diff --git a/CMakeExternals/MITKData.cmake b/CMakeExternals/MITKData.cmake index f1c7d4a47f..33c68acf2a 100644 --- a/CMakeExternals/MITKData.cmake +++ b/CMakeExternals/MITKData.cmake @@ -1,35 +1,35 @@ #----------------------------------------------------------------------------- # MITK Data #----------------------------------------------------------------------------- # Sanity checks if(DEFINED MITK_DATA_DIR AND NOT EXISTS ${MITK_DATA_DIR}) message(FATAL_ERROR "MITK_DATA_DIR variable is defined but corresponds to non-existing directory") endif() set(proj MITK-Data) set(proj_DEPENDENCIES) set(MITK-Data_DEPENDS ${proj}) if(BUILD_TESTING) - set(revision_tag 26c0ae6c) + set(revision_tag 3591d110) # ^^^^^^^^ these are just to check correct length of hash part ExternalProject_Add(${proj} URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/MITK-Data_${revision_tag}.tar.gz UPDATE_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS ${proj_DEPENDENCIES} ) set(MITK_DATA_DIR ${ep_source_dir}/${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif(BUILD_TESTING) diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp index 7c5682f898..980796961a 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp @@ -1,340 +1,349 @@ /*=================================================================== 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_NoiseModel(NULL) , m_FrequencyMap(NULL) , m_kOffset(0) , m_tLine(1) , m_EddyGradientStrength(0.0) , m_SimulateEddyCurrents(false) , m_TE(100) , m_AddGibbsRinging(false) , m_Spikes(0) , m_SpikeAmplitude(1) , m_Wrap(1.0) , 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 DiffusionImageType::Pointer inputImage = static_cast< DiffusionImageType * >( this->ProcessObject::GetInput(0) ); itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion(); typename itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage( inputImage ); duplicator->Update(); typename DiffusionImageType::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_AddGibbsRinging) { upsampledSliceRegion.SetSize(0, xMax*2); upsampledSliceRegion.SetSize(1, yMax*2); } // frequency map slice typename SliceType::Pointer fMap = NULL; if (m_FrequencyMap.IsNotNull()) { fMap = SliceType::New(); fMap->SetLargestPossibleRegion( sliceRegion ); fMap->SetBufferedRegion( sliceRegion ); fMap->SetRequestedRegion( sliceRegion ); fMap->Allocate(); fMap->FillBuffer(0.0); } if (m_Spikes>0 || m_FrequencyMap.IsNotNull() || m_kOffset>0.0 || m_AddGibbsRinging || m_SimulateEddyCurrents || m_Wrap<1.0) { ImageRegion<3> croppedRegion = inputRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Wrap); itk::Point shiftedOrigin = inputImage->GetOrigin(); shiftedOrigin[1] += (inputRegion.GetSize(1)-croppedRegion.GetSize(1))*inputImage->GetSpacing()[1]/2; outputImage = DiffusionImageType::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 DiffusionImageType::PixelType temp; temp.SetSize(inputImage->GetVectorLength()); temp.Fill(0.0); outputImage->FillBuffer(temp); int tempY=croppedRegion.GetSize(1); - if ( tempY%2 == 1 ) - tempY += 1; + tempY += tempY%2; croppedRegion.SetSize(1, tempY); MatrixType transform = inputImage->GetDirection(); for (int i=0; i<3; i++) for (int j=0; j<3; j++) - transform[i][j] *= inputImage->GetSpacing()[j]; + transform[i][j] *= inputImage->GetSpacing()[j]; m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; if (m_FrequencyMap.IsNotNull()) - m_StatusText += this->GetTime()+" > Simulating distortions\n"; + m_StatusText += "Simulating distortions\n"; if (m_AddGibbsRinging) - m_StatusText += this->GetTime()+" > Simulating ringing artifacts\n"; + m_StatusText += "Simulating ringing artifacts\n"; if (m_SimulateEddyCurrents) - m_StatusText += this->GetTime()+" > Simulating eddy currents\n"; + m_StatusText += "Simulating eddy currents\n"; if (m_Spikes>0) - m_StatusText += this->GetTime()+" > Simulating spikes\n"; + m_StatusText += "Simulating spikes\n"; if (m_Wrap<1.0) - m_StatusText += this->GetTime()+" > Simulating aliasing artifacts\n"; + m_StatusText += "Simulating aliasing artifacts\n"; if (m_kOffset>0) - m_StatusText += this->GetTime()+" > Simulating ghosts\n"; + m_StatusText += "Simulating ghosts\n"; std::vector< int > spikeVolume; for (int i=0; iGetIntegerVariate()%inputImage->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(inputImage->GetVectorLength()*inputRegion.GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< 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 (fMap.IsNotNull()) fMap->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D)); } if (m_AddGibbsRinging) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(slice); resampler->SetOutputParametersFromImage(slice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(slice->GetSpacing()/2); resampler->Update(); typename SliceType::Pointer upslice = resampler->GetOutput(); compartmentSlices.push_back(upslice); + + if (fMap.IsNotNull()) + { + itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); + resampler->SetInput(fMap); + resampler->SetOutputParametersFromImage(fMap); + resampler->SetSize(upsampledSliceRegion.GetSize()); + resampler->SetOutputSpacing(fMap->GetSpacing()/2); + resampler->Update(); + fMap = 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->SetCompartmentImages(compartmentSlices); idft->SetkOffset(m_kOffset); idft->SettLine(m_tLine); idft->SetSimulateRelaxation(false); idft->SetFrequencyMap(fMap); idft->SetDiffusionGradientDirection(m_GradientList.at(g)); idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents); idft->SetEddyGradientMagnitude(m_EddyGradientStrength); idft->SetTE(m_TE); idft->SetZ((double)z-(double)inputRegion.GetSize(2)/2.0); idft->SetDirectionMatrix(transform); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikes(numSpikes); idft->SetSpikeAmplitude(m_SpikeAmplitude); 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 DiffusionImageType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; typename DiffusionImageType::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_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 DiffusionImageType::PixelType signal = it1.Get(); 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 3247635b9a..12acaee9d2 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,985 +1,989 @@ /*=================================================================== 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 namespace itk { template< class PixelType > TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter() : m_CircleDummy(false) , m_VolumeAccuracy(10) , m_AddGibbsRinging(false) , m_NumberOfRepetitions(1) , m_EnforcePureFiberVoxels(false) , m_InterpolationShrink(1000) , m_FiberRadius(0) , m_SignalScale(25) , m_kOffset(0) , m_tLine(1) , m_UseInterpolation(false) , m_SimulateRelaxation(true) , m_tInhom(50) , m_TE(100) , m_FrequencyMap(NULL) , m_EddyGradientStrength(0.001) , m_SimulateEddyCurrents(false) , m_Spikes(0) , m_Wrap(1.0) , m_NoiseModel(NULL) , m_SpikeAmplitude(1) , m_AddMotionArtifact(false) , m_UseConstantRandSeed(false) { m_Spacing.Fill(2.5); m_Origin.Fill(0.0); m_DirectionMatrix.SetIdentity(); m_ImageRegion.SetSize(0, 10); m_ImageRegion.SetSize(1, 10); m_ImageRegion.SetSize(2, 10); m_MaxTranslation.Fill(0.0); m_MaxRotation.Fill(0.0); 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 ) { // 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_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_Spacing ); newImage->SetOrigin( m_Origin ); newImage->SetDirection( m_DirectionMatrix ); newImage->SetLargestPossibleRegion( m_ImageRegion ); newImage->SetBufferedRegion( m_ImageRegion ); newImage->SetRequestedRegion( m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); MatrixType transform = m_DirectionMatrix; for (int i=0; i<3; i++) for (int j=0; j<3; j++) { if (j<2) transform[i][j] *= m_UpsampledSpacing[j]; else transform[i][j] *= m_Spacing[j]; } std::vector< unsigned int > spikeVolume; for (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< 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_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_ImageRegion.GetSize(0)); outSize.SetElement(1, 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->SetkOffset(m_kOffset); idft->SettLine(m_tLine); idft->SetTE(m_TE); idft->SetTinhom(m_tInhom); idft->SetSimulateRelaxation(m_SimulateRelaxation); idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents); idft->SetEddyGradientMagnitude(m_EddyGradientStrength); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); idft->SetDirectionMatrix(transform); idft->SetDiffusionGradientDirection(m_FiberModels.at(0)->GetGradientDirection(g)); idft->SetFrequencyMap(fMapSlice); idft->SetSignalScale(m_SignalScale); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikes(numSpikes); idft->SetSpikeAmplitude(m_SpikeAmplitude); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (int 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 (int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; return newImage; } template< class PixelType > void TractsToDWIImageFilter< PixelType >::GenerateData() { m_StartTime = clock(); m_StatusText = "Starting simulation\n"; // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); int numFibers = m_FiberBundle->GetNumFibers(); if (numFibers<=0) itkExceptionMacro("Input fiber bundle contains no fibers!"); if (m_FiberModels.empty()) itkExceptionMacro("No diffusion model for fiber compartments defined!"); if (m_EnforcePureFiberVoxels) while (m_FiberModels.size()>1) m_FiberModels.pop_back(); if (m_NonFiberModels.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); int baselineIndex = m_FiberModels[0]->GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); 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_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Wrap); itk::Point shiftedOrigin = m_Origin; shiftedOrigin[1] += (m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Spacing[1]/2; typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Spacing ); outImage->SetOrigin( shiftedOrigin ); outImage->SetDirection( m_DirectionMatrix ); outImage->SetLargestPossibleRegion( croppedRegion ); outImage->SetBufferedRegion( croppedRegion ); outImage->SetRequestedRegion( croppedRegion ); outImage->SetVectorLength( m_FiberModels[0]->GetNumGradients() ); outImage->Allocate(); typename OutputImageType::PixelType temp; temp.SetSize(m_FiberModels[0]->GetNumGradients()); temp.Fill(0.0); outImage->FillBuffer(temp); // ADJUST GEOMETRY FOR FURTHER PROCESSING // is input slize size a power of two? unsigned int x=m_ImageRegion.GetSize(0); unsigned int y=m_ImageRegion.GetSize(1); ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0; m_ImageRegion.SetSize(0, x+pad[0]); m_ImageRegion.SetSize(1, y+pad[1]); if (m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_FrequencyMap); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_FrequencyMap = zeroPadder->GetOutput(); } if (m_TissueMask.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_TissueMask); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_TissueMask = zeroPadder->GetOutput(); } // apply in-plane upsampling double upsampling = 1; if (m_AddGibbsRinging) upsampling = 2; m_UpsampledSpacing = m_Spacing; m_UpsampledSpacing[0] /= upsampling; m_UpsampledSpacing[1] /= upsampling; m_UpsampledImageRegion = m_ImageRegion; m_UpsampledImageRegion.SetSize(0, m_ImageRegion.GetSize()[0]*upsampling); m_UpsampledImageRegion.SetSize(1, m_ImageRegion.GetSize()[1]*upsampling); m_UpsampledOrigin = m_Origin; m_UpsampledOrigin[0] -= m_Spacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; m_UpsampledOrigin[1] -= m_Spacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; m_UpsampledOrigin[2] -= m_Spacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; // generate double images to store the individual compartment signals std::vector< DoubleDwiType::Pointer > compartments; for (unsigned int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_UpsampledOrigin ); doubleDwi->SetDirection( m_DirectionMatrix ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); doubleDwi->SetVectorLength( m_FiberModels[0]->GetNumGradients() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; pix.SetSize(m_FiberModels[0]->GetNumGradients()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); compartments.push_back(doubleDwi); } // initialize volume fraction images m_VolumeFractions.clear(); for (unsigned int i=0; iSetSpacing( m_UpsampledSpacing ); doubleImg->SetOrigin( m_UpsampledOrigin ); doubleImg->SetDirection( m_DirectionMatrix ); doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleImg->SetBufferedRegion( m_UpsampledImageRegion ); doubleImg->SetRequestedRegion( m_UpsampledImageRegion ); doubleImg->Allocate(); doubleImg->FillBuffer(0); m_VolumeFractions.push_back(doubleImg); } // resample mask image and frequency map to fit upsampled geometry if (m_AddGibbsRinging) { if (m_TissueMask.IsNotNull()) { // rescale mask image (otherwise there are problems with the resampling) itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_TissueMask); 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_TissueMask); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); resampler->Update(); m_TissueMask = resampler->GetOutput(); } // resample frequency map if (m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(m_FrequencyMap); resampler->SetOutputParametersFromImage(m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); resampler->Update(); m_FrequencyMap = resampler->GetOutput(); } } // no input tissue mask is set -> create default bool maskImageSet = true; if (m_TissueMask.IsNull()) { m_StatusText += "No tissue mask set\n"; MITK_INFO << "No tissue mask set"; m_TissueMask = ItkUcharImgType::New(); m_TissueMask->SetSpacing( m_UpsampledSpacing ); m_TissueMask->SetOrigin( m_UpsampledOrigin ); m_TissueMask->SetDirection( m_DirectionMatrix ); m_TissueMask->SetLargestPossibleRegion( m_UpsampledImageRegion ); m_TissueMask->SetBufferedRegion( m_UpsampledImageRegion ); m_TissueMask->SetRequestedRegion( m_UpsampledImageRegion ); m_TissueMask->Allocate(); m_TissueMask->FillBuffer(1); maskImageSet = false; } else { m_StatusText += "Using tissue mask\n"; MITK_INFO << "Using tissue mask"; } m_ImageRegion = croppedRegion; x=m_ImageRegion.GetSize(0); y=m_ImageRegion.GetSize(1); if ( x%2 == 1 ) m_ImageRegion.SetSize(0, x+1); if ( y%2 == 1 ) 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(); fiberBundle->ResampleFibers(minSpacing/m_VolumeAccuracy); double mmRadius = m_FiberRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/m_VolumeAccuracy; double interpFact = 2*atan(-0.5*m_InterpolationShrink); double maxVolume = 0; double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; if (m_AddMotionArtifact) { if (m_RandomMotion) { m_StatusText += "Adding random motion artifacts:\n"; m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_MaxRotation) + "°\n"; m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_MaxTranslation) + "mm\n"; } else { m_StatusText += "Adding linear motion artifacts:\n"; m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_MaxRotation) + "°\n"; m_StatusText += "Maximum translation: " + boost::lexical_cast(m_MaxTranslation) + "mm\n"; } MITK_INFO << "Adding motion artifacts"; MITK_INFO << "Maximum rotation: " << m_MaxRotation; MITK_INFO << "Maxmimum translation: " << m_MaxTranslation; } maxVolume = 0; m_StatusText += "\n"+this->GetTime()+" > Generating signal of " + boost::lexical_cast(m_FiberModels.size()) + " fiber compartments\n"; MITK_INFO << "Generating signal of " << m_FiberModels.size() << " fiber