NumGradients = 0; m_NumBaseline = 0; for( unsigned int i=0; im_GradientDirections.size(); i++) { if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList) +void mitk::SignalGenerationParameters::SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList) { m_NumGradients = 0; m_NumBaseline = 0; m_GradientDirections.clear(); for( unsigned int i=0; iSize(); i++) { GradientType g; g[0] = gradientList->at(i)[0]; g[1] = gradientList->at(i)[1]; g[2] = gradientList->at(i)[2]; m_GradientDirections.push_back(g); if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SaveParameters(string filename) { if(filename.empty()) return; if(".ffp"!=filename.substr(filename.size()-4, 4)) filename += ".ffp"; boost::property_tree::ptree parameters; // fiber generation parameters parameters.put("fiberfox.fibers.realtime", m_FiberGen.m_RealTimeFibers); parameters.put("fiberfox.fibers.showadvanced", m_FiberGen.m_AdvancedOptions); parameters.put("fiberfox.fibers.distribution", m_FiberGen.m_Distribution); parameters.put("fiberfox.fibers.variance", m_FiberGen.m_Variance); parameters.put("fiberfox.fibers.density", m_FiberGen.m_FiberDensity); parameters.put("fiberfox.fibers.spline.sampling", m_FiberGen.m_Sampling); parameters.put("fiberfox.fibers.spline.tension", m_FiberGen.m_Tension); parameters.put("fiberfox.fibers.spline.continuity", m_FiberGen.m_Continuity); parameters.put("fiberfox.fibers.spline.bias", m_FiberGen.m_Bias); parameters.put("fiberfox.fibers.constantradius", m_FiberGen.m_ConstantRadius); parameters.put("fiberfox.fibers.rotation.x", m_FiberGen.m_Rotation[0]); parameters.put("fiberfox.fibers.rotation.y", m_FiberGen.m_Rotation[1]); parameters.put("fiberfox.fibers.rotation.z", m_FiberGen.m_Rotation[2]); parameters.put("fiberfox.fibers.translation.x", m_FiberGen.m_Translation[0]); parameters.put("fiberfox.fibers.translation.y", m_FiberGen.m_Translation[1]); parameters.put("fiberfox.fibers.translation.z", m_FiberGen.m_Translation[2]); parameters.put("fiberfox.fibers.scale.x", m_FiberGen.m_Scale[0]); parameters.put("fiberfox.fibers.scale.y", m_FiberGen.m_Scale[1]); parameters.put("fiberfox.fibers.scale.z", m_FiberGen.m_Scale[2]); parameters.put("fiberfox.fibers.includeFiducials", m_FiberGen.m_IncludeFiducials); // image generation parameters parameters.put("fiberfox.image.basic.size.x", m_SignalGen.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", m_SignalGen.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", m_SignalGen.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", m_SignalGen.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", m_SignalGen.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", m_SignalGen.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.origin.x", m_SignalGen.m_ImageOrigin[0]); parameters.put("fiberfox.image.basic.origin.y", m_SignalGen.m_ImageOrigin[1]); parameters.put("fiberfox.image.basic.origin.z", m_SignalGen.m_ImageOrigin[2]); parameters.put("fiberfox.image.basic.direction.1", m_SignalGen.m_ImageDirection[0][0]); parameters.put("fiberfox.image.basic.direction.2", m_SignalGen.m_ImageDirection[0][1]); parameters.put("fiberfox.image.basic.direction.3", m_SignalGen.m_ImageDirection[0][2]); parameters.put("fiberfox.image.basic.direction.4", m_SignalGen.m_ImageDirection[1][0]); parameters.put("fiberfox.image.basic.direction.5", m_SignalGen.m_ImageDirection[1][1]); parameters.put("fiberfox.image.basic.direction.6", m_SignalGen.m_ImageDirection[1][2]); parameters.put("fiberfox.image.basic.direction.7", m_SignalGen.m_ImageDirection[2][0]); parameters.put("fiberfox.image.basic.direction.8", m_SignalGen.m_ImageDirection[2][1]); parameters.put("fiberfox.image.basic.direction.9", m_SignalGen.m_ImageDirection[2][2]); parameters.put("fiberfox.image.signalScale", m_SignalGen.m_SignalScale); parameters.put("fiberfox.image.tEcho", m_SignalGen.m_tEcho); parameters.put("fiberfox.image.tLine", m_SignalGen.m_tLine); parameters.put("fiberfox.image.tInhom", m_SignalGen.m_tInhom); parameters.put("fiberfox.image.bvalue", m_SignalGen.m_Bvalue); parameters.put("fiberfox.image.simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); parameters.put("fiberfox.image.axonRadius", m_SignalGen.m_AxonRadius); parameters.put("fiberfox.image.diffusiondirectionmode", m_SignalGen.m_DiffusionDirectionMode); parameters.put("fiberfox.image.fiberseparationthreshold", m_SignalGen.m_FiberSeparationThreshold); parameters.put("fiberfox.image.artifacts.addnoise", m_SignalGen.m_DoAddNoise); parameters.put("fiberfox.image.artifacts.addghosts", m_SignalGen.m_DoAddGhosts); parameters.put("fiberfox.image.artifacts.addaliasing", m_SignalGen.m_DoAddAliasing); parameters.put("fiberfox.image.artifacts.addspikes", m_SignalGen.m_DoAddSpikes); parameters.put("fiberfox.image.artifacts.addeddycurrents", m_SignalGen.m_DoAddEddyCurrents); parameters.put("fiberfox.image.artifacts.spikesnum", m_SignalGen.m_Spikes); parameters.put("fiberfox.image.artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); parameters.put("fiberfox.image.artifacts.eddyStrength", m_SignalGen.m_EddyStrength); parameters.put("fiberfox.image.artifacts.eddyTau", m_SignalGen.m_Tau); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); parameters.put("fiberfox.image.artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); parameters.put("fiberfox.image.doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); parameters.put("fiberfox.image.artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); parameters.put("fiberfox.image.artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); parameters.put("fiberfox.image.artifacts.doAddDistortions", m_SignalGen.m_DoAddDistortions); parameters.put("fiberfox.image.artifacts.translation0", m_SignalGen.m_Translation[0]); parameters.put("fiberfox.image.artifacts.translation1", m_SignalGen.m_Translation[1]); parameters.put("fiberfox.image.artifacts.translation2", m_SignalGen.m_Translation[2]); parameters.put("fiberfox.image.artifacts.rotation0", m_SignalGen.m_Rotation[0]); parameters.put("fiberfox.image.artifacts.rotation1", m_SignalGen.m_Rotation[1]); parameters.put("fiberfox.image.artifacts.rotation2", m_SignalGen.m_Rotation[2]); parameters.put("fiberfox.image.signalmodelstring", m_Misc.m_SignalModelString); parameters.put("fiberfox.image.artifactmodelstring", m_Misc.m_ArtifactModelString); parameters.put("fiberfox.image.outpath", m_Misc.m_OutputPath); parameters.put("fiberfox.image.outputvolumefractions", m_Misc.m_OutputVolumeFractions); parameters.put("fiberfox.image.showadvanced", m_Misc.m_AdvancedOptions); - parameters.put("fiberfox.image.basic.numgradients", m_NumGradients); + parameters.put("fiberfox.image.basic.numgradients", m_SignalGen.GetNumWeightedVolumes()); if (m_NoiseModel!=NULL) { parameters.put("fiberfox.image.artifacts.noisevariance", m_NoiseModel->GetNoiseVariance()); if (dynamic_cast*>(m_NoiseModel)) parameters.put("fiberfox.image.artifacts.noisetype", "rice"); else if (dynamic_cast*>(m_NoiseModel)) parameters.put("fiberfox.image.artifacts.noisetype", "chisquare"); } for (int i=0; i* signalModel = NULL; if (i(i)+".type", "fiber"); } else { signalModel = m_NonFiberModelList.at(i-m_FiberModelList.size()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".type", "non-fiber"); } if (dynamic_cast*>(signalModel)) { mitk::StickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".stick.d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".stick.t2", model->GetT2()); } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.d1", model->GetDiffusivity1()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.d2", model->GetDiffusivity2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.d3", model->GetDiffusivity3()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.t2", model->GetT2()); } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.minFA", model->GetFaRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.maxFA", model->GetFaRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.minADC", model->GetAdcRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.maxADC", model->GetAdcRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.numSamples", model->GetMaxNumKernels()); } else if (dynamic_cast*>(signalModel)) { mitk::BallModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ball.d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ball.t2", model->GetT2()); } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".astrosticks.d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".astrosticks.t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".astrosticks.randomize", model->GetRandomizeSticks()); } else if (dynamic_cast*>(signalModel)) { mitk::DotModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".dot.t2", model->GetT2()); } - parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ID", signalModel->m_CompartmentId); + + if (signalModel!=NULL) + { + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ID", signalModel->m_CompartmentId); + +// if (signalModel->GetVolumeFractionImage().IsNotNull()) +// { +// try{ +// itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); +// writer->SetFileName(filename+"_VOLUME"+boost::lexical_cast(signalModel->m_CompartmentId)+".nrrd"); +// writer->SetInput(signalModel->GetVolumeFractionImage()); +// writer->Update(); +// MITK_INFO << "Volume fraction image for compartment "+boost::lexical_cast(signalModel->m_CompartmentId)+" saved."; +// } +// catch(...) +// { +// } +// } + } } boost::property_tree::xml_writer_settings writerSettings(' ', 2); boost::property_tree::xml_parser::write_xml(filename, parameters, std::locale(), writerSettings); + +// if (m_SignalGen.m_DoAddDistortions) +// { +// try{ +// itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); +// writer->SetFileName(filename+"_FMAP.nrrd"); +// writer->SetInput(m_SignalGen.m_FrequencyMap); +// writer->Update(); +// } +// catch(...) +// { +// MITK_INFO << "No frequency map saved."; +// } +// } + +// try{ +// itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); +// writer->SetFileName(filename+"_MASK.nrrd"); +// writer->SetInput(m_SignalGen.m_MaskImage); +// writer->Update(); +// } +// catch(...) +// { +// MITK_INFO << "No mask image saved."; +// } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::LoadParameters(string filename) { if(filename.empty()) return; boost::property_tree::ptree parameterTree; boost::property_tree::xml_parser::read_xml(filename, parameterTree); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel!=NULL) delete m_NoiseModel; BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_FiberGen.m_RealTimeFibers = v1.second.get("realtime", m_FiberGen.m_RealTimeFibers); m_FiberGen.m_AdvancedOptions = v1.second.get("showadvanced", m_FiberGen.m_AdvancedOptions); m_FiberGen.m_Distribution = v1.second.get("distribution", m_FiberGen.m_Distribution); m_FiberGen.m_Variance = v1.second.get("variance", m_FiberGen.m_Variance); m_FiberGen.m_FiberDensity = v1.second.get("density", m_FiberGen.m_FiberDensity); m_FiberGen.m_Sampling = v1.second.get("spline.sampling", m_FiberGen.m_Sampling); m_FiberGen.m_Tension = v1.second.get("spline.tension", m_FiberGen.m_Tension); m_FiberGen.m_Continuity = v1.second.get("spline.continuity", m_FiberGen.m_Continuity); m_FiberGen.m_Bias = v1.second.get("spline.bias", m_FiberGen.m_Bias); m_FiberGen.m_ConstantRadius = v1.second.get("constantradius", m_FiberGen.m_ConstantRadius); m_FiberGen.m_Rotation[0] = v1.second.get("rotation.x", m_FiberGen.m_Rotation[0]); m_FiberGen.m_Rotation[1] = v1.second.get("rotation.y", m_FiberGen.m_Rotation[1]); m_FiberGen.m_Rotation[2] = v1.second.get("rotation.z", m_FiberGen.m_Rotation[2]); m_FiberGen.m_Translation[0] = v1.second.get("translation.x", m_FiberGen.m_Translation[0]); m_FiberGen.m_Translation[1] = v1.second.get("translation.y", m_FiberGen.m_Translation[1]); m_FiberGen.m_Translation[2] = v1.second.get("translation.z", m_FiberGen.m_Translation[2]); m_FiberGen.m_Scale[0] = v1.second.get("scale.x", m_FiberGen.m_Scale[0]); m_FiberGen.m_Scale[1] = v1.second.get("scale.y", m_FiberGen.m_Scale[1]); m_FiberGen.m_Scale[2] = v1.second.get("scale.z", m_FiberGen.m_Scale[2]); m_FiberGen.m_IncludeFiducials = v1.second.get("includeFiducials", m_FiberGen.m_IncludeFiducials); } else if ( v1.first == "image" ) { - m_SignalGen.m_ImageRegion.SetSize(0, v1.second.get("basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0))); - m_SignalGen.m_ImageRegion.SetSize(1, v1.second.get("basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1))); - m_SignalGen.m_ImageRegion.SetSize(2, v1.second.get("basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2))); - m_SignalGen.m_ImageSpacing[0] = v1.second.get("basic.spacing.x",m_SignalGen.m_ImageSpacing[0]); - m_SignalGen.m_ImageSpacing[1] = v1.second.get("basic.spacing.y",m_SignalGen.m_ImageSpacing[1]); - m_SignalGen.m_ImageSpacing[2] = v1.second.get("basic.spacing.z",m_SignalGen.m_ImageSpacing[2]); - m_SignalGen.m_ImageOrigin[0] = v1.second.get("basic.origin.x",m_SignalGen.m_ImageOrigin[0]); - m_SignalGen.m_ImageOrigin[1] = v1.second.get("basic.origin.y",m_SignalGen.m_ImageOrigin[1]); - m_SignalGen.m_ImageOrigin[2] = v1.second.get("basic.origin.z",m_SignalGen.m_ImageOrigin[2]); - m_SignalGen.m_ImageDirection[0][0] = v1.second.get("basic.direction.1",m_SignalGen.m_ImageDirection[0][0]); - m_SignalGen.m_ImageDirection[0][1] = v1.second.get("basic.direction.2",m_SignalGen.m_ImageDirection[0][1]); - m_SignalGen.m_ImageDirection[0][2] = v1.second.get("basic.direction.3",m_SignalGen.m_ImageDirection[0][2]); - m_SignalGen.m_ImageDirection[1][0] = v1.second.get("basic.direction.4",m_SignalGen.m_ImageDirection[1][0]); - m_SignalGen.m_ImageDirection[1][1] = v1.second.get("basic.direction.5",m_SignalGen.m_ImageDirection[1][1]); - m_SignalGen.m_ImageDirection[1][2] = v1.second.get("basic.direction.6",m_SignalGen.m_ImageDirection[1][2]); - m_SignalGen.m_ImageDirection[2][0] = v1.second.get("basic.direction.7",m_SignalGen.m_ImageDirection[2][0]); - m_SignalGen.m_ImageDirection[2][1] = v1.second.get("basic.direction.8",m_SignalGen.m_ImageDirection[2][1]); - m_SignalGen.m_ImageDirection[2][2] = v1.second.get("basic.direction.9",m_SignalGen.m_ImageDirection[2][2]); + m_SignalGen.m_ImageRegion.SetSize(0, v1.second.get("basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0))); + m_SignalGen.m_ImageRegion.SetSize(1, v1.second.get("basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1))); + m_SignalGen.m_ImageRegion.SetSize(2, v1.second.get("basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2))); + m_SignalGen.m_ImageSpacing[0] = v1.second.get("basic.spacing.x",m_SignalGen.m_ImageSpacing[0]); + m_SignalGen.m_ImageSpacing[1] = v1.second.get("basic.spacing.y",m_SignalGen.m_ImageSpacing[1]); + m_SignalGen.m_ImageSpacing[2] = v1.second.get("basic.spacing.z",m_SignalGen.m_ImageSpacing[2]); + m_SignalGen.m_ImageOrigin[0] = v1.second.get("basic.origin.x",m_SignalGen.m_ImageOrigin[0]); + m_SignalGen.m_ImageOrigin[1] = v1.second.get("basic.origin.y",m_SignalGen.m_ImageOrigin[1]); + m_SignalGen.m_ImageOrigin[2] = v1.second.get("basic.origin.z",m_SignalGen.m_ImageOrigin[2]); + m_SignalGen.m_ImageDirection[0][0] = v1.second.get("basic.direction.1",m_SignalGen.m_ImageDirection[0][0]); + m_SignalGen.m_ImageDirection[0][1] = v1.second.get("basic.direction.2",m_SignalGen.m_ImageDirection[0][1]); + m_SignalGen.m_ImageDirection[0][2] = v1.second.get("basic.direction.3",m_SignalGen.m_ImageDirection[0][2]); + m_SignalGen.m_ImageDirection[1][0] = v1.second.get("basic.direction.4",m_SignalGen.m_ImageDirection[1][0]); + m_SignalGen.m_ImageDirection[1][1] = v1.second.get("basic.direction.5",m_SignalGen.m_ImageDirection[1][1]); + m_SignalGen.m_ImageDirection[1][2] = v1.second.get("basic.direction.6",m_SignalGen.m_ImageDirection[1][2]); + m_SignalGen.m_ImageDirection[2][0] = v1.second.get("basic.direction.7",m_SignalGen.m_ImageDirection[2][0]); + m_SignalGen.m_ImageDirection[2][1] = v1.second.get("basic.direction.8",m_SignalGen.m_ImageDirection[2][1]); + m_SignalGen.m_ImageDirection[2][2] = v1.second.get("basic.direction.9",m_SignalGen.m_ImageDirection[2][2]); m_SignalGen.m_SignalScale = v1.second.get("signalScale", m_SignalGen.m_SignalScale); m_SignalGen.m_tEcho = v1.second.get("tEcho", m_SignalGen.m_tEcho); m_SignalGen.m_tLine = v1.second.get("tLine", m_SignalGen.m_tLine); m_SignalGen.m_tInhom = v1.second.get("tInhom", m_SignalGen.m_tInhom); m_SignalGen.m_Bvalue = v1.second.get("bvalue", m_SignalGen.m_Bvalue); m_SignalGen.m_SimulateKspaceAcquisition = v1.second.get("simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); m_SignalGen.m_AxonRadius = v1.second.get("axonRadius", m_SignalGen.m_AxonRadius); int mode = v1.second.get("diffusiondirectionmode", 0); switch (mode) { case 0: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; break; case 1: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::MAIN_FIBER_DIRECTIONS; break; case 2: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::RANDOM_DIRECTIONS; break; default: m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; } m_SignalGen.m_FiberSeparationThreshold = v1.second.get("fiberseparationthreshold", m_SignalGen.m_FiberSeparationThreshold); m_SignalGen.m_DoAddNoise = v1.second.get("artifacts.addnoise", m_SignalGen.m_DoAddNoise); m_SignalGen.m_DoAddGhosts = v1.second.get("artifacts.addghosts", m_SignalGen.m_DoAddGhosts); m_SignalGen.m_DoAddAliasing = v1.second.get("artifacts.addaliasing", m_SignalGen.m_DoAddAliasing); m_SignalGen.m_DoAddSpikes = v1.second.get("artifacts.addspikes", m_SignalGen.m_DoAddSpikes); m_SignalGen.m_DoAddEddyCurrents = v1.second.get("artifacts.addeddycurrents", m_SignalGen.m_DoAddEddyCurrents); m_SignalGen.m_Spikes = v1.second.get("artifacts.spikesnum", m_SignalGen.m_Spikes); m_SignalGen.m_SpikeAmplitude = v1.second.get("artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); m_SignalGen.m_KspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); m_SignalGen.m_EddyStrength = v1.second.get("artifacts.eddyStrength", m_SignalGen.m_EddyStrength); m_SignalGen.m_Tau = v1.second.get("artifacts.eddyTau", m_SignalGen.m_Tau); m_SignalGen.m_CroppingFactor = v1.second.get("artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); m_SignalGen.m_DoAddGibbsRinging = v1.second.get("artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); m_SignalGen.m_DoSimulateRelaxation = v1.second.get("doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); m_SignalGen.m_DoDisablePartialVolume = v1.second.get("doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); m_SignalGen.m_DoAddMotion = v1.second.get("artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); m_SignalGen.m_DoRandomizeMotion = v1.second.get("artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); m_SignalGen.m_DoAddDistortions = v1.second.get("artifacts.doAddDistortions", m_SignalGen.m_DoAddDistortions); m_SignalGen.m_Translation[0] = v1.second.get("artifacts.translation0", m_SignalGen.m_Translation[0]); m_SignalGen.m_Translation[1] = v1.second.get("artifacts.translation1", m_SignalGen.m_Translation[1]); m_SignalGen.m_Translation[2] = v1.second.get("artifacts.translation2", m_SignalGen.m_Translation[2]); m_SignalGen.m_Rotation[0] = v1.second.get("artifacts.rotation0", m_SignalGen.m_Rotation[0]); m_SignalGen.m_Rotation[1] = v1.second.get("artifacts.rotation1", m_SignalGen.m_Rotation[1]); m_SignalGen.m_Rotation[2] = v1.second.get("artifacts.rotation2", m_SignalGen.m_Rotation[2]); m_Misc.m_SignalModelString = v1.second.get("signalmodelstring", m_Misc.m_SignalModelString); m_Misc.m_ArtifactModelString = v1.second.get("artifactmodelstring", m_Misc.m_ArtifactModelString); m_Misc.m_OutputPath = v1.second.get("outpath", m_Misc.m_OutputPath); m_Misc.m_OutputVolumeFractions = v1.second.get("outputvolumefractions", m_Misc.m_OutputVolumeFractions); m_Misc.m_AdvancedOptions = v1.second.get("showadvanced", m_Misc.m_AdvancedOptions); - m_NumGradients = v1.second.get("numgradients", m_NumGradients); - GenerateGradientHalfShell(); + m_SignalGen.SetNumWeightedVolumes(v1.second.get("numgradients", m_SignalGen.GetNumWeightedVolumes())); try { if (v1.second.get("artifacts.noisetype")=="rice") { m_NoiseModel = new mitk::RicianNoiseModel(); m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); } } catch(...) {} try { if (v1.second.get("artifacts.noisetype")=="chisquare") { m_NoiseModel = new mitk::ChiSquareNoiseModel(); m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); } } catch(...){ } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") ) { + mitk::DiffusionSignalModel* signalModel = NULL; try // stick model { mitk::StickModel* model = new mitk::StickModel(); model->SetDiffusivity(v2.second.get("stick.d")); model->SetT2(v2.second.get("stick.t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); + signalModel = model; } catch (...) { } try // tensor model { mitk::TensorModel* model = new mitk::TensorModel(); model->SetDiffusivity1(v2.second.get("tensor.d1")); model->SetDiffusivity2(v2.second.get("tensor.d2")); model->SetDiffusivity3(v2.second.get("tensor.d3")); model->SetT2(v2.second.get("tensor.t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); + signalModel = model; } catch (...) { } try // ball model { mitk::BallModel* model = new mitk::BallModel(); model->SetDiffusivity(v2.second.get("ball.d")); model->SetT2(v2.second.get("ball.t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); + signalModel = model; } catch (...) { } try // astrosticks model { mitk::AstroStickModel* model = new AstroStickModel(); model->SetDiffusivity(v2.second.get("astrosticks.d")); model->SetT2(v2.second.get("astrosticks.t2")); model->SetRandomizeSticks(v2.second.get("astrosticks.randomize")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); + signalModel = model; } catch (...) { } try // dot model { mitk::DotModel* model = new mitk::DotModel(); model->SetT2(v2.second.get("dot.t2")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); + signalModel = model; } catch (...) { } try // prototype model { mitk::RawShModel* model = new mitk::RawShModel(); model->SetMaxNumKernels(v2.second.get("prototype.numSamples")); model->SetFaRange(v2.second.get("prototype.minFA"), v2.second.get("prototype.maxFA")); model->SetAdcRange(v2.second.get("prototype.minADC"), v2.second.get("prototype.maxADC")); model->m_CompartmentId = v2.second.get("ID"); if (v2.second.get("type")=="fiber") m_FiberModelList.push_back(model); else if (v2.second.get("type")=="non-fiber") m_NonFiberModelList.push_back(model); + signalModel = model; } catch (...) { } + +// if (signalModel!=NULL) +// { +// try{ +// itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); +// reader->SetFileName(filename+"_VOLUME"+v2.second.get("ID")+".nrrd"); +// reader->Update(); +// signalModel->SetVolumeFractionImage(reader->GetOutput()); +// } +// catch(...) +// { +// } +// } } } } + +// if (m_SignalGen.m_DoAddDistortions) +// { +// try{ +// itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); +// reader->SetFileName(filename+"_FMAP.nrrd"); +// reader->Update(); +// m_SignalGen.m_FrequencyMap = reader->GetOutput(); +// } +// catch(...) +// { +// MITK_INFO << "No frequency map saved."; +// } +// } + +// try{ +// itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); +// reader->SetFileName(filename+"_MASK.nrrd"); +// reader->Update(); +// m_SignalGen.m_MaskImage = reader->GetOutput(); +// } +// catch(...) +// { +// MITK_INFO << "No mask image saved."; +// } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::PrintSelf() { MITK_INFO << "Not implemented :("; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h index 28f4aa0ce3..54fc362adc 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h @@ -1,206 +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 _MITK_FiberfoxParameters_H #define _MITK_FiberfoxParameters_H #include #include #include #include #include #include #include #include using namespace std; namespace mitk { /** Fiber generation */ struct FiberGenerationParameters { bool m_RealTimeFibers; bool m_AdvancedOptions; int m_Distribution; double m_Variance; unsigned int m_FiberDensity; double m_Sampling; double m_Tension; double m_Continuity; double m_Bias; bool m_ConstantRadius; mitk::Vector3D m_Rotation; mitk::Vector3D m_Translation; mitk::Vector3D m_Scale; bool m_IncludeFiducials; }; /** Signal generation */ -struct SignalGenerationParameters +class SignalGenerationParameters { +public: typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; + typedef itk::Vector GradientType; + typedef std::vector GradientListType; enum DiffusionDirectionMode { FIBER_TANGENT_DIRECTIONS, MAIN_FIBER_DIRECTIONS, RANDOM_DIRECTIONS }; /** input/output image specifications */ itk::ImageRegion<3> m_ImageRegion; ///< Image size. itk::Vector m_ImageSpacing; ///< Image voxel size. itk::Point m_ImageOrigin; ///< Image origin. itk::Matrix m_ImageDirection; ///< Image rotation matrix. /** Other acquisitions parameters */ double m_SignalScale; ///< Scaling factor for output signal (before noise is added). double m_tEcho; ///< Echo time TE. double m_tLine; ///< k-space line readout time. double m_tInhom; ///< T2' double m_Bvalue; ///< Acquisition b-value bool m_SimulateKspaceAcquisition;///< double m_AxonRadius; ///< Determines compartment volume fractions (0 == automatic axon radius estimation) DiffusionDirectionMode m_DiffusionDirectionMode; ///< Determines how the main diffusion direction of the signal models is selected double m_FiberSeparationThreshold; ///< Used for random and and mein fiber deriction DiffusionDirectionMode /** Artifacts */ unsigned int m_Spikes; ///< Number of spikes randomly appearing in the image double m_SpikeAmplitude; ///< amplitude of spikes relative to the largest signal intensity (magnitude of complex) double m_KspaceLineOffset; ///< Causes N/2 ghosts. Larger offset means stronger ghost. double m_EddyStrength; ///< Strength of eddy current induced gradients in mT/m. double m_Tau; ///< Eddy current decay constant (in ms) double m_CroppingFactor; ///< FOV size in y-direction is multiplied by this factor. Causes aliasing artifacts. - ItkDoubleImgType::Pointer m_FrequencyMap; ///< If != NULL, distortions are added to the image using this frequency map. ItkUcharImgType::Pointer m_MaskImage; ///< Signal is only genrated inside of the mask image. bool m_DoAddNoise; bool m_DoAddGhosts; bool m_DoAddAliasing; bool m_DoAddSpikes; bool m_DoAddEddyCurrents; bool m_DoAddGibbsRinging; ///< Add Gibbs ringing artifact bool m_DoSimulateRelaxation; ///< Add T2 relaxation effects bool m_DoAddDistortions; ///< Add magnetic field distortions bool m_DoDisablePartialVolume; ///< Disable partial volume effects. Each voxel is either all fiber or all non-fiber. bool m_DoAddMotion; ///< Enable motion artifacts. bool m_DoRandomizeMotion; ///< Toggles between random and linear motion. itk::Vector m_Translation; ///< Maximum translational motion. itk::Vector m_Rotation; ///< Maximum rotational motion. + + inline void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions) + + inline std::vector< int > GetBaselineIndices(); + inline unsigned int GetFirstBaselineIndex(); + inline bool IsBaselineIndex(unsigned int idx); + + inline unsigned int GetNumWeightedVolumes(); ///< Get number of diffusion-weighted image volumes + inline unsigned int GetNumBaselineVolumes(); ///< Get number of non-diffusion-weighted image volumes + inline unsigned int GetNumVolumes(); ///< Get number of baseline and diffusion-weighted image volumes + inline GradientListType GetGradientDirections(); ///< Return gradient direction container + inline GradientType GetGradientDirection(unsigned int i); + + inline void SetNumWeightedVolumes(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. + inline void SetGradienDirections(GradientListType gradientList); + inline void SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList); + +protected: + + unsigned int m_NumGradients; ///< Number of diffusion-weighted image volumes. + unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes. + GradientListType m_GradientDirections; ///< Total number of image volumes. }; /** GUI persistence, input, output, ... */ struct MiscFiberfoxParameters { mitk::DataNode::Pointer m_ResultNode; ///< Stores resulting image. mitk::DataNode::Pointer m_ParentNode; ///< Parent node of result node. string m_SignalModelString; ///< Appendet to the name of the result node string m_ArtifactModelString; ///< Appendet to the name of the result node string m_OutputPath; ///< Image is automatically saved to the specified folder after simulation is finished. bool m_OutputVolumeFractions; bool m_AdvancedOptions; }; /** * \brief Datastructure to manage the Fiberfox signal generation parameters. * */ template< class ScalarType = double > class FiberfoxParameters { public: - typedef itk::Image ItkDoubleImgType; - typedef itk::Image ItkUcharImgType; - typedef DiffusionSignalModel DiffusionModelType; - typedef std::vector< DiffusionModelType* > DiffusionModelListType; - typedef typename DiffusionModelType::GradientListType GradientListType; - typedef typename DiffusionModelType::GradientType GradientType; - typedef DiffusionNoiseModel NoiseModelType; + typedef itk::Image ItkDoubleImgType; + typedef itk::Image ItkUcharImgType; + typedef DiffusionSignalModel DiffusionModelType; + typedef std::vector< DiffusionModelType* > DiffusionModelListType; + typedef DiffusionNoiseModel NoiseModelType; FiberfoxParameters(); ~FiberfoxParameters(); /** Get same parameter object with different template parameter */ template< class OutType > FiberfoxParameters< OutType > CopyParameters() { FiberfoxParameters< OutType > out; out.m_FiberGen = m_FiberGen; out.m_SignalGen = m_SignalGen; out.m_Misc = m_Misc; - out.SetNumWeightedGradients(m_NumGradients); - if (m_NoiseModel!=NULL) { if (dynamic_cast*>(m_NoiseModel)) out.m_NoiseModel = new mitk::RicianNoiseModel(); else if (dynamic_cast*>(m_NoiseModel)) out.m_NoiseModel = new mitk::ChiSquareNoiseModel(); out.m_NoiseModel->SetNoiseVariance(m_NoiseModel->GetNoiseVariance()); } - // TODO: copy constructor für singalmodelle, gradienten + // TODO: copy signal models +// for (int i=0; i* outModel = NULL; +// mitk::DiffusionSignalModel* signalModel = NULL; +// if (i*>(signalModel)) +// { +// outModel = new mitk::StickModel(); +// } +// else if (dynamic_cast*>(signalModel)) +// { +// outModel = new mitk::TensorModel(); +// } +// else if (dynamic_cast*>(signalModel)) +// { +// outModel = new mitk::RawShModel(); +// } +// else if (dynamic_cast*>(signalModel)) +// { +// outModel = new mitk::BallModel(); +// } +// else if (dynamic_cast*>(signalModel)) +// { +// outModel = new mitk::AstroStickModel(); +// } +// else if (dynamic_cast*>(signalModel)) +// { +// outModel = new mitk::DotModel(); +// } +// } return out; } FiberGenerationParameters m_FiberGen; SignalGenerationParameters m_SignalGen; MiscFiberfoxParameters m_Misc; /** Signal generation */ DiffusionModelListType m_FiberModelList; ///< Intra- and inter-axonal compartments. DiffusionModelListType m_NonFiberModelList; ///< Extra-axonal compartments. NoiseModelType* m_NoiseModel; ///< If != NULL, noise is added to the image. void PrintSelf(); ///< Print parameters to stdout. void SaveParameters(string filename); ///< Save image generation parameters to .ffp file. void LoadParameters(string filename); ///< Load image generation parameters from .ffp file. - void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions) - - std::vector< int > GetBaselineIndices(); - unsigned int GetFirstBaselineIndex(); - bool IsBaselineIndex(unsigned int idx); - - unsigned int GetNumWeightedVolumes(); - unsigned int GetNumBaselineVolumes(); - unsigned int GetNumVolumes(); - GradientListType GetGradientDirections(); - GradientType GetGradientDirection(unsigned int i); - - void SetNumWeightedGradients(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. - void SetGradienDirections(GradientListType gradientList); - void SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList); - -protected: - - unsigned int m_NumGradients; ///< Number of diffusion-weighted image volumes. - unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes. - GradientListType m_GradientDirections; ///< Total number of image volumes. - }; } #include "mitkFiberfoxParameters.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp index bf63c80ff2..b5f199e112 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.cpp @@ -1,127 +1,127 @@ /*=================================================================== 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. ===================================================================*/ #include #include #include using namespace mitk; template< class ScalarType > AstroStickModel< ScalarType >::AstroStickModel() : m_BValue(1000) , m_Diffusivity(0.001) , m_NumSticks(42) , m_RandomizeSticks(false) { this->m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); this->m_RandGen->SetSeed(); - vnl_matrix_fixed* sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell(); + vnl_matrix_fixed* sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell(); for (unsigned int i=0; iget(0,i); stick[1] = sticks->get(1,i); stick[2] = sticks->get(2,i); stick.Normalize(); m_Sticks.push_back(stick); } } template< class ScalarType > AstroStickModel< ScalarType >::~AstroStickModel() { } template< class ScalarType > ScalarType AstroStickModel< ScalarType >::SimulateMeasurement(unsigned int dir) { ScalarType signal = 0; if (dir>=this->m_GradientList.size()) return signal; ScalarType b = -m_BValue*m_Diffusivity; if (m_RandomizeSticks) // random number of sticks m_NumSticks = 30 + this->m_RandGen->GetIntegerVariate()%31; GradientType g = this->m_GradientList[dir]; ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) // is weighted direction { for (unsigned int j=0; j typename AstroStickModel< ScalarType >::GradientType AstroStickModel< ScalarType >::GetRandomDirection() { GradientType vec; vec[0] = this->m_RandGen->GetNormalVariate(); vec[1] = this->m_RandGen->GetNormalVariate(); vec[2] = this->m_RandGen->GetNormalVariate(); vec.Normalize(); return vec; } template< class ScalarType > typename AstroStickModel< ScalarType >::PixelType AstroStickModel< ScalarType >::SimulateMeasurement() { PixelType signal; signal.SetSize(this->m_GradientList.size()); ScalarType b = -m_BValue*m_Diffusivity; if (m_RandomizeSticks) m_NumSticks = 30 + this->m_RandGen->GetIntegerVariate()%31; for( unsigned int i=0; im_GradientList.size(); i++) { GradientType g = this->m_GradientList[i]; ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) { for (unsigned int j=0; j #include namespace mitk { /** * \brief Generates the diffusion signal using a collection of idealised cylinder with zero radius: e^(-bd(ng)²) * */ template< class ScalarType = double > class AstroStickModel : public DiffusionSignalModel< ScalarType > { public: AstroStickModel(); ~AstroStickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); + void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } void SetRandomizeSticks(bool randomize=true){ m_RandomizeSticks=randomize; } ///< Random stick configuration in each voxel - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal - void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant - ScalarType GetDiffusivity() { return m_Diffusivity; } + void SetBvalue(double bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + void SetDiffusivity(double diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + double GetDiffusivity() { return m_Diffusivity; } bool GetRandomizeSticks() { return m_RandomizeSticks; } void SetNumSticks(unsigned int order) { vnl_matrix sticks; switch (order) { case 1: m_NumSticks = 12; sticks = itk::PointShell<12, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 2: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 3: m_NumSticks = 92; sticks = itk::PointShell<92, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 4: m_NumSticks = 162; sticks = itk::PointShell<162, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 5: m_NumSticks = 252; sticks = itk::PointShell<252, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; default: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; } for (int i=0; i namespace mitk { /** * \brief Generates direction independent diffusion measurement employing a scalar diffusion constant d: e^(-bd) * */ template< class ScalarType = double > class BallModel : public DiffusionSignalModel< ScalarType > { public: BallModel(); ~BallModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - void SetDiffusivity(ScalarType D) { m_Diffusivity = D; } - ScalarType GetDiffusivity() { return m_Diffusivity; } - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } + void SetDiffusivity(double D) { m_Diffusivity = D; } + double GetDiffusivity() { return m_Diffusivity; } + void SetBvalue(double bValue) { m_BValue = bValue; } void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } protected: - ScalarType m_Diffusivity; ///< Scalar diffusion constant - ScalarType m_BValue; ///< b-value used to generate the artificial signal + double m_Diffusivity; ///< Scalar diffusion constant + double m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkBallModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp index 5f05467ad5..ebad8020a0 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp @@ -1,257 +1,257 @@ /*=================================================================== 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. ===================================================================*/ #include #include #include #include #include #include using namespace mitk; using namespace boost::math; template< class ScalarType > RawShModel< ScalarType >::RawShModel() : m_ShOrder(0) , m_ModelIndex(-1) , m_MaxNumKernels(1000) { this->m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); this->m_RandGen->SetSeed(); m_AdcRange.first = 0; m_AdcRange.second = 0.004; m_FaRange.first = 0; m_FaRange.second = 1; } template< class ScalarType > RawShModel< ScalarType >::~RawShModel() { } template< class ScalarType > void RawShModel< ScalarType >::Clear() { m_ShCoefficients.clear(); m_PrototypeMaxDirection.clear(); m_B0Signal.clear(); } template< class ScalarType > void RawShModel< ScalarType >::RandomModel() { m_ModelIndex = this->m_RandGen->GetIntegerVariate(m_B0Signal.size()-1); } template< class ScalarType > unsigned int RawShModel< ScalarType >::GetNumberOfKernels() { return m_B0Signal.size(); } // convert cartesian to spherical coordinates template< class ScalarType > void RawShModel< ScalarType >::Cart2Sph( GradientListType gradients ) { m_SphCoords.set_size(gradients.size(), 2); m_SphCoords.fill(0.0); for (unsigned int i=0; i 0.0001 ) { gradients[i].Normalize(); m_SphCoords(i,0) = acos(gradients[i][2]); // theta m_SphCoords(i,1) = atan2(gradients[i][1], gradients[i][0]); // phi } } } template< class ScalarType > void RawShModel< ScalarType >::SetFiberDirection(GradientType fiberDirection) { this->m_FiberDirection = fiberDirection; this->m_FiberDirection.Normalize(); RandomModel(); GradientType axis = itk::CrossProduct(this->m_FiberDirection, m_PrototypeMaxDirection.at(m_ModelIndex)); axis.Normalize(); vnl_quaternion rotation(axis.GetVnlVector(), acos(dot_product(this->m_FiberDirection.GetVnlVector(), m_PrototypeMaxDirection.at(m_ModelIndex).GetVnlVector()))); rotation.normalize(); GradientListType gradients; for (unsigned int i=0; im_GradientList.size(); i++) { GradientType dir = this->m_GradientList.at(i); if( dir.GetNorm() > 0.0001 ) { dir.Normalize(); vnl_vector_fixed< double, 3 > vnlDir = rotation.rotate(dir.GetVnlVector()); dir[0] = vnlDir[0]; dir[1] = vnlDir[1]; dir[2] = vnlDir[2]; dir.Normalize(); } gradients.push_back(dir); } Cart2Sph( gradients ); } template< class ScalarType > -bool RawShModel< ScalarType >::SetShCoefficients(vnl_vector< double > shCoefficients, ScalarType b0 ) +bool RawShModel< ScalarType >::SetShCoefficients(vnl_vector< double > shCoefficients, double b0 ) { m_ShOrder = 2; while ( (m_ShOrder*m_ShOrder + m_ShOrder + 2)/2 + m_ShOrder <= shCoefficients.size() ) m_ShOrder += 2; m_ShOrder -= 2; m_ModelIndex = m_B0Signal.size(); m_B0Signal.push_back(b0); m_ShCoefficients.push_back(shCoefficients); // itk::OrientationDistributionFunction odf; // GradientListType gradients; // for (unsigned int i=0; im_GradientList ); // PixelType signal = SimulateMeasurement(); // int minDirIdx = 0; // double min = itk::NumericTraits::max(); // for (unsigned int i=0; ib0 || signal[i]<0) // { // MITK_INFO << "Corrupted signal value detected. Kernel rejected."; // m_B0Signal.pop_back(); // m_ShCoefficients.pop_back(); // return false; // } // if (signal[i]m_GradientList.at(minDirIdx); // maxDir.Normalize(); // m_PrototypeMaxDirection.push_back(maxDir); Cart2Sph( this->m_GradientList ); m_ModelIndex = -1; return true; } template< class ScalarType > ScalarType RawShModel< ScalarType >::SimulateMeasurement(unsigned int dir) { ScalarType signal = 0; if (m_ModelIndex==-1) RandomModel(); if (dir>=this->m_GradientList.size()) return signal; int j, m; double mag, plm; if (this->m_GradientList[dir].GetNorm()>0.001) { j=0; for (int l=0; l<=m_ShOrder; l=l+2) for (m=-l; m<=l; m++) { plm = legendre_p(l,abs(m),cos(m_SphCoords(dir,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; double basis; if (m<0) basis = sqrt(2.0)*mag*cos(fabs((double)m)*m_SphCoords(dir,1)); else if (m==0) basis = mag; else basis = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*m_SphCoords(dir,1)); signal += m_ShCoefficients.at(m_ModelIndex)[j]*basis; j++; } } else signal = m_B0Signal.at(m_ModelIndex); m_ModelIndex = -1; return signal; } template< class ScalarType > typename RawShModel< ScalarType >::PixelType RawShModel< ScalarType >::SimulateMeasurement() { if (m_ModelIndex==-1) RandomModel(); PixelType signal; signal.SetSize(this->m_GradientList.size()); int M = this->m_GradientList.size(); int j, m; double mag, plm; vnl_matrix< double > shBasis; shBasis.set_size(M, m_ShCoefficients.at(m_ModelIndex).size()); shBasis.fill(0.0); for (int p=0; pm_GradientList[p].GetNorm()>0.001) { j=0; for (int l=0; l<=m_ShOrder; l=l+2) for (m=-l; m<=l; m++) { plm = legendre_p(l,abs(m),cos(m_SphCoords(p,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; if (m<0) shBasis(p,j) = sqrt(2.0)*mag*cos(fabs((double)m)*m_SphCoords(p,1)); else if (m==0) shBasis(p,j) = mag; else shBasis(p,j) = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*m_SphCoords(p,1)); j++; } double val = 0; for (unsigned int cidx=0; cidx namespace mitk { /** * \brief The spherical harmonic representation of a prototype diffusion weighted MR signal is used to obtain the direction dependent signal. * */ template< class ScalarType = double > class RawShModel : public DiffusionSignalModel< ScalarType > { public: RawShModel(); ~RawShModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; typedef itk::Matrix< double, 3, 3 > MatrixType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - bool SetShCoefficients(vnl_vector< double > shCoefficients, ScalarType b0); + bool SetShCoefficients(vnl_vector< double > shCoefficients, double b0); void SetFiberDirection(GradientType fiberDirection); void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } void SetFaRange(double min, double max){ m_FaRange.first = min; m_FaRange.second = max; } void SetAdcRange(double min, double max){ m_AdcRange.first = min; m_AdcRange.second = max; } void SetMaxNumKernels(unsigned int max){ m_MaxNumKernels = max; } unsigned int GetNumberOfKernels(); std::pair< double, double > GetFaRange(){ return m_FaRange; } std::pair< double, double > GetAdcRange(){ return m_AdcRange; } unsigned int GetMaxNumKernels(){ return m_MaxNumKernels; } void Clear(); vector< GradientType > m_PrototypeMaxDirection; protected: void Cart2Sph( GradientListType gradients ); void RandomModel(); std::pair< double, double > m_AdcRange; std::pair< double, double > m_FaRange; vector< vnl_vector< double > > m_ShCoefficients; - vector< ScalarType > m_B0Signal; + vector< double > m_B0Signal; vnl_matrix m_SphCoords; unsigned int m_ShOrder; int m_ModelIndex; unsigned int m_MaxNumKernels; }; } #include "mitkRawShModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h index 1523592cab..bb9ff5e5b5 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h @@ -1,63 +1,63 @@ /*=================================================================== 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 _MITK_StickModel_H #define _MITK_StickModel_H #include namespace mitk { /** * \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²) * */ template< class ScalarType = double > class StickModel : public DiffusionSignalModel< ScalarType > { public: StickModel(); ~StickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal - void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant - ScalarType GetDiffusivity() { return m_Diffusivity; } + void SetBvalue(double bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + void SetDiffusivity(double diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + double GetDiffusivity() { return m_Diffusivity; } void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } protected: - ScalarType m_Diffusivity; ///< Scalar diffusion constant - ScalarType m_BValue; ///< b-value used to generate the artificial signal + double m_Diffusivity; ///< Scalar diffusion constant + double