compartments"; boost::progress_display disp(numFibers*m_FiberModels.at(0)->GetNumGradients()); ofstream logFile; logFile.open("fiberfox_motion.log"); logFile << "0 rotation: 0,0,0; translation: 0,0,0\n"; // get transform for motion artifacts FiberBundleType fiberBundleTransformed = fiberBundle; VectorType rotation = m_MaxRotation/m_FiberModels.at(0)->GetNumGradients(); VectorType translation = m_MaxTranslation/m_FiberModels.at(0)->GetNumGradients(); // creat image to hold transformed mask (motion artifact) ItkUcharImgType::Pointer tempTissueMask = ItkUcharImgType::New(); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_TissueMask); duplicator->Update(); tempTissueMask = duplicator->GetOutput(); // second upsampling needed for motion artifacts ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; itk::Vector 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; ItkUcharImgType::Pointer upsampledTissueMask = ItkUcharImgType::New(); itk::ResampleImageFilter::Pointer upsampler = itk::ResampleImageFilter::New(); upsampler->SetInput(m_TissueMask); upsampler->SetOutputParametersFromImage(m_TissueMask); upsampler->SetSize(upsampledImageRegion.GetSize()); upsampler->SetOutputSpacing(upsampledSpacing); upsampler->SetOutputOrigin(upsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); upsampler->SetInterpolator(nn_interpolator); upsampler->Update(); upsampledTissueMask = upsampler->GetOutput(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned int lastTick = 0; for (int g=0; gGetNumGradients(); g++) { vtkPolyData* fiberPolyData = fiberBundleTransformed->GetFiberPolyData(); ItkDoubleImgType::Pointer intraAxonalVolume = ItkDoubleImgType::New(); intraAxonalVolume->SetSpacing( m_UpsampledSpacing ); intraAxonalVolume->SetOrigin( m_UpsampledOrigin ); intraAxonalVolume->SetDirection( m_DirectionMatrix ); intraAxonalVolume->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolume->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolume->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolume->Allocate(); intraAxonalVolume->FillBuffer(0); // generate fiber signal 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; tempTissueMask->TransformPhysicalPointToIndex(vertex, idx); tempTissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!m_UseInterpolation) // use nearest neighbour interpolation { if (!tempTissueMask->GetLargestPossibleRegion().IsInside(idx) || tempTissueMask->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment for (unsigned int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(idx); pix[g] += segmentVolume*m_FiberModels[k]->SimulateMeasurement(g); doubleDwi->SetPixel(idx, pix ); double vol = intraAxonalVolume->GetPixel(idx) + segmentVolume; intraAxonalVolume->SetPixel(idx, vol ); if (g==0 && vol>maxVolume) maxVolume = vol; } continue; } double frac_x = contIndex[0] - idx[0]; double frac_y = contIndex[1] - idx[1]; double frac_z = contIndex[2] - idx[2]; if (frac_x<0) { idx[0] -= 1; frac_x += 1; } if (frac_y<0) { idx[1] -= 1; frac_y += 1; } if (frac_z<0) { idx[2] -= 1; frac_z += 1; } frac_x = atan((0.5-frac_x)*m_InterpolationShrink)/interpFact + 0.5; frac_y = atan((0.5-frac_y)*m_InterpolationShrink)/interpFact + 0.5; frac_z = atan((0.5-frac_z)*m_InterpolationShrink)/interpFact + 0.5; // use trilinear interpolation itk::Index<3> newIdx; for (int x=0; x<2; x++) { frac_x = 1-frac_x; for (int y=0; y<2; y++) { frac_y = 1-frac_y; for (int z=0; z<2; z++) { frac_z = 1-frac_z; newIdx[0] = idx[0]+x; newIdx[1] = idx[1]+y; newIdx[2] = idx[2]+z; double frac = frac_x*frac_y*frac_z; // is position valid? if (!tempTissueMask->GetLargestPossibleRegion().IsInside(newIdx) || tempTissueMask->GetPixel(newIdx)<=0) continue; // generate signal for each fiber compartment for (unsigned int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(newIdx); pix[g] += segmentVolume*frac*m_FiberModels[k]->SimulateMeasurement(g); doubleDwi->SetPixel(newIdx, pix ); double vol = intraAxonalVolume->GetPixel(idx) + segmentVolume; intraAxonalVolume->SetPixel(idx, vol ); if (g==0 && vol>maxVolume) maxVolume = vol; } } } } } ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } // generate non-fiber signal ImageRegionIterator it3(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); double fact = 1; if (m_FiberRadius<0.0001) fact = voxelVolume/maxVolume; while(!it3.IsAtEnd()) { if (it3.Get()>0) { DoubleDwiType::IndexType index = it3.GetIndex(); // get fiber volume fraction DoubleDwiType::Pointer fiberDwi = compartments.at(0); DoubleDwiType::PixelType fiberPix = fiberDwi->GetPixel(index); // intra axonal compartment if (fact>1) // auto scale intra-axonal if no fiber radius is specified { fiberPix[g] *= fact; fiberDwi->SetPixel(index, fiberPix); } double f = intraAxonalVolume->GetPixel(index)*fact; if (f>voxelVolume || (f>0.0 && m_EnforcePureFiberVoxels) ) // more fiber than space in voxel? { fiberPix[g] *= voxelVolume/f; fiberDwi->SetPixel(index, fiberPix); m_VolumeFractions.at(0)->SetPixel(index, 1); } else { m_VolumeFractions.at(0)->SetPixel(index, f/voxelVolume); double nonf = voxelVolume-f; // non-fiber volume double inter = 0; if (m_FiberModels.size()>1) inter = nonf * f/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f double other = nonf - inter; // rest of compartment double singleinter = inter/(m_FiberModels.size()-1); // adjust non-fiber and intra-axonal signal for (unsigned int i=1; iGetPixel(index); if (f>0) pix[g] /= f; pix[g] *= singleinter; doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume); } for (unsigned int i=0; iGetPixel(index); // if (dynamic_cast< mitk::AstroStickModel* >(m_NonFiberModels.at(i))) // { // mitk::AstroStickModel* model = dynamic_cast< mitk::AstroStickModel* >(m_NonFiberModels.at(i)); // model->SetSeed(8111984); // } pix[g] += m_NonFiberModels[i]->SimulateMeasurement(g)*other*m_NonFiberModels[i]->GetWeight(); doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(i+m_FiberModels.size())->SetPixel(index, other/voxelVolume*m_NonFiberModels[i]->GetWeight()); } } } ++it3; } // move fibers if (m_AddMotionArtifact) { if (m_RandomMotion) { fiberBundleTransformed = fiberBundle->GetDeepCopy(); rotation[0] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[0]*2)-m_MaxRotation[0]; rotation[1] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[1]*2)-m_MaxRotation[1]; rotation[2] = m_RandGen->GetVariateWithClosedRange(m_MaxRotation[2]*2)-m_MaxRotation[2]; translation[0] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[0]*2)-m_MaxTranslation[0]; translation[1] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[1]*2)-m_MaxTranslation[1]; translation[2] = m_RandGen->GetVariateWithClosedRange(m_MaxTranslation[2]*2)-m_MaxTranslation[2]; } // rotate mask image if (maskImageSet) { ImageRegionIterator maskIt(upsampledTissueMask, upsampledTissueMask->GetLargestPossibleRegion()); tempTissueMask->FillBuffer(0); while(!maskIt.IsAtEnd()) { if (maskIt.Get()<=0) { ++maskIt; continue; } DoubleDwiType::IndexType index = maskIt.GetIndex(); itk::Point point; upsampledTissueMask->TransformIndexToPhysicalPoint(index, point); if (m_RandomMotion) point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); else point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0]*(g+1),rotation[1]*(g+1),rotation[2]*(g+1),translation[0]*(g+1),translation[1]*(g+1),translation[2]*(g+1)); tempTissueMask->TransformPhysicalPointToIndex(point, index); if (tempTissueMask->GetLargestPossibleRegion().IsInside(index)) tempTissueMask->SetPixel(index,100); ++maskIt; } } // rotate fibers logFile << g+1 << " rotation:" << rotation[0] << "," << rotation[1] << "," << rotation[2] << ";"; logFile << " translation:" << translation[0] << "," << translation[1] << "," << translation[2] << "\n"; fiberBundleTransformed->TransformFibers(rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); } } logFile.close(); m_StatusText += "\n\n"; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } // do k-space stuff DoubleDwiType::Pointer doubleOutImage; if (m_Spikes>0 || m_FrequencyMap.IsNotNull() || m_kOffset>0 || m_SimulateRelaxation || m_SimulateEddyCurrents || m_AddGibbsRinging || m_Wrap<1.0) { m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; MITK_INFO << "Adjusting complex signal:"; if (m_SimulateRelaxation) - m_StatusText += " > Simulating signal relaxation\n"; + m_StatusText += "Simulating signal relaxation\n"; if (m_FrequencyMap.IsNotNull()) - m_StatusText += " > Simulating distortions\n"; + m_StatusText += "Simulating distortions\n"; if (m_AddGibbsRinging) - m_StatusText += " > Simulating ringing artifacts\n"; + m_StatusText += "Simulating ringing artifacts\n"; if (m_SimulateEddyCurrents) - m_StatusText += " > Simulating eddy currents\n"; + m_StatusText += "Simulating eddy currents\n"; if (m_Spikes>0) - m_StatusText += " > Simulating spikes\n"; + m_StatusText += "Simulating spikes\n"; if (m_Wrap<1.0) - m_StatusText += " > Simulating aliasing artifacts\n"; + m_StatusText += "Simulating aliasing artifacts\n"; if (m_kOffset>0) - m_StatusText += " > Simulating ghosts\n"; + m_StatusText += "Simulating ghosts\n"; doubleOutImage = DoKspaceStuff(compartments); m_SignalScale = 1; } else { m_StatusText += this->GetTime()+" > Summing compartments\n"; MITK_INFO << "Summing compartments"; doubleOutImage = compartments.at(0); for (unsigned int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); adder->SetInput2(compartments.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_SignalScale>1) + m_StatusText += " Scaling signal\n"; + if (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_FiberModels[0]->GetNumGradients()); 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 (int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename OutputImageType::IndexType index = it4.GetIndex(); signal = doubleOutImage->GetPixel(index)*m_SignalScale; if (m_NoiseModel!=NULL) { DoubleDwiType::PixelType accu = signal; accu.Fill(0.0); for (unsigned int i=0; iAddNoise(temp); accu += temp; } signal = accu/m_NumberOfRepetitions; } for (unsigned int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]>window) window = signal[i]; if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]SetNthOutput(0, outImage); m_StatusText += "\n\n"; m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); } 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 > std::string TractsToDWIImageFilter< PixelType >::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; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt index f1e0030d09..749ee7b7ac 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt @@ -1,12 +1,12 @@ MITK_CREATE_MODULE_TESTS() mitkAddCustomModuleTest(mitkFiberBundleXReaderWriterTest mitkFiberBundleXReaderWriterTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib) mitkAddCustomModuleTest(mitkGibbsTrackingTest mitkGibbsTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage.qbi ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/gibbsTrackingParameters.gtp ${MITK_DATA_DIR}/DiffusionImaging/gibbsTractogram.fib) mitkAddCustomModuleTest(mitkStreamlineTrackingTest mitkStreamlineTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/tensorImage.dti ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/streamlineTractogramInterpolated.fib) #mitkAddCustomModuleTest(mitkPeakExtractionTest mitkPeakExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_SHCoeffs.nrrd ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_VectorField.fib) mitkAddCustomModuleTest(mitkLocalFiberPlausibilityTest mitkLocalFiberPlausibilityTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_0.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_1.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_NUM_DIRECTIONS.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_VECTOR_FIELD.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE_IGNORE.nrrd) mitkAddCustomModuleTest(mitkFiberTransformationTest mitkFiberTransformationTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_transformed.fib) mitkAddCustomModuleTest(mitkFiberExtractionTest mitkFiberExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_extracted.fib ${MITK_DATA_DIR}/DiffusionImaging/ROI1.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI2.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI3.pf ${MITK_DATA_DIR}/DiffusionImaging/ROIIMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_inside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_outside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_passing-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_ending-in-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_subtracted.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_added.fib) mitkAddCustomModuleTest(mitkFiberGenerationTest mitkFiberGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_0.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_1.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_2.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/uniform.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib) -#mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationTest mitkFiberfoxSignalGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickAstrosticks_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickDot_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/TensorBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickTensorBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickTensorBallAstrosticks_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gibbsringing.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/ghost.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/aliasing.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/eddy.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/linearmotion.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/randommotion.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/spikes.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/riciannoise.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/chisquarenoise.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/distortions.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fieldmap.nrrd) -#mitkAddCustomModuleTest(mitkFiberfoxAddArtifactsToDwiTest mitkFiberfoxAddArtifactsToDwiTest) +mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationTest mitkFiberfoxSignalGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickAstrosticks_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickDot_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/TensorBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickTensorBall_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/StickTensorBallAstrosticks_RELAX.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gibbsringing.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/ghost.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/aliasing.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/eddy.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/linearmotion.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/randommotion.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/spikes.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/riciannoise.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/chisquarenoise.