m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkStickModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h index 06f16f8731..6376b7de8a 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h @@ -1,72 +1,72 @@ /*=================================================================== 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 _MITK_TensorModel_H #define _MITK_TensorModel_H #include #include namespace mitk { /** * \brief Generates diffusion measurement employing a second rank tensor model: e^(-bg^TDg) * */ template< class ScalarType = double > class TensorModel : public DiffusionSignalModel< ScalarType > { public: TensorModel(); ~TensorModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef itk::DiffusionTensor3D< ScalarType > ItkTensorType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } - void SetDiffusivity1(ScalarType d1){ m_KernelTensorMatrix[0][0] = d1; } - void SetDiffusivity2(ScalarType d2){ m_KernelTensorMatrix[1][1] = d2; } - void SetDiffusivity3(ScalarType d3){ m_KernelTensorMatrix[2][2] = d3; } - ScalarType GetDiffusivity1() { return m_KernelTensorMatrix[0][0]; } - ScalarType GetDiffusivity2() { return m_KernelTensorMatrix[1][1]; } - ScalarType GetDiffusivity3() { return m_KernelTensorMatrix[2][2]; } + void SetBvalue(double bValue) { m_BValue = bValue; } + void SetDiffusivity1(double d1){ m_KernelTensorMatrix[0][0] = d1; } + void SetDiffusivity2(double d2){ m_KernelTensorMatrix[1][1] = d2; } + void SetDiffusivity3(double d3){ m_KernelTensorMatrix[2][2] = d3; } + double GetDiffusivity1() { return m_KernelTensorMatrix[0][0]; } + double GetDiffusivity2() { return m_KernelTensorMatrix[1][1]; } + double GetDiffusivity3() { return m_KernelTensorMatrix[2][2]; } void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } protected: /** Calculates tensor matrix from FA and ADC **/ void UpdateKernelTensor(); GradientType m_KernelDirection; ///< Direction of the kernel tensors principal eigenvector - vnl_matrix_fixed m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values - ScalarType m_BValue; ///< b-value used to generate the artificial signal + vnl_matrix_fixed m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values + double m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkTensorModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp index e170a82360..bef3714322 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp @@ -1,181 +1,181 @@ /*=================================================================== 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. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /**Documentation * Test the Fiberfox simulation functions (diffusion weighted image -> diffusion weighted image) */ class mitkFiberfoxAddArtifactsToDwiTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkFiberfoxAddArtifactsToDwiTestSuite); MITK_TEST(Spikes); MITK_TEST(GibbsRinging); MITK_TEST(Ghost); MITK_TEST(Aliasing); MITK_TEST(Eddy); MITK_TEST(RicianNoise); MITK_TEST(ChiSquareNoise); MITK_TEST(Distortions); CPPUNIT_TEST_SUITE_END(); private: mitk::DiffusionImage::Pointer m_InputDwi; FiberfoxParameters m_Parameters; public: void setUp() { // reference files m_InputDwi = dynamic_cast*>(mitk::IOUtil::LoadDataNode(GetTestDataFilePath("DiffusionImaging/Fiberfox/StickBall_RELAX.dwi"))->GetData()); // parameter setup m_Parameters = FiberfoxParameters(); m_Parameters.m_SignalGen.m_ImageRegion = m_InputDwi->GetVectorImage()->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = m_InputDwi->GetVectorImage()->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = m_InputDwi->GetVectorImage()->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = m_InputDwi->GetVectorImage()->GetDirection(); m_Parameters.m_SignalGen.m_Bvalue = m_InputDwi->GetReferenceBValue(); - m_Parameters.SetGradienDirections(m_InputDwi->GetDirections()); + m_Parameters.m_SignalGen.SetGradienDirections(m_InputDwi->GetDirections()); } bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2) { typedef itk::VectorImage< short, 3 > DwiImageType; try{ itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (it1.Get()!=it2.Get()) return false; ++it1; ++it2; } } catch(...) { return false; } return true; } void StartSimulation(string testFileName) { mitk::DiffusionImage::Pointer refImage = NULL; if (!testFileName.empty()) CPPUNIT_ASSERT(refImage = dynamic_cast*>(mitk::IOUtil::LoadDataNode(testFileName)->GetData())); itk::AddArtifactsToDwiImageFilter< short >::Pointer artifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); artifactsToDwiFilter->SetUseConstantRandSeed(true); artifactsToDwiFilter->SetInput(m_InputDwi->GetVectorImage()); artifactsToDwiFilter->SetParameters(m_Parameters); CPPUNIT_ASSERT_NO_THROW(artifactsToDwiFilter->Update()); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( artifactsToDwiFilter->GetOutput() ); testImage->SetReferenceBValue( m_Parameters.m_SignalGen.m_Bvalue); - testImage->SetDirections( m_Parameters.GetGradientDirections()); + testImage->SetDirections( m_Parameters.m_SignalGen.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { CPPUNIT_ASSERT_MESSAGE(testFileName, CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage())); } } void Spikes() { m_Parameters.m_SignalGen.m_Spikes = 5; m_Parameters.m_SignalGen.m_SpikeAmplitude = 1; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/spikes2.dwi") ); } void GibbsRinging() { m_Parameters.m_SignalGen.m_DoAddGibbsRinging = true; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/gibbsringing2.dwi") ); } void Ghost() { m_Parameters.m_SignalGen.m_KspaceLineOffset = 0.25; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/ghost2.dwi") ); } void Aliasing() { m_Parameters.m_SignalGen.m_CroppingFactor = 0.4; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/aliasing2.dwi") ); } void Eddy() { m_Parameters.m_SignalGen.m_EddyStrength = 0.05; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/eddy2.dwi") ); } void RicianNoise() { mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); m_Parameters.m_NoiseModel = ricianNoiseModel; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/riciannoise2.dwi") ); delete m_Parameters.m_NoiseModel; } void ChiSquareNoise() { mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetNoiseVariance(1000000); chiSquareNoiseModel->SetSeed(0); m_Parameters.m_NoiseModel = chiSquareNoiseModel; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/chisquarenoise2.dwi") ); delete m_Parameters.m_NoiseModel; } void Distortions() { mitk::Image::Pointer mitkFMap = dynamic_cast(mitk::IOUtil::LoadDataNode( GetTestDataFilePath("DiffusionImaging/Fiberfox/Fieldmap.nrrd") )->GetData()); typedef itk::Image ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage(mitkFMap, fMap); m_Parameters.m_SignalGen.m_FrequencyMap = fMap; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/distortions2.dwi") ); } }; MITK_TEST_SUITE_REGISTRATION(mitkFiberfoxAddArtifactsToDwi) diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp index a21db5e488..1f28408a0a 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp @@ -1,276 +1,276 @@ /*=================================================================== 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. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /**Documentation * Test the Fiberfox simulation functions (fiberBundle -> diffusion weighted image) */ bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2) { typedef itk::VectorImage< short, 3 > DwiImageType; try{ itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (it1.Get()!=it2.Get()) return false; ++it1; ++it2; } } catch(...) { return false; } return true; } void StartSimulation(FiberfoxParameters parameters, FiberBundleX::Pointer fiberBundle, mitk::DiffusionImage::Pointer refImage, string message) { itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetUseConstantRandSeed(true); tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( tractsToDwiFilter->GetOutput() ); testImage->SetReferenceBValue(parameters.m_SignalGen.m_Bvalue); - testImage->SetDirections(parameters.GetGradientDirections()); + testImage->SetDirections(parameters.m_SignalGen.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { bool cond = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()); if (!cond) { MITK_INFO << "Saving test and rference image to " << mitk::IOUtil::GetTempPath(); mitk::IOUtil::SaveBaseData(testImage, mitk::IOUtil::GetTempPath()+"testImage.dwi"); mitk::IOUtil::SaveBaseData(refImage, mitk::IOUtil::GetTempPath()+"refImage.dwi"); } MITK_TEST_CONDITION_REQUIRED(cond, message); } } int mitkFiberfoxSignalGenerationTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkFiberfoxSignalGenerationTest"); MITK_TEST_CONDITION_REQUIRED(argc>=19,"check for input data"); // input fiber bundle FiberBundleXReader::Pointer fibReader = FiberBundleXReader::New(); fibReader->SetFileName(argv[1]); fibReader->Update(); FiberBundleX::Pointer fiberBundle = dynamic_cast(fibReader->GetOutput()); // reference diffusion weighted images mitk::DiffusionImage::Pointer stickBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); mitk::DiffusionImage::Pointer stickAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); mitk::DiffusionImage::Pointer stickDot = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); mitk::DiffusionImage::Pointer tensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData()); mitk::DiffusionImage::Pointer stickTensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData()); mitk::DiffusionImage::Pointer stickTensorBallAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData()); mitk::DiffusionImage::Pointer gibbsringing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[8])->GetData()); mitk::DiffusionImage::Pointer ghost = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[9])->GetData()); mitk::DiffusionImage::Pointer aliasing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[10])->GetData()); mitk::DiffusionImage::Pointer eddy = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[11])->GetData()); mitk::DiffusionImage::Pointer linearmotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[12])->GetData()); mitk::DiffusionImage::Pointer randommotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[13])->GetData()); mitk::DiffusionImage::Pointer spikes = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[14])->GetData()); mitk::DiffusionImage::Pointer riciannoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[15])->GetData()); mitk::DiffusionImage::Pointer chisquarenoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[16])->GetData()); mitk::DiffusionImage::Pointer distortions = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[17])->GetData()); mitk::Image::Pointer mitkFMap = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[18])->GetData()); typedef itk::Image ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage(mitkFMap, fMap); FiberfoxParameters parameters; parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_SignalGen.m_SignalScale = 10000; parameters.m_SignalGen.m_ImageRegion = stickBall->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = stickBall->GetVectorImage()->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = stickBall->GetVectorImage()->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = stickBall->GetVectorImage()->GetDirection(); parameters.m_SignalGen.m_Bvalue = stickBall->GetReferenceBValue(); - parameters.SetGradienDirections(stickBall->GetDirections()); + parameters.m_SignalGen.SetGradienDirections(stickBall->GetDirections()); // intra and inter axonal compartments mitk::StickModel stickModel; stickModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); stickModel.SetT2(110); stickModel.SetDiffusivity(0.001); - stickModel.SetGradientList(parameters.GetGradientDirections()); + stickModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::TensorModel tensorModel; tensorModel.SetT2(110); stickModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); tensorModel.SetDiffusivity1(0.001); tensorModel.SetDiffusivity2(0.00025); tensorModel.SetDiffusivity3(0.00025); - tensorModel.SetGradientList(parameters.GetGradientDirections()); + tensorModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); // extra axonal compartment models mitk::BallModel ballModel; ballModel.SetT2(80); ballModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); ballModel.SetDiffusivity(0.001); - ballModel.SetGradientList(parameters.GetGradientDirections()); + ballModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::AstroStickModel astrosticksModel; astrosticksModel.SetT2(80); astrosticksModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); astrosticksModel.SetDiffusivity(0.001); astrosticksModel.SetRandomizeSticks(true); astrosticksModel.SetSeed(0); - astrosticksModel.SetGradientList(parameters.GetGradientDirections()); + astrosticksModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::DotModel dotModel; dotModel.SetT2(80); - dotModel.SetGradientList(parameters.GetGradientDirections()); + dotModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); // noise models mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); // Rician noise mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetNoiseVariance(1000000); chiSquareNoiseModel->SetSeed(0); try{ // Stick-Ball parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickBall, argv[2]); // Srick-Astrosticks parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickAstrosticks, argv[3]); // Stick-Dot parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&dotModel); StartSimulation(parameters, fiberBundle, stickDot, argv[4]); // Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, tensorBall, argv[5]); // Stick-Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickTensorBall, argv[6]); // Stick-Tensor-Ball-Astrosticks parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickTensorBallAstrosticks, argv[7]); // Gibbs ringing parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); parameters.m_SignalGen.m_DoAddGibbsRinging = true; StartSimulation(parameters, fiberBundle, gibbsringing, argv[8]); // Ghost parameters.m_SignalGen.m_DoAddGibbsRinging = false; parameters.m_SignalGen.m_KspaceLineOffset = 0.25; StartSimulation(parameters, fiberBundle, ghost, argv[9]); // Aliasing parameters.m_SignalGen.m_KspaceLineOffset = 0; parameters.m_SignalGen.m_CroppingFactor = 0.4; parameters.m_SignalGen.m_SignalScale = 1000; StartSimulation(parameters, fiberBundle, aliasing, argv[10]); // Eddy currents parameters.m_SignalGen.m_CroppingFactor = 1; parameters.m_SignalGen.m_SignalScale = 10000; parameters.m_SignalGen.m_EddyStrength = 0.05; StartSimulation(parameters, fiberBundle, eddy, argv[11]); // Motion (linear) parameters.m_SignalGen.m_EddyStrength = 0.0; parameters.m_SignalGen.m_DoAddMotion = true; parameters.m_SignalGen.m_DoRandomizeMotion = false; parameters.m_SignalGen.m_Translation[1] = 10; parameters.m_SignalGen.m_Rotation[2] = 90; StartSimulation(parameters, fiberBundle, linearmotion, argv[12]); // Motion (random) parameters.m_SignalGen.m_DoRandomizeMotion = true; parameters.m_SignalGen.m_Translation[1] = 5; parameters.m_SignalGen.m_Rotation[2] = 45; StartSimulation(parameters, fiberBundle, randommotion, argv[13]); // Spikes parameters.m_SignalGen.m_DoAddMotion = false; parameters.m_SignalGen.m_Spikes = 5; parameters.m_SignalGen.m_SpikeAmplitude = 1; StartSimulation(parameters, fiberBundle, spikes, argv[14]); // Rician noise parameters.m_SignalGen.m_Spikes = 0; parameters.m_NoiseModel = ricianNoiseModel; StartSimulation(parameters, fiberBundle, riciannoise, argv[15]); delete parameters.m_NoiseModel; // Chi-square noise parameters.m_NoiseModel = chiSquareNoiseModel; StartSimulation(parameters, fiberBundle, chisquarenoise, argv[16]); delete parameters.m_NoiseModel; // Distortions parameters.m_NoiseModel = NULL; parameters.m_SignalGen.m_FrequencyMap = fMap; StartSimulation(parameters, fiberBundle, distortions, argv[17]); } catch (std::exception &e) { MITK_TEST_CONDITION_REQUIRED(false, e.what()); } // always end with this! MITK_TEST_END(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp index 222ede5bf9..6bfae0165d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2604 +1,2647 @@ /*=================================================================== 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. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ switch (m_FilterType) { case 0: m_View->m_TractsToDwiFilter->Update(); break; case 1: m_View->m_ArtifactsToDwiFilter->Update(); break; } } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); - - m_StickModel1.m_CompartmentId = 1; - m_StickModel2.m_CompartmentId = 2; - m_TensorModel1.m_CompartmentId = 1; - m_TensorModel2.m_CompartmentId = 2; - m_ZeppelinModel1.m_CompartmentId = 1; - m_ZeppelinModel2.m_CompartmentId = 2; - m_BallModel1.m_CompartmentId = 3; - m_BallModel2.m_CompartmentId = 4; - m_AstrosticksModel1.m_CompartmentId = 3; - m_AstrosticksModel2.m_CompartmentId = 4; - m_DotModel1.m_CompartmentId = 3; - m_DotModel2.m_CompartmentId = 4; - m_PrototypeModel1.m_CompartmentId = 1; - m_PrototypeModel3.m_CompartmentId = 3; - m_PrototypeModel4.m_CompartmentId = 4; } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; switch (m_Worker.m_FilterType) { case 0: m_TractsToDwiFilter->SetAbortGenerateData(true); break; case 1: m_ArtifactsToDwiFilter->SetAbortGenerateData(true); break; } m_Controls->m_AbortSimulationButton->setEnabled(false); m_Controls->m_AbortSimulationButton->setText("Aborting simulation ..."); } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_AbortSimulationButton->setEnabled(true); m_Controls->m_AbortSimulationButton->setText("Abort simulation"); m_Controls->m_GenerateImageButton->setVisible(true); m_ThreadIsRunning = false; QString statusText; FiberfoxParameters parameters; mitk::DiffusionImage::Pointer mitkImage = mitk::DiffusionImage::New(); switch (m_Worker.m_FilterType) { case 0: { statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage->SetVectorImage( m_TractsToDwiFilter->GetOutput() ); mitkImage->SetReferenceBValue(parameters.m_SignalGen.m_Bvalue); - mitkImage->SetDirections(parameters.GetGradientDirections()); + mitkImage->SetDirections(parameters.m_SignalGen.GetGradientDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_Misc.m_ResultNode->SetData( mitkImage ); parameters.m_Misc.m_ResultNode->SetName(parameters.m_Misc.m_ParentNode->GetName() - +"_D"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(0)).toStdString() - +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(1)).toStdString() - +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(2)).toStdString() - +"_S"+QString::number(parameters.m_SignalGen.m_ImageSpacing[0]).toStdString() + +"_D"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(0)).toStdString() + +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(1)).toStdString() + +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(2)).toStdString() + +"_S"+QString::number(parameters.m_SignalGen.m_ImageSpacing[0]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[1]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(parameters.m_SignalGen.m_Bvalue).toStdString() +"_"+parameters.m_Misc.m_SignalModelString +parameters.m_Misc.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); parameters.m_Misc.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(parameters.m_Misc.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_Misc.m_ParentNode); } } m_TractsToDwiFilter = NULL; break; } case 1: { statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); if (m_ArtifactsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_ArtifactsToDwiFilter->GetParameters().CopyParameters(); mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(parameters.m_Misc.m_ParentNode->GetData()); mitkImage = mitk::DiffusionImage::New(); mitkImage->SetVectorImage( m_ArtifactsToDwiFilter->GetOutput() ); mitkImage->SetReferenceBValue(diffImg->GetReferenceBValue()); mitkImage->SetDirections(diffImg->GetDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_Misc.m_ResultNode->SetData( mitkImage ); parameters.m_Misc.m_ResultNode->SetName(parameters.m_Misc.m_ParentNode->GetName()+parameters.m_Misc.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); m_ArtifactsToDwiFilter = NULL; break; } } mitk::BaseData::Pointer basedata = parameters.m_Misc.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_Misc.m_OutputPath.empty()) { try{ QString outputFileName(parameters.m_Misc.m_OutputPath.c_str()); outputFileName += parameters.m_Misc.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::SaveBaseData(mitkImage, outputFileName.toStdString()); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_SignalGen.m_FrequencyMap = NULL; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText; switch (m_Worker.m_FilterType) { case 0: statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); break; case 1: statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); break; } if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); statusText = "
"+statusText+"
"; m_Controls->m_SimulationStatusText->setText(statusText); QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); m_Controls->m_PrototypeWidget2->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_PrototypeWidget3->SetMinFa(0.0); m_Controls->m_PrototypeWidget3->SetMaxFa(0.15); m_Controls->m_PrototypeWidget4->SetMinFa(0.0); m_Controls->m_PrototypeWidget4->SetMaxFa(0.15); m_Controls->m_PrototypeWidget3->SetMinAdc(0.0); m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001); m_Controls->m_PrototypeWidget4->SetMinAdc(0.003); m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetPredicate(finalPredicate); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); } } template< class ScalarType > FiberfoxParameters< ScalarType > QmitkFiberfoxView::UpdateImageParameters() { FiberfoxParameters< ScalarType > parameters; parameters.m_Misc.m_OutputPath = ""; parameters.m_FiberGen.m_AdvancedOptions = m_Controls->m_AdvancedOptionsBox->isChecked(); parameters.m_Misc.m_AdvancedOptions = m_Controls->m_AdvancedOptionsBox_2->isChecked(); string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { parameters.m_Misc.m_OutputPath = outputPath; parameters.m_Misc.m_OutputPath += "/"; } if (m_MaskImageNode.IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_MaskImageNode->GetData()); mitk::CastToItkImage(mitkMaskImage, parameters.m_SignalGen.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(parameters.m_SignalGen.m_MaskImage); duplicator->Update(); parameters.m_SignalGen.m_MaskImage = duplicator->GetOutput(); } if (m_SelectedDWI.IsNotNull()) // use parameters of selected DWI { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); parameters.m_SignalGen.m_ImageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = dwi->GetVectorImage()->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = dwi->GetVectorImage()->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = dwi->GetVectorImage()->GetDirection(); parameters.m_SignalGen.m_Bvalue = dwi->GetReferenceBValue(); - parameters.SetGradienDirections(dwi->GetDirections()); + parameters.m_SignalGen.SetGradienDirections(dwi->GetDirections()); } else if (m_SelectedImage.IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); - parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); + parameters.m_SignalGen.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); parameters.m_SignalGen.m_Bvalue = m_Controls->m_BvalueBox->value(); } else // use GUI parameters { parameters.m_SignalGen.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); parameters.m_SignalGen.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); parameters.m_SignalGen.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); parameters.m_SignalGen.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); parameters.m_SignalGen.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); parameters.m_SignalGen.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); parameters.m_SignalGen.m_ImageOrigin[0] = parameters.m_SignalGen.m_ImageSpacing[0]/2; parameters.m_SignalGen.m_ImageOrigin[1] = parameters.m_SignalGen.m_ImageSpacing[1]/2; parameters.m_SignalGen.m_ImageOrigin[2] = parameters.m_SignalGen.m_ImageSpacing[2]/2; parameters.m_SignalGen.m_ImageDirection.SetIdentity(); - parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); + parameters.m_SignalGen.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); parameters.m_SignalGen.m_Bvalue = m_Controls->m_BvalueBox->value(); - parameters.GenerateGradientHalfShell(); + parameters.m_SignalGen.GenerateGradientHalfShell(); } // signal relaxation parameters.m_SignalGen.m_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); parameters.m_SignalGen.m_SimulateKspaceAcquisition = parameters.m_SignalGen.m_DoSimulateRelaxation; if (parameters.m_SignalGen.m_DoSimulateRelaxation && m_SelectedBundles.size()>0 ) parameters.m_Misc.m_ArtifactModelString += "_RELAX"; // N/2 ghosts parameters.m_SignalGen.m_DoAddGhosts = m_Controls->m_AddGhosts->isChecked(); if (m_Controls->m_AddGhosts->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_GHOST"; parameters.m_SignalGen.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(parameters.m_SignalGen.m_KspaceLineOffset)); } else parameters.m_SignalGen.m_KspaceLineOffset = 0; // Aliasing parameters.m_SignalGen.m_DoAddAliasing = m_Controls->m_AddAliasing->isChecked(); if (m_Controls->m_AddAliasing->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_ALIASING"; parameters.m_SignalGen.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Spikes parameters.m_SignalGen.m_DoAddSpikes = m_Controls->m_AddSpikes->isChecked(); if (m_Controls->m_AddSpikes->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_SignalGen.m_Spikes = m_Controls->m_SpikeNumBox->value(); parameters.m_SignalGen.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); parameters.m_Misc.m_ArtifactModelString += "_SPIKES"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_SignalGen.m_Spikes)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SignalGen.m_SpikeAmplitude)); } // gibbs ringing parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); parameters.m_Misc.m_ArtifactModelString += "_RINGING"; } // add distortions parameters.m_SignalGen.m_DoAddDistortions = m_Controls->m_AddDistortions->isChecked(); if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); + if (m_SelectedImage.IsNull()) // use geometry of frequency map + { + parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); + parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); + parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); + parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); + } + if (parameters.m_SignalGen.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && parameters.m_SignalGen.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && parameters.m_SignalGen.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(itkImg); duplicator->Update(); parameters.m_SignalGen.m_FrequencyMap = duplicator->GetOutput(); parameters.m_Misc.m_ArtifactModelString += "_DISTORTED"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } } parameters.m_SignalGen.m_EddyStrength = 0; parameters.m_SignalGen.m_DoAddEddyCurrents = m_Controls->m_AddEddy->isChecked(); if (m_Controls->m_AddEddy->isChecked()) { parameters.m_SignalGen.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); parameters.m_Misc.m_ArtifactModelString += "_EDDY"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_SignalGen.m_EddyStrength)); } // Motion parameters.m_SignalGen.m_DoAddMotion = m_Controls->m_AddMotion->isChecked(); parameters.m_SignalGen.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); parameters.m_SignalGen.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); parameters.m_SignalGen.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); parameters.m_SignalGen.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); parameters.m_SignalGen.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); parameters.m_SignalGen.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); parameters.m_SignalGen.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); if ( m_Controls->m_AddMotion->isChecked() && m_SelectedBundles.size()>0 ) { parameters.m_Misc.m_ArtifactModelString += "_MOTION"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(parameters.m_SignalGen.m_DoRandomizeMotion)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(parameters.m_SignalGen.m_Translation[0])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(parameters.m_SignalGen.m_Translation[1])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(parameters.m_SignalGen.m_Translation[2])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[0])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[1])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[2])); } // other imaging parameters parameters.m_SignalGen.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); parameters.m_SignalGen.m_tInhom = m_Controls->m_T2starBox->value(); parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); parameters.m_SignalGen.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); parameters.m_SignalGen.m_AxonRadius = m_Controls->m_FiberRadius->value(); parameters.m_SignalGen.m_SignalScale = m_Controls->m_SignalScaleBox->value(); // adjust echo time if needed if ( parameters.m_SignalGen.m_tEcho < parameters.m_SignalGen.m_ImageRegion.GetSize(1)*parameters.m_SignalGen.m_tLine ) { this->m_Controls->m_TEbox->setValue( parameters.m_SignalGen.m_ImageRegion.GetSize(1)*parameters.m_SignalGen.m_tLine ); parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(parameters.m_SignalGen.m_tEcho)+" ms"); } // Noise parameters.m_SignalGen.m_DoAddNoise = m_Controls->m_AddNoise->isChecked(); if (m_Controls->m_AddNoise->isChecked()) { double noiseVariance = m_Controls->m_NoiseLevel->value(); { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); break; } case 1: { parameters.m_NoiseModel = new mitk::ChiSquareNoiseModel(); parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); break; } default: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); } } } parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); parameters.m_Misc.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } // adjusting line readout time to the adapted image size needed for the DFT unsigned int y = parameters.m_SignalGen.m_ImageRegion.GetSize(1); y += y%2; if ( y>parameters.m_SignalGen.m_ImageRegion.GetSize(1) ) parameters.m_SignalGen.m_tLine *= (double)parameters.m_SignalGen.m_ImageRegion.GetSize(1)/y; // signal models - m_PrototypeModel1.Clear(); - m_PrototypeModel3.Clear(); - m_PrototypeModel4.Clear(); - - // compartment 1 - switch (m_Controls->m_Compartment1Box->currentIndex()) { - case 0: - mitk::StickModel* model = new mitk::StickModel(); - model->SetGradientList(parameters.GetGradientDirections()); - model->SetBvalue(parameters.m_SignalGen.m_Bvalue); - model->SetDiffusivity(m_Controls->m_StickWidget1->GetD()); - model->SetT2(m_Controls->m_StickWidget1->GetT2()); - parameters.m_FiberModelList.push_back(model); - parameters.m_Misc.m_SignalModelString += "Stick"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_StickModel1.GetT2()) ); - break; - case 1: - m_ZeppelinModel1.SetGradientList(parameters.GetGradientDirections()); - m_ZeppelinModel1.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_ZeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); - m_ZeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); - m_ZeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); - m_ZeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); - parameters.m_FiberModelList.push_back(&m_ZeppelinModel1); - parameters.m_Misc.m_SignalModelString += "Zeppelin"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); - break; - case 2: - m_TensorModel1.SetGradientList(parameters.GetGradientDirections()); - m_TensorModel1.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_TensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); - m_TensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); - m_TensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); - m_TensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); - parameters.m_FiberModelList.push_back(&m_TensorModel1); - parameters.m_Misc.m_SignalModelString += "Tensor"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); - break; - case 3: - parameters.m_SignalGen.m_SimulateKspaceAcquisition = false; - m_PrototypeModel1.SetGradientList(parameters.GetGradientDirections()); - m_PrototypeModel1.SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); - m_PrototypeModel1.SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); - m_PrototypeModel1.SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); - parameters.m_FiberModelList.push_back(&m_PrototypeModel1); - parameters.m_Misc.m_SignalModelString += "Prototype"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); - break; - } - - // compartment 2 - switch (m_Controls->m_Compartment2Box->currentIndex()) - { - case 0: - break; - case 1: - m_StickModel2.SetGradientList(parameters.GetGradientDirections()); - m_StickModel2.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_StickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); - m_StickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); - parameters.m_FiberModelList.push_back(&m_StickModel2); - parameters.m_Misc.m_SignalModelString += "Stick"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_StickModel2.GetT2()) ); - break; - case 2: - m_ZeppelinModel2.SetGradientList(parameters.GetGradientDirections()); - m_ZeppelinModel2.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_ZeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); - m_ZeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); - m_ZeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); - m_ZeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); - parameters.m_FiberModelList.push_back(&m_ZeppelinModel2); - parameters.m_Misc.m_SignalModelString += "Zeppelin"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); - break; - case 3: - m_TensorModel2.SetGradientList(parameters.GetGradientDirections()); - m_TensorModel2.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_TensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); - m_TensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); - m_TensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); - m_TensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); - parameters.m_FiberModelList.push_back(&m_TensorModel2); - parameters.m_Misc.m_SignalModelString += "Tensor"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); - break; - } - - // compartment 3 - switch (m_Controls->m_Compartment3Box->currentIndex()) - { - case 0: - m_BallModel1.SetGradientList(parameters.GetGradientDirections()); - m_BallModel1.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_BallModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); - m_BallModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); - parameters.m_NonFiberModelList.push_back(&m_BallModel1); - parameters.m_Misc.m_SignalModelString += "Ball"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_BallModel1.GetT2()) ); - break; - case 1: - m_AstrosticksModel1.SetGradientList(parameters.GetGradientDirections()); - m_AstrosticksModel1.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_AstrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); - m_AstrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); - m_AstrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); - parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel1); - parameters.m_Misc.m_SignalModelString += "Astrosticks"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_AstrosticksModel1.GetT2()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); - break; - case 2: - m_DotModel1.SetGradientList(parameters.GetGradientDirections()); - m_DotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); - parameters.m_NonFiberModelList.push_back(&m_DotModel1); - parameters.m_Misc.m_SignalModelString += "Dot"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_DotModel1.GetT2()) ); - break; - case 3: - parameters.m_SignalGen.m_SimulateKspaceAcquisition = false; - m_PrototypeModel3.SetGradientList(parameters.GetGradientDirections()); - m_PrototypeModel3.SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); - m_PrototypeModel3.SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); - m_PrototypeModel3.SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); - parameters.m_NonFiberModelList.push_back(&m_PrototypeModel3); - parameters.m_Misc.m_SignalModelString += "Prototype"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); - break; - } - - // compartment 4 - ItkDoubleImgType::Pointer comp4VolumeImage = NULL; - ItkDoubleImgType::Pointer comp3VolumeImage = NULL; - if (m_Controls->m_Compartment4Box->currentIndex()>0) - { - mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); - if (volumeNode.IsNull()) + // compartment 1 + switch (m_Controls->m_Compartment1Box->currentIndex()) + { + case 0: { - QMessageBox::information( NULL, "Information", "No volume fraction image selected! Second extra-axonal compartment has been disabled for this simultation."); - MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; + mitk::StickModel* model = new mitk::StickModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity(m_Controls->m_StickWidget1->GetD()); + model->SetT2(m_Controls->m_StickWidget1->GetT2()); + model->m_CompartmentId = 1; + parameters.m_FiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Stick"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); + break; } - else + case 1: { - MITK_INFO << "Rescaling volume fraction image..."; - comp4VolumeImage = ItkDoubleImgType::New(); - mitk::Image* img = dynamic_cast(volumeNode->GetData()); - CastToItkImage< ItkDoubleImgType >(img, comp4VolumeImage); - - double max = itk::NumericTraits::min(); - double min = itk::NumericTraits::max(); - - itk::ImageRegionIterator< ItkDoubleImgType > it(comp4VolumeImage, comp4VolumeImage->GetLargestPossibleRegion()); - while(!it.IsAtEnd()) - { - if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) - { - it.Set(0.0); - ++it; - continue; - } - - if (it.Get()>max) - max = it.Get(); - if (it.Get()::Pointer scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); - scaler->SetInput(comp4VolumeImage); - scaler->SetShift(-min); - scaler->SetScale(1.0/(max-min)); - scaler->Update(); - comp4VolumeImage = scaler->GetOutput(); - - // itk::ImageFileWriter< ItkDoubleImgType >::Pointer wr = itk::ImageFileWriter< ItkDoubleImgType >::New(); - // wr->SetInput(comp4VolumeImage); - // wr->SetFileName("/local/comp4.nrrd"); - // wr->Update(); - - // if (max>1 || min<0) // are volume fractions between 0 and 1? - // { - // itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); - // rescaler->SetInput(0, comp4VolumeImage); - // rescaler->SetOutputMaximum(1); - // rescaler->SetOutputMinimum(0); - // rescaler->Update(); - // comp4VolumeImage = rescaler->GetOutput(); - // } - - itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); - inverter->SetMaximum(1.0); - inverter->SetInput(comp4VolumeImage); - inverter->Update(); - comp3VolumeImage = inverter->GetOutput(); + mitk::TensorModel* model = new mitk::TensorModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); + model->SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); + model->SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); + model->SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); + model->m_CompartmentId = 1; + parameters.m_FiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Zeppelin"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); + break; + } + case 2: + { + mitk::TensorModel* model = new mitk::TensorModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); + model->SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); + model->SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); + model->SetT2(m_Controls->m_TensorWidget1->GetT2()); + model->m_CompartmentId = 1; + parameters.m_FiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Tensor"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); + break; + } + case 3: + { + mitk::RawShModel* model = new mitk::RawShModel(); + parameters.m_SignalGen.m_SimulateKspaceAcquisition = false; + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); + model->SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); + model->SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); + model->m_CompartmentId = 1; + parameters.m_FiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Prototype"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); + break; + } } - } - if (comp4VolumeImage.IsNotNull()) - switch (m_Controls->m_Compartment4Box->currentIndex()) + // compartment 2 + switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: { - m_BallModel2.SetGradientList(parameters.GetGradientDirections()); - m_BallModel2.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); - m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); - m_BallModel2.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_BallModel2); - parameters.m_Misc.m_SignalModelString += "Ball"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) ); + mitk::StickModel* model = new mitk::StickModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity(m_Controls->m_StickWidget2->GetD()); + model->SetT2(m_Controls->m_StickWidget2->GetT2()); + model->m_CompartmentId = 2; + parameters.m_FiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Stick"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { - m_AstrosticksModel2.SetGradientList(parameters.GetGradientDirections()); - m_AstrosticksModel2.SetBvalue(parameters.m_SignalGen.m_Bvalue); - m_AstrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); - m_AstrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); - m_AstrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - m_AstrosticksModel2.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel2); - parameters.m_Misc.m_SignalModelString += "Astrosticks"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); + mitk::TensorModel* model = new mitk::TensorModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); + model->SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); + model->SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); + model->SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); + model->m_CompartmentId = 2; + parameters.m_FiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Zeppelin"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { - m_DotModel2.SetGradientList(parameters.GetGradientDirections()); - m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); - m_DotModel2.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_DotModel2); + mitk::TensorModel* model = new mitk::TensorModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); + model->SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); + model->SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); + model->SetT2(m_Controls->m_TensorWidget2->GetT2()); + model->m_CompartmentId = 2; + parameters.m_FiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Tensor"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); + break; + } + } + + // compartment 3 + switch (m_Controls->m_Compartment3Box->currentIndex()) + { + case 0: + { + mitk::BallModel* model = new mitk::BallModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity(m_Controls->m_BallWidget1->GetD()); + model->SetT2(m_Controls->m_BallWidget1->GetT2()); + model->m_CompartmentId = 3; + parameters.m_NonFiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Ball"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); + break; + } + case 1: + { + mitk::AstroStickModel* model = new mitk::AstroStickModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); + model->SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); + model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); + model->m_CompartmentId = 3; + parameters.m_NonFiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Astrosticks"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); + break; + } + case 2: + { + mitk::DotModel* model = new mitk::DotModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetT2(m_Controls->m_DotWidget1->GetT2()); + model->m_CompartmentId = 3; + parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Dot"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } - case 4: + case 3: { + mitk::RawShModel* model = new mitk::RawShModel(); parameters.m_SignalGen.m_SimulateKspaceAcquisition = false; - m_PrototypeModel4.SetGradientList(parameters.GetGradientDirections()); - m_PrototypeModel4.SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); - m_PrototypeModel4.SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); - m_PrototypeModel4.SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); - m_PrototypeModel4.