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/distortions.dwi ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fieldmap.nrrd) +mitkAddCustomModuleTest(mitkFiberfoxAddArtifactsToDwiTest mitkFiberfoxAddArtifactsToDwiTest) diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp index efbe9fd0fd..b0afe6cc25 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp @@ -1,215 +1,216 @@ /*=================================================================== 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 #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: - vector< string > m_Files; mitk::DiffusionImage::Pointer m_InputDwi; FiberfoxParameters m_Parameters; - mitk::RicianNoiseModel* m_RicianNoiseModel; - mitk::ChiSquareNoiseModel* m_ChiSquareNoiseModel; public: void setUp() { RegisterDiffusionCoreObjectFactory(); // reference files - m_Files.push_back( GetTestDataFilePath("DiffusionImaging/Fiberfox/StickBall_RELAX.dwi") ); - m_Files.push_back( GetTestDataFilePath("DiffusionImaging/Fiberfox/spikes2.dwi") ); - m_Files.push_back( GetTestDataFilePath("DiffusionImaging/Fiberfox/gibbsringing.dwi") ); - - m_InputDwi = dynamic_cast*>(mitk::IOUtil::LoadDataNode(m_Files.at(0))->GetData()); + m_InputDwi = dynamic_cast*>(mitk::IOUtil::LoadDataNode(GetTestDataFilePath("DiffusionImaging/Fiberfox/StickBall_RELAX.dwi"))->GetData()); // parameter setup + m_Parameters = FiberfoxParameters(); m_Parameters.m_ImageRegion = m_InputDwi->GetVectorImage()->GetLargestPossibleRegion(); m_Parameters.m_ImageSpacing = m_InputDwi->GetVectorImage()->GetSpacing(); m_Parameters.m_ImageOrigin = m_InputDwi->GetVectorImage()->GetOrigin(); m_Parameters.m_ImageDirection = m_InputDwi->GetVectorImage()->GetDirection(); m_Parameters.m_Bvalue = m_InputDwi->GetB_Value(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = m_InputDwi->GetDirections(); m_Parameters.m_NumGradients = 0; for (unsigned int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; m_Parameters.m_GradientDirections.push_back(g); if (dirs->at(i).magnitude()>0.0001) m_Parameters.m_NumGradients++; } - - // noise models - m_RicianNoiseModel = new mitk::RicianNoiseModel(); - m_RicianNoiseModel->SetNoiseVariance(1000000); - m_RicianNoiseModel->SetSeed(0); - - // Rician noise - m_ChiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); - m_ChiSquareNoiseModel->SetDOF(500000); - m_ChiSquareNoiseModel->SetSeed(0); } 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->SettLine(m_Parameters.m_tLine); artifactsToDwiFilter->SetkOffset(m_Parameters.m_KspaceLineOffset); artifactsToDwiFilter->SetNoiseModel(m_Parameters.m_NoiseModelShort); artifactsToDwiFilter->SetGradientList(m_Parameters.m_GradientDirections); artifactsToDwiFilter->SetTE(m_Parameters.m_tEcho); artifactsToDwiFilter->SetSimulateEddyCurrents(m_Parameters.m_DoSimulateEddyCurrents); artifactsToDwiFilter->SetEddyGradientStrength(m_Parameters.m_EddyStrength); artifactsToDwiFilter->SetAddGibbsRinging(m_Parameters.m_AddGibbsRinging); artifactsToDwiFilter->SetFrequencyMap(m_Parameters.m_FrequencyMap); artifactsToDwiFilter->SetSpikeAmplitude(m_Parameters.m_SpikeAmplitude); artifactsToDwiFilter->SetSpikes(m_Parameters.m_Spikes); artifactsToDwiFilter->SetWrap(m_Parameters.m_Wrap); - artifactsToDwiFilter->Update(); + CPPUNIT_ASSERT_NO_THROW(artifactsToDwiFilter->Update()); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( artifactsToDwiFilter->GetOutput() ); testImage->SetB_Value(m_Parameters.m_Bvalue); testImage->SetDirections(m_Parameters.m_GradientDirections); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { CPPUNIT_ASSERT_MESSAGE(testFileName, CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage())); } else { - MITK_INFO << "Saving test image to " << testFileName; NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); - writer->SetFileName(testFileName); + writer->SetFileName("/local/distortions2.dwi"); writer->SetInput(testImage); writer->Update(); } } void Spikes() { m_Parameters.m_Spikes = 5; m_Parameters.m_SpikeAmplitude = 1; - StartSimulation(m_Files.at(1)); - m_Parameters.m_Spikes = 0; + StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/spikes2.dwi") ); } void GibbsRinging() { - // Gibbs ringing m_Parameters.m_AddGibbsRinging = true; - StartSimulation(m_Files.at(2)); - m_Parameters.m_AddGibbsRinging = false; - - // // Ghost - // parameters.m_AddGibbsRinging = false; - // parameters.m_KspaceLineOffset = 0.25; - // StartSimulation(parameters, fiberBundle, ghost, argv[9]); - - // // Aliasing - // parameters.m_KspaceLineOffset = 0; - // parameters.m_Wrap = 0.4; - // parameters.m_SignalScale = 1000; - // StartSimulation(parameters, fiberBundle, aliasing, argv[10]); - - // // Eddy currents - // parameters.m_Wrap = 1; - // parameters.m_SignalScale = 10000; - // parameters.m_DoSimulateEddyCurrents = true; - // parameters.m_EddyStrength = 0.05; - // StartSimulation(parameters, fiberBundle, eddy, argv[11]); - - // // Rician noise - // parameters.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_FrequencyMap = fMap; - // StartSimulation(parameters, fiberBundle, distortions, argv[17]); + StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/gibbsringing2.dwi") ); + } + + void Ghost() + { + m_Parameters.m_KspaceLineOffset = 0.25; + StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/ghost2.dwi") ); + } + + void Aliasing() + { + m_Parameters.m_Wrap = 0.4; + StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/aliasing2.dwi") ); + } + + void Eddy() + { + m_Parameters.m_DoSimulateEddyCurrents = true; + m_Parameters.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->SetDOF(500000); + 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_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 68305c8537..a6628b1bf8 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp @@ -1,327 +1,325 @@ /*=================================================================== 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 #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->SetSimulateEddyCurrents(parameters.m_DoSimulateEddyCurrents); tractsToDwiFilter->SetEddyGradientStrength(parameters.m_EddyStrength); tractsToDwiFilter->SetAddGibbsRinging(parameters.m_AddGibbsRinging); tractsToDwiFilter->SetSimulateRelaxation(parameters.m_DoSimulateRelaxation); tractsToDwiFilter->SetImageRegion(parameters.m_ImageRegion); tractsToDwiFilter->SetSpacing(parameters.m_ImageSpacing); tractsToDwiFilter->SetOrigin(parameters.m_ImageOrigin); tractsToDwiFilter->SetDirectionMatrix(parameters.m_ImageDirection); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->SetFiberModels(parameters.m_FiberModelList); tractsToDwiFilter->SetNonFiberModels(parameters.m_NonFiberModelList); tractsToDwiFilter->SetNoiseModel(parameters.m_NoiseModel); tractsToDwiFilter->SetkOffset(parameters.m_KspaceLineOffset); tractsToDwiFilter->SettLine(parameters.m_tLine); tractsToDwiFilter->SettInhom(parameters.m_tInhom); tractsToDwiFilter->SetTE(parameters.m_tEcho); tractsToDwiFilter->SetNumberOfRepetitions(parameters.m_Repetitions); tractsToDwiFilter->SetEnforcePureFiberVoxels(parameters.m_DoDisablePartialVolume); tractsToDwiFilter->SetInterpolationShrink(parameters.m_InterpolationShrink); tractsToDwiFilter->SetFiberRadius(parameters.m_AxonRadius); tractsToDwiFilter->SetSignalScale(parameters.m_SignalScale); if (parameters.m_InterpolationShrink>0) tractsToDwiFilter->SetUseInterpolation(true); tractsToDwiFilter->SetTissueMask(parameters.m_MaskImage); tractsToDwiFilter->SetFrequencyMap(parameters.m_FrequencyMap); tractsToDwiFilter->SetSpikeAmplitude(parameters.m_SpikeAmplitude); tractsToDwiFilter->SetSpikes(parameters.m_Spikes); tractsToDwiFilter->SetWrap(parameters.m_Wrap); tractsToDwiFilter->SetAddMotionArtifact(parameters.m_DoAddMotion); tractsToDwiFilter->SetMaxTranslation(parameters.m_Translation); tractsToDwiFilter->SetMaxRotation(parameters.m_Rotation); tractsToDwiFilter->SetRandomMotion(parameters.m_RandomMotion); tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( tractsToDwiFilter->GetOutput() ); testImage->SetB_Value(parameters.m_Bvalue); testImage->SetDirections(parameters.m_GradientDirections); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { MITK_TEST_CONDITION_REQUIRED(CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()), message); } else { MITK_INFO << "Saving test image to " << message; NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(message); writer->SetInput(testImage); writer->Update(); } } int mitkFiberfoxSignalGenerationTest(int argc, char* argv[]) { RegisterDiffusionCoreObjectFactory(); 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_DoSimulateRelaxation = true; parameters.m_SignalScale = 10000; parameters.m_ImageRegion = stickBall->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_ImageSpacing = stickBall->GetVectorImage()->GetSpacing(); parameters.m_ImageOrigin = stickBall->GetVectorImage()->GetOrigin(); parameters.m_ImageDirection = stickBall->GetVectorImage()->GetDirection(); parameters.m_Bvalue = stickBall->GetB_Value(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = stickBall->GetDirections(); parameters.m_NumGradients = 0; for (unsigned int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; parameters.m_GradientDirections.push_back(g); if (dirs->at(i).magnitude()>0.0001) parameters.m_NumGradients++; } // intra and inter axonal compartments mitk::StickModel stickModel; stickModel.SetBvalue(parameters.m_Bvalue); stickModel.SetT2(110); stickModel.SetDiffusivity(0.001); stickModel.SetGradientList(parameters.m_GradientDirections); mitk::TensorModel tensorModel; tensorModel.SetT2(110); stickModel.SetBvalue(parameters.m_Bvalue); tensorModel.SetDiffusivity1(0.001); tensorModel.SetDiffusivity2(0.00025); tensorModel.SetDiffusivity3(0.00025); tensorModel.SetGradientList(parameters.m_GradientDirections); // extra axonal compartment models mitk::BallModel ballModel; ballModel.SetT2(80); ballModel.SetBvalue(parameters.m_Bvalue); ballModel.SetDiffusivity(0.001); ballModel.SetGradientList(parameters.m_GradientDirections); mitk::AstroStickModel astrosticksModel; astrosticksModel.SetT2(80); astrosticksModel.SetBvalue(parameters.m_Bvalue); astrosticksModel.SetDiffusivity(0.001); astrosticksModel.SetRandomizeSticks(true); astrosticksModel.SetSeed(0); astrosticksModel.SetGradientList(parameters.m_GradientDirections); mitk::DotModel dotModel; dotModel.SetT2(80); dotModel.SetGradientList(parameters.m_GradientDirections); // noise models mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); // Rician noise mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetDOF(500000); 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_AddGibbsRinging = true; StartSimulation(parameters, fiberBundle, gibbsringing, argv[8]); // Ghost parameters.m_AddGibbsRinging = false; parameters.m_KspaceLineOffset = 0.25; StartSimulation(parameters, fiberBundle, ghost, argv[9]); // Aliasing parameters.m_KspaceLineOffset = 0; parameters.m_Wrap = 0.4; parameters.m_SignalScale = 1000; StartSimulation(parameters, fiberBundle, aliasing, argv[10]); // Eddy currents parameters.m_Wrap = 1; parameters.m_SignalScale = 10000; parameters.m_DoSimulateEddyCurrents = true; parameters.m_EddyStrength = 0.05; StartSimulation(parameters, fiberBundle, eddy, argv[11]); // Motion (linear) parameters.m_DoSimulateEddyCurrents = false; parameters.m_EddyStrength = 0.0; parameters.m_DoAddMotion = true; parameters.m_RandomMotion = false; parameters.m_Translation[1] = 10; parameters.m_Rotation[2] = 90; StartSimulation(parameters, fiberBundle, linearmotion, argv[12]); // Motion (random) parameters.m_RandomMotion = true; parameters.m_Translation[1] = 5; parameters.m_Rotation[2] = 45; StartSimulation(parameters, fiberBundle, randommotion, argv[13]); // Spikes parameters.m_DoAddMotion = false; parameters.m_Spikes = 5; parameters.m_SpikeAmplitude = 1; StartSimulation(parameters, fiberBundle, spikes, argv[14]); // Rician noise parameters.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_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/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp index ae209c2ac3..ddffd87b70 100755 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp @@ -1,142 +1,142 @@ /*=================================================================== 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 using namespace std; int mitkStreamlineTrackingTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkStreamlineTrackingTest"); MITK_TEST_CONDITION_REQUIRED(argc>3,"check for input data") string dtiFileName = argv[1]; string maskFileName = argv[2]; string referenceFileName = argv[3]; MITK_INFO << "DTI file: " << dtiFileName; MITK_INFO << "Mask file: " << maskFileName; MITK_INFO << "Reference fiber file: " << referenceFileName; float minFA = 0.05; float minCurv = -1; float stepSize = -1; float tendf = 1; float tendg = 0; float minLength = 20; int numSeeds = 1; bool interpolate = true; try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); // load input image const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( dtiFileName, s1, s2, false ); MITK_INFO << "Loading tensor image ..."; typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(mitkTensorImage, itk_dti); MITK_INFO << "Loading seed image ..."; typedef itk::Image< unsigned char, 3 > ItkUCharImageType; mitk::Image::Pointer mitkSeedImage = mitk::IOUtil::LoadImage(maskFileName); MITK_INFO << "Loading mask image ..."; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(maskFileName); // instantiate tracker typedef itk::StreamlineTrackingFilter< float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(itk_dti); filter->SetSeedsPerVoxel(numSeeds); filter->SetFaThreshold(minFA); filter->SetMinCurvatureRadius(minCurv); filter->SetStepSize(stepSize); filter->SetF(tendf); filter->SetG(tendg); filter->SetInterpolate(interpolate); filter->SetMinTractLength(minLength); filter->SetNumberOfThreads(1); if (mitkSeedImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(mitkSeedImage, mask); filter->SetSeedImage(mask); } if (mitkMaskImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(mitkMaskImage, mask); filter->SetMaskImage(mask); } filter->Update(); vtkSmartPointer fiberBundle = filter->GetFiberPolyData(); mitk::FiberBundleX::Pointer fib1 = mitk::FiberBundleX::New(fiberBundle); infile = mitk::BaseDataIO::LoadBaseDataFromFile( referenceFileName, s1, s2, false ); mitk::FiberBundleX::Pointer fib2 = dynamic_cast(infile.at(0).GetPointer()); MITK_TEST_CONDITION_REQUIRED(fib2.IsNotNull(), "Check if reference tractogram is not null."); if (!fib1->Equals(fib2)) { - MITK_INFO << "TEST FAILED. TRACTOGRAMS ARE NOT EQUAL!"; + MITK_WARN << "TEST FAILED. TRACTOGRAMS ARE NOT EQUAL!"; mitk::FiberBundleXWriter::Pointer writer = mitk::FiberBundleXWriter::New(); - writer->SetFileName("/tmp/testBundle.fib"); + writer->SetFileName("testBundle.fib"); writer->SetInputFiberBundleX(fib1); writer->Update(); - writer->SetFileName("/tmp/refBundle.fib"); + writer->SetFileName("refBundle.fib"); writer->SetInputFiberBundleX(fib2); writer->Update(); } //MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2), "Check if tractograms are equal."); } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } 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 d2bd4f1d1f..ce5da412c9 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2331 +1,2343 @@ /*=================================================================== 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 #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_OutputPath("") , 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); } 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; } } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_ImageGenParametersBackup = m_ImageGenParameters; 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_GenerateImageButton->setVisible(true); //m_Controls->m_SimulationStatusText->setVisible(false); m_ThreadIsRunning = false; mitk::DiffusionImage::Pointer mitkImage = mitk::DiffusionImage::New(); switch (m_Worker.m_FilterType) { case 0: { if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } mitkImage->SetVectorImage( m_TractsToDwiFilter->GetOutput() ); mitkImage->SetB_Value(m_ImageGenParametersBackup.m_Bvalue); mitkImage->SetDirections(m_ImageGenParametersBackup.m_GradientDirections); mitkImage->InitializeFromVectorImage(); m_ImageGenParametersBackup.m_ResultNode->SetData( mitkImage ); m_ImageGenParametersBackup.m_ResultNode->SetName(m_ImageGenParametersBackup.m_ParentNode->GetName() +"_D"+QString::number(m_ImageGenParametersBackup.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(m_ImageGenParametersBackup.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(m_ImageGenParametersBackup.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(m_ImageGenParametersBackup.m_ImageSpacing[0]).toStdString() +"-"+QString::number(m_ImageGenParametersBackup.m_ImageSpacing[1]).toStdString() +"-"+QString::number(m_ImageGenParametersBackup.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(m_ImageGenParametersBackup.m_Bvalue).toStdString() +"_"+m_ImageGenParametersBackup.m_SignalModelString +m_ImageGenParametersBackup.m_ArtifactModelString); GetDataStorage()->Add(m_ImageGenParametersBackup.m_ResultNode, m_ImageGenParametersBackup.m_ParentNode); m_ImageGenParametersBackup.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 (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(m_ImageGenParametersBackup.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, m_ImageGenParametersBackup.m_ParentNode); } } break; } case 1: { if (m_ArtifactsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_ImageGenParametersBackup.m_ParentNode->GetData()); mitkImage = mitk::DiffusionImage::New(); mitkImage->SetVectorImage( m_ArtifactsToDwiFilter->GetOutput() ); mitkImage->SetB_Value(diffImg->GetB_Value()); mitkImage->SetDirections(diffImg->GetDirections()); mitkImage->InitializeFromVectorImage(); m_ImageGenParametersBackup.m_ResultNode->SetData( mitkImage ); m_ImageGenParametersBackup.m_ResultNode->SetName(m_ImageGenParametersBackup.m_ParentNode->GetName()+m_ImageGenParameters.m_ArtifactModelString); GetDataStorage()->Add(m_ImageGenParametersBackup.m_ResultNode, m_ImageGenParametersBackup.m_ParentNode); break; } } mitk::BaseData::Pointer basedata = m_ImageGenParametersBackup.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!m_ImageGenParametersBackup.m_OutputPath.empty()) { try{ QString status("Saving output image to "); status += QString(m_ImageGenParametersBackup.m_OutputPath.c_str()); status += m_ImageGenParametersBackup.m_ResultNode->GetName().c_str(); status += ".dwi"; m_Controls->m_SimulationStatusText->append(status); mitk::NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(m_ImageGenParametersBackup.m_OutputPath+m_ImageGenParametersBackup.m_ResultNode->GetName()+".dwi"); writer->SetInput(mitkImage); writer->Update(); 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!"); } } m_ImageGenParameters.m_FrequencyMap = NULL; m_ImageGenParametersBackup.m_FrequencyMap = NULL; m_TractsToDwiFilter = 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); } } // 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_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); 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())); } } void QmitkFiberfoxView::UpdateImageParameters() { m_ImageGenParameters.m_NonFiberModelList.clear(); m_ImageGenParameters.m_FiberModelList.clear(); m_ImageGenParameters.m_SignalModelString = ""; m_ImageGenParameters.m_ArtifactModelString = ""; m_ImageGenParameters.m_ResultNode = mitk::DataNode::New(); m_ImageGenParameters.m_FrequencyMap = NULL; m_ImageGenParameters.m_GradientDirections.clear(); m_ImageGenParameters.m_Spikes = 0; m_ImageGenParameters.m_SpikeAmplitude = 1; m_ImageGenParameters.m_Wrap = 1; m_ImageGenParameters.m_OutputPath = m_OutputPath; if (m_SelectedDWI.IsNotNull()) // use parameters of selected DWI { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); m_ImageGenParameters.m_ImageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); m_ImageGenParameters.m_ImageSpacing = dwi->GetVectorImage()->GetSpacing(); m_ImageGenParameters.m_ImageOrigin = dwi->GetVectorImage()->GetOrigin(); m_ImageGenParameters.m_ImageDirection = dwi->GetVectorImage()->GetDirection(); m_ImageGenParameters.m_Bvalue = dwi->GetB_Value(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections(); m_ImageGenParameters.m_NumGradients = 0; for (int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; m_ImageGenParameters.m_GradientDirections.push_back(g); if (dirs->at(i).magnitude()>0.0001) m_ImageGenParameters.m_NumGradients++; } } 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); m_ImageGenParameters.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_ImageGenParameters.m_ImageSpacing = itkImg->GetSpacing(); m_ImageGenParameters.m_ImageOrigin = itkImg->GetOrigin(); m_ImageGenParameters.m_ImageDirection = itkImg->GetDirection(); m_ImageGenParameters.m_NumGradients = m_Controls->m_NumGradientsBox->value(); m_ImageGenParameters.m_GradientDirections = GenerateHalfShell(m_Controls->m_NumGradientsBox->value()); m_ImageGenParameters.m_Bvalue = m_Controls->m_BvalueBox->value(); } else // use GUI parameters { m_ImageGenParameters.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); m_ImageGenParameters.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); m_ImageGenParameters.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); m_ImageGenParameters.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); m_ImageGenParameters.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); m_ImageGenParameters.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); m_ImageGenParameters.m_ImageOrigin[0] = m_ImageGenParameters.m_ImageSpacing[0]/2; m_ImageGenParameters.m_ImageOrigin[1] = m_ImageGenParameters.m_ImageSpacing[1]/2; m_ImageGenParameters.m_ImageOrigin[2] = m_ImageGenParameters.m_ImageSpacing[2]/2; m_ImageGenParameters.m_ImageDirection.SetIdentity(); m_ImageGenParameters.m_NumGradients = m_Controls->m_NumGradientsBox->value(); m_ImageGenParameters.m_GradientDirections = GenerateHalfShell(m_Controls->m_NumGradientsBox->value());; m_ImageGenParameters.m_Bvalue = m_Controls->m_BvalueBox->value(); } // signal relaxation m_ImageGenParameters.m_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); if (m_ImageGenParameters.m_DoSimulateRelaxation && m_SelectedBundles.size()>0 ) m_ImageGenParameters.m_ArtifactModelString += "_RELAX"; // N/2 ghosts if (m_Controls->m_AddGhosts->isChecked()) { m_ImageGenParameters.m_ArtifactModelString += "_GHOST"; m_ImageGenParameters.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(m_ImageGenParameters.m_KspaceLineOffset)); } else m_ImageGenParameters.m_KspaceLineOffset = 0; // Aliasing if (m_Controls->m_AddAliasing->isChecked()) { m_ImageGenParameters.m_ArtifactModelString += "_ALIASING"; m_ImageGenParameters.m_Wrap = (100-m_Controls->m_WrapBox->value())/100; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Motion m_ImageGenParameters.m_DoAddMotion = m_Controls->m_AddMotion->isChecked(); m_ImageGenParameters.m_RandomMotion = m_Controls->m_RandomMotion->isChecked(); m_ImageGenParameters.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); m_ImageGenParameters.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); m_ImageGenParameters.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); m_ImageGenParameters.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); m_ImageGenParameters.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); m_ImageGenParameters.