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_PrototypeModel4); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); + model->SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); + model->SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); + model->m_CompartmentId = 3; + parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Prototype"; - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); break; } } + // compartment 4 + ItkDoubleImgType::Pointer comp4VolumeImage = NULL; + ItkDoubleImgType::Pointer comp3VolumeImage = NULL; + if (m_Controls->m_Compartment4Box->currentIndex()>0) + { + mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); + if (volumeNode.IsNull()) + { + QMessageBox::information( NULL, "Information", "No volume fraction image selected! Second extra-axonal compartment has been disabled for this simultation."); + MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; + } + else + { + MITK_INFO << "Rescaling volume fraction image..."; + comp4VolumeImage = ItkDoubleImgType::New(); + mitk::Image* img = dynamic_cast(volumeNode->GetData()); + CastToItkImage< ItkDoubleImgType >(img, comp4VolumeImage); + + double max = itk::NumericTraits::min(); + double min = itk::NumericTraits::max(); + + itk::ImageRegionIterator< ItkDoubleImgType > it(comp4VolumeImage, comp4VolumeImage->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) + { + if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) + { + it.Set(0.0); + ++it; + continue; + } + + if (it.Get()>max) + max = it.Get(); + if (it.Get()::Pointer scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); + scaler->SetInput(comp4VolumeImage); + scaler->SetShift(-min); + scaler->SetScale(1.0/(max-min)); + scaler->Update(); + comp4VolumeImage = scaler->GetOutput(); + + // itk::ImageFileWriter< ItkDoubleImgType >::Pointer wr = itk::ImageFileWriter< ItkDoubleImgType >::New(); + // wr->SetInput(comp4VolumeImage); + // wr->SetFileName("/local/comp4.nrrd"); + // wr->Update(); + + // if (max>1 || min<0) // are volume fractions between 0 and 1? + // { + // itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); + // rescaler->SetInput(0, comp4VolumeImage); + // rescaler->SetOutputMaximum(1); + // rescaler->SetOutputMinimum(0); + // rescaler->Update(); + // comp4VolumeImage = rescaler->GetOutput(); + // } + + itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); + inverter->SetMaximum(1.0); + inverter->SetInput(comp4VolumeImage); + inverter->Update(); + comp3VolumeImage = inverter->GetOutput(); + } + } + + if (comp4VolumeImage.IsNotNull()) + { + switch (m_Controls->m_Compartment4Box->currentIndex()) + { + case 0: + break; + case 1: + { + mitk::BallModel* model = new mitk::BallModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity(m_Controls->m_BallWidget2->GetD()); + model->SetT2(m_Controls->m_BallWidget2->GetT2()); + model->SetVolumeFractionImage(comp4VolumeImage); + model->m_CompartmentId = 4; + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + parameters.m_NonFiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Ball"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); + break; + } + case 2: + { + mitk::AstroStickModel* model = new mitk::AstroStickModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetBvalue(parameters.m_SignalGen.m_Bvalue); + model->SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); + model->SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); + model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + model->SetVolumeFractionImage(comp4VolumeImage); + model->m_CompartmentId = 4; + parameters.m_NonFiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Astrosticks"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); + break; + } + case 3: + { + mitk::DotModel* model = new mitk::DotModel(); + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetT2(m_Controls->m_DotWidget2->GetT2()); + model->SetVolumeFractionImage(comp4VolumeImage); + model->m_CompartmentId = 4; + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + parameters.m_NonFiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Dot"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); + break; + } + case 4: + { + mitk::RawShModel* model = new mitk::RawShModel(); + parameters.m_SignalGen.m_SimulateKspaceAcquisition = false; + model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); + model->SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); + model->SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); + model->SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); + model->SetVolumeFractionImage(comp4VolumeImage); + model->m_CompartmentId = 4; + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + parameters.m_NonFiberModelList.push_back(model); + parameters.m_Misc.m_SignalModelString += "Prototype"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); + break; + } + } + } + } + parameters.m_SignalGen.m_FiberSeparationThreshold = m_Controls->m_SeparationAngleBox->value(); switch (m_Controls->m_DiffusionDirectionBox->currentIndex()) { case 0: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; break; case 1: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::MAIN_FIBER_DIRECTIONS; break; case 2: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::RANDOM_DIRECTIONS; parameters.m_SignalGen.m_DoAddMotion = false; parameters.m_SignalGen.m_DoAddGibbsRinging = false; parameters.m_SignalGen.m_KspaceLineOffset = 0.0; parameters.m_SignalGen.m_FrequencyMap = NULL; parameters.m_SignalGen.m_CroppingFactor = 1.0; parameters.m_SignalGen.m_EddyStrength = 0; break; default: parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; } parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(parameters.m_SignalGen.m_SignalScale)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(parameters.m_SignalGen.m_AxonRadius)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(parameters.m_SignalGen.m_tInhom)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(parameters.m_SignalGen.m_tLine)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(parameters.m_SignalGen.m_tEcho)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(parameters.m_SignalGen.m_Bvalue)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(parameters.m_SignalGen.m_DoDisablePartialVolume)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(parameters.m_SignalGen.m_DoSimulateRelaxation)); parameters.m_Misc.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); parameters.m_FiberGen.m_RealTimeFibers = m_Controls->m_RealTimeFibers->isChecked(); parameters.m_FiberGen.m_AdvancedOptions = m_Controls->m_AdvancedOptionsBox->isChecked(); parameters.m_FiberGen.m_Distribution = m_Controls->m_DistributionBox->currentIndex(); parameters.m_FiberGen.m_Variance = m_Controls->m_VarianceBox->value(); parameters.m_FiberGen.m_FiberDensity = m_Controls->m_FiberDensityBox->value(); parameters.m_FiberGen.m_IncludeFiducials = m_Controls->m_IncludeFiducials->isChecked(); parameters.m_FiberGen.m_ConstantRadius = m_Controls->m_ConstantRadiusBox->isChecked(); parameters.m_FiberGen.m_Sampling = m_Controls->m_FiberSamplingBox->value(); parameters.m_FiberGen.m_Tension = m_Controls->m_TensionBox->value(); parameters.m_FiberGen.m_Continuity = m_Controls->m_ContinuityBox->value(); parameters.m_FiberGen.m_Bias = m_Controls->m_BiasBox->value(); parameters.m_FiberGen.m_Rotation[0] = m_Controls->m_XrotBox->value(); parameters.m_FiberGen.m_Rotation[1] = m_Controls->m_YrotBox->value(); parameters.m_FiberGen.m_Rotation[2] = m_Controls->m_ZrotBox->value(); parameters.m_FiberGen.m_Translation[0] = m_Controls->m_XtransBox->value(); parameters.m_FiberGen.m_Translation[1] = m_Controls->m_YtransBox->value(); parameters.m_FiberGen.m_Translation[2] = m_Controls->m_ZtransBox->value(); parameters.m_FiberGen.m_Scale[0] = m_Controls->m_XscaleBox->value(); parameters.m_FiberGen.m_Scale[1] = m_Controls->m_YscaleBox->value(); parameters.m_FiberGen.m_Scale[2] = m_Controls->m_ZscaleBox->value(); return parameters; } void QmitkFiberfoxView::SaveParameters() { FiberfoxParameters<> ffParamaters = UpdateImageParameters(); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); ffParamaters.SaveParameters(filename.toStdString()); m_ParameterFile = filename; } void QmitkFiberfoxView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; FiberfoxParameters<> parameters; parameters.LoadParameters(filename.toStdString()); m_Controls->m_RealTimeFibers->setChecked(parameters.m_FiberGen.m_RealTimeFibers); m_Controls->m_AdvancedOptionsBox->setChecked(parameters.m_FiberGen.m_AdvancedOptions); m_Controls->m_DistributionBox->setCurrentIndex(parameters.m_FiberGen.m_Distribution); m_Controls->m_VarianceBox->setValue(parameters.m_FiberGen.m_Variance); m_Controls->m_FiberDensityBox->setValue(parameters.m_FiberGen.m_FiberDensity); m_Controls->m_IncludeFiducials->setChecked(parameters.m_FiberGen.m_IncludeFiducials); m_Controls->m_ConstantRadiusBox->setChecked(parameters.m_FiberGen.m_ConstantRadius); m_Controls->m_FiberSamplingBox->setValue(parameters.m_FiberGen.m_Sampling); m_Controls->m_TensionBox->setValue(parameters.m_FiberGen.m_Tension); m_Controls->m_ContinuityBox->setValue(parameters.m_FiberGen.m_Continuity); m_Controls->m_BiasBox->setValue(parameters.m_FiberGen.m_Bias); m_Controls->m_XrotBox->setValue(parameters.m_FiberGen.m_Rotation[0]); m_Controls->m_YrotBox->setValue(parameters.m_FiberGen.m_Rotation[1]); m_Controls->m_ZrotBox->setValue(parameters.m_FiberGen.m_Rotation[2]); m_Controls->m_XtransBox->setValue(parameters.m_FiberGen.m_Translation[0]); m_Controls->m_YtransBox->setValue(parameters.m_FiberGen.m_Translation[1]); m_Controls->m_ZtransBox->setValue(parameters.m_FiberGen.m_Translation[2]); m_Controls->m_XscaleBox->setValue(parameters.m_FiberGen.m_Scale[0]); m_Controls->m_YscaleBox->setValue(parameters.m_FiberGen.m_Scale[1]); m_Controls->m_ZscaleBox->setValue(parameters.m_FiberGen.m_Scale[2]); // image generation parameters m_Controls->m_SizeX->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(0)); m_Controls->m_SizeY->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(1)); m_Controls->m_SizeZ->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(2)); m_Controls->m_SpacingX->setValue(parameters.m_SignalGen.m_ImageSpacing[0]); m_Controls->m_SpacingY->setValue(parameters.m_SignalGen.m_ImageSpacing[1]); m_Controls->m_SpacingZ->setValue(parameters.m_SignalGen.m_ImageSpacing[2]); - m_Controls->m_NumGradientsBox->setValue(parameters.GetNumWeightedVolumes()); + m_Controls->m_NumGradientsBox->setValue(parameters.m_SignalGen.GetNumWeightedVolumes()); m_Controls->m_BvalueBox->setValue(parameters.m_SignalGen.m_Bvalue); m_Controls->m_AdvancedOptionsBox_2->setChecked(parameters.m_Misc.m_AdvancedOptions); m_Controls->m_SignalScaleBox->setValue(parameters.m_SignalGen.m_SignalScale); m_Controls->m_TEbox->setValue(parameters.m_SignalGen.m_tEcho); m_Controls->m_LineReadoutTimeBox->setValue(parameters.m_SignalGen.m_tLine); m_Controls->m_T2starBox->setValue(parameters.m_SignalGen.m_tInhom); m_Controls->m_FiberRadius->setValue(parameters.m_SignalGen.m_AxonRadius); m_Controls->m_RelaxationBox->setChecked(parameters.m_SignalGen.m_DoSimulateRelaxation); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(parameters.m_SignalGen.m_DoDisablePartialVolume); m_Controls->m_VolumeFractionsBox->setChecked(parameters.m_Misc.m_OutputVolumeFractions); if (parameters.m_NoiseModel!=NULL) { m_Controls->m_AddNoise->setChecked(parameters.m_SignalGen.m_DoAddNoise); if (dynamic_cast*>(parameters.m_NoiseModel)) m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); else if (dynamic_cast*>(parameters.m_NoiseModel)) m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); m_Controls->m_NoiseLevel->setValue(parameters.m_NoiseModel->GetNoiseVariance()); } else m_Controls->m_AddNoise->setChecked(false); m_Controls->m_AddGhosts->setChecked(parameters.m_SignalGen.m_DoAddGhosts); m_Controls->m_kOffsetBox->setValue(parameters.m_SignalGen.m_KspaceLineOffset); m_Controls->m_AddAliasing->setChecked(parameters.m_SignalGen.m_DoAddAliasing); m_Controls->m_WrapBox->setValue(100*(1-parameters.m_SignalGen.m_CroppingFactor)); m_Controls->m_AddDistortions->setChecked(parameters.m_SignalGen.m_DoAddDistortions); m_Controls->m_AddSpikes->setChecked(parameters.m_SignalGen.m_DoAddSpikes); m_Controls->m_SpikeNumBox->setValue(parameters.m_SignalGen.m_Spikes); m_Controls->m_SpikeScaleBox->setValue(parameters.m_SignalGen.m_SpikeAmplitude); m_Controls->m_AddEddy->setChecked(parameters.m_SignalGen.m_DoAddEddyCurrents); m_Controls->m_EddyGradientStrength->setValue(parameters.m_SignalGen.m_EddyStrength); m_Controls->m_AddGibbsRinging->setChecked(parameters.m_SignalGen.m_DoAddGibbsRinging); m_Controls->m_AddMotion->setChecked(parameters.m_SignalGen.m_DoAddMotion); m_Controls->m_RandomMotion->setChecked(parameters.m_SignalGen.m_DoRandomizeMotion); m_Controls->m_MaxTranslationBoxX->setValue(parameters.m_SignalGen.m_Translation[0]); m_Controls->m_MaxTranslationBoxY->setValue(parameters.m_SignalGen.m_Translation[1]); m_Controls->m_MaxTranslationBoxZ->setValue(parameters.m_SignalGen.m_Translation[2]); m_Controls->m_MaxRotationBoxX->setValue(parameters.m_SignalGen.m_Rotation[0]); m_Controls->m_MaxRotationBoxY->setValue(parameters.m_SignalGen.m_Rotation[1]); m_Controls->m_MaxRotationBoxZ->setValue(parameters.m_SignalGen.m_Rotation[2]); m_Controls->m_DiffusionDirectionBox->setCurrentIndex(parameters.m_SignalGen.m_DiffusionDirectionMode); m_Controls->m_SeparationAngleBox->setValue(parameters.m_SignalGen.m_FiberSeparationThreshold); m_Controls->m_Compartment1Box->setCurrentIndex(0); m_Controls->m_Compartment2Box->setCurrentIndex(0); m_Controls->m_Compartment3Box->setCurrentIndex(0); m_Controls->m_Compartment4Box->setCurrentIndex(0); for (unsigned int i=0; i* signalModel = NULL; if (im_CompartmentId) { case 1: { if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget1->SetT2(model->GetT2()); m_Controls->m_StickWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment1Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget1->SetT2(model->GetT2()); m_Controls->m_TensorWidget1->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget1->SetD2(model->GetDiffusivity1()); m_Controls->m_TensorWidget1->SetD3(model->GetDiffusivity1()); m_Controls->m_Compartment1Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget1->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget1->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget1->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget1->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget1->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment1Box->setCurrentIndex(3); break; } break; } case 2: { if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget2->SetT2(model->GetT2()); m_Controls->m_StickWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment2Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget2->SetT2(model->GetT2()); m_Controls->m_TensorWidget2->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget2->SetD2(model->GetDiffusivity1()); m_Controls->m_TensorWidget2->SetD3(model->GetDiffusivity1()); m_Controls->m_Compartment2Box->setCurrentIndex(3); break; } break; } case 3: { if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget1->SetT2(model->GetT2()); m_Controls->m_BallWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment3Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget1->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget1->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment3Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget1->SetT2(model->GetT2()); m_Controls->m_Compartment3Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget3->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget3->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget3->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget3->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget3->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment3Box->setCurrentIndex(3); break; } break; } case 4: { if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget2->SetT2(model->GetT2()); m_Controls->m_BallWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment4Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget2->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget2->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment4Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget2->SetT2(model->GetT2()); m_Controls->m_Compartment4Box->setCurrentIndex(3); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget4->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget4->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget4->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget4->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget4->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment4Box->setCurrentIndex(4); break; } break; } } } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget3->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 4: m_Controls->m_PrototypeWidget4->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for(unsigned int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for(unsigned int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); node->SetBoolProperty("planarfigure.3drendering", true); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( node ); } UpdateGui(); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (unsigned int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (unsigned int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { if (m_SelectedBundles.empty() && m_SelectedDWI.IsNull()) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); } else if (!m_SelectedBundles.empty()) SimulateImageFromFibers(m_SelectedBundles.at(0)); else if (m_SelectedDWI.IsNotNull()) SimulateForExistingDwi(m_SelectedDWI); } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { if (!dynamic_cast*>(imageNode->GetData())) return; FiberfoxParameters parameters = UpdateImageParameters(); if (parameters.m_NoiseModel==NULL && parameters.m_SignalGen.m_Spikes==0 && parameters.m_SignalGen.m_FrequencyMap.IsNull() && parameters.m_SignalGen.m_KspaceLineOffset<=0.000001 && !parameters.m_SignalGen.m_DoAddGibbsRinging && !(parameters.m_SignalGen.m_EddyStrength>0) && parameters.m_SignalGen.m_CroppingFactor>0.999) { QMessageBox::information( NULL, "Simulation cancelled", "No valid artifact enabled! Motion artifacts and relaxation effects can NOT be added to an existing diffusion weighted image."); return; } mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(imageNode->GetData()); m_ArtifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); m_ArtifactsToDwiFilter->SetInput(diffImg->GetVectorImage()); parameters.m_Misc.m_ParentNode = imageNode; m_ArtifactsToDwiFilter->SetParameters(parameters); m_Worker.m_FilterType = 1; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) return; FiberfoxParameters parameters = UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); parameters.m_Misc.m_ParentNode = fiberNode; if (m_SelectedDWI.IsNotNull()) { mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedDWI->GetData()); bool doSampling = false; for (unsigned int i=0; i* >(parameters.m_FiberModelList[i]) ) doSampling = true; for (unsigned int i=0; i* >(parameters.m_NonFiberModelList[i]) ) doSampling = true; // sample prototype signals if ( doSampling ) { const int shOrder = 2; typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); filter->SetBValue(diffImg->GetReferenceBValue()); filter->Update(); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = filter->GetOutput(); const int NumCoeffs = (shOrder*shOrder + shOrder + 2)/2 + shOrder; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); qballfilter->SetBValue(diffImg->GetReferenceBValue()); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); QballFilterType::CoefficientImageType::Pointer itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput(diffImg->GetVectorImage()); adcFilter->SetGradientDirections(diffImg->GetDirections()); adcFilter->SetB_value(diffImg->GetReferenceBValue()); adcFilter->Update(); ItkDoubleImgType::Pointer adcImage = adcFilter->GetOutput(); int b0Index; for (unsigned int i=0; iGetDirectionsWithoutMeasurementFrame()->Size(); i++) if ( diffImg->GetDirectionsWithoutMeasurementFrame()->GetElement(i).magnitude()<0.001 ) { b0Index = i; break; } double max = 0; { itk::ImageRegionIterator< itk::VectorImage< short, 3 > > it(diffImg->GetVectorImage(), diffImg->GetVectorImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) { ++it; continue; } if (it.Get()[b0Index]>max) max = it.Get()[b0Index]; ++it; } } MITK_INFO << "Sampling signal kernels."; itk::ImageRegionIterator< itk::Image< itk::DiffusionTensor3D< double >, 3 > > it(tensorImage, tensorImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { bool skipPixel = false; if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) { ++it; continue; } for (unsigned int i=0; iGetDirections()->Size(); i++) { if (diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]!=diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i] || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]<=0 || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]>diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]) { skipPixel = true; break; } } if (skipPixel) { ++it; continue; } typedef itk::DiffusionTensor3D TensorType; TensorType::EigenValuesArrayType eigenvalues; TensorType::EigenVectorsMatrixType eigenvectors; TensorType tensor = it.Get(); double FA = tensor.GetFractionalAnisotropy(); double ADC = adcImage->GetPixel(it.GetIndex()); QballFilterType::CoefficientImageType::PixelType itkv = itkFeatureImage->GetPixel(it.GetIndex()); vnl_vector_fixed< double, NumCoeffs > coeffs; for (unsigned int c=0; c* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) { tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); itk::Vector dir; dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); model->m_PrototypeMaxDirection.push_back(dir); MITK_INFO << "WM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } } } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) MITK_INFO << "CSF/GM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } } ++it; } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); if ( model && model->GetNumberOfKernels()<=0 ) { QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for fiber compartment "+QString::number(i)); return; } } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); if ( model && model->GetNumberOfKernels()<=0 ) { QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for non-fiber compartment "+QString::number(i)); return; } } } } else if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 || m_Controls->m_Compartment4Box->currentIndex()==4 ) { QMessageBox::information( NULL, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } m_TractsToDwiFilter->SetParameters(parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Worker.m_FilterType = 0; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for(unsigned int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { for (std::vector::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); pe->Modified(); } } } } } else { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); pe->Modified(); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } for (std::vector::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); newNode->SetBoolProperty("planarfigure.3drendering", true); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_MaskImageNode.IsNotNull() || m_SelectedImage.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (!m_SelectedBundles.empty()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = NULL; m_MaskImageNode = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isbinary = false; node->GetPropertyValue("binary", isbinary); if (isbinary) { m_MaskImageNode = node; m_Controls->m_TissueMaskLabel->setText(m_MaskImageNode->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(node->GetData())) m_SelectedImages.clear(); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( nonConstNode ); } MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG string outputPath = QFileDialog::getExistingDirectory(NULL, "Save images to...", QString(outputPath.c_str())).toStdString(); if (outputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { outputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str())); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h index fc4f611076..dbe58f859b 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h @@ -1,228 +1,209 @@ /*=================================================================== 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. ===================================================================*/ #include #include #include #include "ui_QmitkFiberfoxViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief View for fiber based diffusion software phantoms (Fiberfox). See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details. \sa QmitkFunctionality \ingroup Functionalities */ // Forward Qt class declarations using namespace std; class QmitkFiberfoxView; class QmitkFiberfoxWorker : public QObject { Q_OBJECT public: QmitkFiberfoxWorker(QmitkFiberfoxView* view); int m_FilterType; public slots: void run(); private: QmitkFiberfoxView* m_View; }; class QmitkFiberfoxView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const string VIEW_ID; QmitkFiberfoxView(); virtual ~QmitkFiberfoxView(); virtual void CreateQtPartControl(QWidget *parent); void SetFocus(); typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef vector GradientListType; template vector > MakeGradientList(); protected slots: void SetOutputPath(); ///< path where image is automatically saved to after the simulation is finished void LoadParameters(); ///< load fiberfox parameters void SaveParameters(); ///< save fiberfox parameters void BeforeThread(); void AfterThread(); void KillThread(); ///< abort simulation void UpdateSimulationStatus(); ///< print simulation progress and satus messages void OnDrawROI(); ///< adds new ROI, handles interactors etc. void OnAddBundle(); ///< adds new fiber bundle to datastorage void OnFlipButton(); ///< negate one coordinate of the fiber waypoints in the selcted planar figure. needed in case of unresolvable twists void GenerateFibers(); ///< generate fibers from the selected ROIs void GenerateImage(); ///< start image simulation void JoinBundles(); ///< merges selcted fiber bundles into one void CopyBundles(); ///< add copy of the selected bundle to the datamanager void ApplyTransform(); ///< rotate and shift selected bundles void AlignOnGrid(); ///< shift selected fiducials to nearest voxel center void Comp1ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 1 void Comp2ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 2 void Comp3ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 3 void Comp4ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 4 void ShowAdvancedOptions(int state); /** update fibers if any parameter changes */ void OnFiberDensityChanged(int value); void OnFiberSamplingChanged(double value); void OnTensionChanged(double value); void OnContinuityChanged(double value); void OnBiasChanged(double value); void OnVarianceChanged(double value); void OnDistributionChanged(int value); void OnConstantRadius(int value); /** update GUI elements */ void OnAddNoise(int value); void OnAddGhosts(int value); void OnAddDistortions(int value); void OnAddEddy(int value); void OnAddSpikes(int value); void OnAddAliasing(int value); void OnAddMotion(int value); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList&); GradientListType GenerateHalfShell(int NPoints); ///< generate vectors distributed over the halfsphere Ui::QmitkFiberfoxViewControls* m_Controls; void SimulateForExistingDwi(mitk::DataNode* imageNode); ///< add artifacts to existing diffusion weighted image void SimulateImageFromFibers(mitk::DataNode* fiberNode); ///< simulate new diffusion weighted image template< class ScalarType > FiberfoxParameters< ScalarType > UpdateImageParameters(); ///< update fiberfox paramater object (template parameter defines noise model type) void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection void PlanarFigureSelected( itk::Object* object, const itk::EventObject& ); void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts void NodeAdded( const mitk::DataNode* node ); ///< add observers void NodeRemoved(const mitk::DataNode* node); ///< remove observers /** structure to keep track of planar figures and observers */ struct QmitkPlanarFigureData { QmitkPlanarFigureData() : m_Figure(0) , m_EndPlacementObserverTag(0) , m_SelectObserverTag(0) , m_StartInteractionObserverTag(0) , m_EndInteractionObserverTag(0) , m_Flipped(0) { } mitk::PlanarFigure* m_Figure; unsigned int m_EndPlacementObserverTag; unsigned int m_SelectObserverTag; unsigned int m_StartInteractionObserverTag; unsigned int m_EndInteractionObserverTag; unsigned int m_Flipped; }; std::map m_DataNodeToPlanarFigureData; ///< map each planar figure uniquely to a QmitkPlanarFigureData mitk::DataNode::Pointer m_SelectedFiducial; ///< selected planar ellipse mitk::DataNode::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedDWI; vector< mitk::DataNode::Pointer > m_SelectedBundles; vector< mitk::DataNode::Pointer > m_SelectedBundles2; vector< mitk::DataNode::Pointer > m_SelectedFiducials; vector< mitk::DataNode::Pointer > m_SelectedImages; mitk::DataNode::Pointer m_MaskImageNode; - /** intra and inter axonal compartments */ - mitk::StickModel m_StickModel1; - mitk::StickModel m_StickModel2; - mitk::TensorModel m_ZeppelinModel1; - mitk::TensorModel m_ZeppelinModel2; - mitk::TensorModel m_TensorModel1; - mitk::TensorModel m_TensorModel2; - mitk::RawShModel m_PrototypeModel1; - - /** extra axonal compartment models */ - mitk::BallModel m_BallModel1; - mitk::BallModel m_BallModel2; - mitk::AstroStickModel m_AstrosticksModel1; - mitk::AstroStickModel m_AstrosticksModel2; - mitk::DotModel m_DotModel1; - mitk::DotModel m_DotModel2; - mitk::RawShModel m_PrototypeModel3; - mitk::RawShModel m_PrototypeModel4; - QString m_ParameterFile; ///< parameter file name // GUI thread QmitkFiberfoxWorker m_Worker; ///< runs filter QThread m_Thread; ///< worker thread bool m_ThreadIsRunning; QTimer* m_SimulationTimer; QTime m_SimulationTime; QString m_SimulationStatusText; /** Image filters that do all the simulations. */ itk::TractsToDWIImageFilter< short >::Pointer m_TractsToDwiFilter; itk::AddArtifactsToDwiImageFilter< short >::Pointer m_ArtifactsToDwiFilter; friend class QmitkFiberfoxWorker; };