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); if ( m_Controls->m_AddMotion->isChecked() && m_SelectedBundles.size()>0 ) { m_ImageGenParameters.m_ArtifactModelString += "_MOTION"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(m_ImageGenParameters.m_RandomMotion)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(m_ImageGenParameters.m_Translation[0])); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(m_ImageGenParameters.m_Translation[1])); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(m_ImageGenParameters.m_Translation[2])); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(m_ImageGenParameters.m_Rotation[0])); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(m_ImageGenParameters.m_Rotation[1])); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(m_ImageGenParameters.m_Rotation[2])); } // other imaging parameters m_ImageGenParameters.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); m_ImageGenParameters.m_tInhom = m_Controls->m_T2starBox->value(); m_ImageGenParameters.m_tEcho = m_Controls->m_TEbox->value(); m_ImageGenParameters.m_Repetitions = m_Controls->m_RepetitionsBox->value(); m_ImageGenParameters.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); m_ImageGenParameters.m_InterpolationShrink = m_Controls->m_InterpolationShrink->value(); m_ImageGenParameters.m_AxonRadius = m_Controls->m_FiberRadius->value(); m_ImageGenParameters.m_SignalScale = m_Controls->m_SignalScaleBox->value(); if (m_Controls->m_AddSpikes->isChecked()) { m_ImageGenParameters.m_Spikes = m_Controls->m_SpikeNumBox->value(); m_ImageGenParameters.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); m_ImageGenParameters.m_ArtifactModelString += "_SPIKES"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(m_ImageGenParameters.m_Spikes)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(m_ImageGenParameters.m_SpikeAmplitude)); } // adjust echo time if needed if ( m_ImageGenParameters.m_tEcho < m_ImageGenParameters.m_ImageRegion.GetSize(1)*m_ImageGenParameters.m_tLine ) { this->m_Controls->m_TEbox->setValue( m_ImageGenParameters.m_ImageRegion.GetSize(1)*m_ImageGenParameters.m_tLine ); m_ImageGenParameters.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(m_ImageGenParameters.m_tEcho)+" ms"); } // rician noise if (m_Controls->m_AddNoise->isChecked()) { if (m_ImageGenParameters.m_NoiseModel!=NULL) delete m_ImageGenParameters.m_NoiseModel; if (m_ImageGenParameters.m_NoiseModelShort!=NULL) delete m_ImageGenParameters.m_NoiseModelShort; double noiseVariance = m_Controls->m_NoiseLevel->value(); { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { mitk::RicianNoiseModel* rician = new mitk::RicianNoiseModel(); rician->SetNoiseVariance(noiseVariance); m_ImageGenParameters.m_NoiseModel = rician; m_ImageGenParameters.m_ArtifactModelString += "_RICIAN-"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); break; } case 1: { mitk::ChiSquareNoiseModel* chiSquare = new mitk::ChiSquareNoiseModel(); chiSquare->SetDOF(noiseVariance/2); m_ImageGenParameters.m_NoiseModel = chiSquare; m_ImageGenParameters.m_ArtifactModelString += "_CHISQUARED-"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); break; } default: { mitk::RicianNoiseModel* rician = new mitk::RicianNoiseModel(); rician->SetNoiseVariance(noiseVariance); m_ImageGenParameters.m_NoiseModel = rician; m_ImageGenParameters.m_ArtifactModelString += "_RICIAN-"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); } } } { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { mitk::RicianNoiseModel* rician = new mitk::RicianNoiseModel(); rician->SetNoiseVariance(noiseVariance); m_ImageGenParameters.m_NoiseModelShort = rician; break; } case 1: { mitk::ChiSquareNoiseModel* chiSquare = new mitk::ChiSquareNoiseModel(); chiSquare->SetDOF(noiseVariance/2); m_ImageGenParameters.m_NoiseModelShort = chiSquare; break; } default: { mitk::RicianNoiseModel* rician = new mitk::RicianNoiseModel(); rician->SetNoiseVariance(noiseVariance); m_ImageGenParameters.m_NoiseModelShort = rician; } } } m_ImageGenParameters.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } else { if (m_ImageGenParameters.m_NoiseModel!=NULL) { delete m_ImageGenParameters.m_NoiseModel; m_ImageGenParameters.m_NoiseModel = NULL; } if (m_ImageGenParameters.m_NoiseModelShort!=NULL) { delete m_ImageGenParameters.m_NoiseModelShort; m_ImageGenParameters.m_NoiseModelShort = NULL; } } // gibbs ringing m_ImageGenParameters.m_AddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); m_ImageGenParameters.m_ArtifactModelString += "_RINGING"; } // adjusting line readout time to the adapted image size needed for the DFT int y = m_ImageGenParameters.m_ImageRegion.GetSize(1); if ( y%2 == 1 ) y += 1; if ( y>m_ImageGenParameters.m_ImageRegion.GetSize(1) ) m_ImageGenParameters.m_tLine *= (double)m_ImageGenParameters.m_ImageRegion.GetSize(1)/y; // add distortions 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_ImageGenParameters.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && m_ImageGenParameters.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && m_ImageGenParameters.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { m_ImageGenParameters.m_FrequencyMap = itkImg; m_ImageGenParameters.m_ArtifactModelString += "_DISTORTED"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } } m_ImageGenParameters.m_DoSimulateEddyCurrents = m_Controls->m_AddEddy->isChecked(); m_ImageGenParameters.m_EddyStrength = 0; if (m_Controls->m_AddEddy->isChecked()) { m_ImageGenParameters.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); m_ImageGenParameters.m_ArtifactModelString += "_EDDY"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(m_ImageGenParameters.m_EddyStrength)); } // signal models m_ImageGenParameters.m_Comp3Weight = 1; m_ImageGenParameters.m_Comp4Weight = 0; if (m_Controls->m_Compartment4Box->currentIndex()>0) { m_ImageGenParameters.m_Comp4Weight = m_Controls->m_Comp4FractionBox->value(); m_ImageGenParameters.m_Comp3Weight -= m_ImageGenParameters.m_Comp4Weight; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.weight", DoubleProperty::New(m_ImageGenParameters.m_Comp3Weight)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.weight", DoubleProperty::New(m_ImageGenParameters.m_Comp4Weight)); } // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: m_StickModel1.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_StickModel1.SetBvalue(m_ImageGenParameters.m_Bvalue); m_StickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); m_StickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); m_ImageGenParameters.m_FiberModelList.push_back(&m_StickModel1); m_ImageGenParameters.m_SignalModelString += "Stick"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_StickModel1.GetT2()) ); break; case 1: m_ZeppelinModel1.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_ZeppelinModel1.SetBvalue(m_ImageGenParameters.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()); m_ImageGenParameters.m_FiberModelList.push_back(&m_ZeppelinModel1); m_ImageGenParameters.m_SignalModelString += "Zeppelin"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; case 2: m_TensorModel1.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_TensorModel1.SetBvalue(m_ImageGenParameters.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()); m_ImageGenParameters.m_FiberModelList.push_back(&m_TensorModel1); m_ImageGenParameters.m_SignalModelString += "Tensor"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: m_StickModel2.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_StickModel2.SetBvalue(m_ImageGenParameters.m_Bvalue); m_StickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); m_StickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); m_ImageGenParameters.m_FiberModelList.push_back(&m_StickModel2); m_ImageGenParameters.m_SignalModelString += "Stick"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_StickModel2.GetT2()) ); break; case 2: m_ZeppelinModel2.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_ZeppelinModel2.SetBvalue(m_ImageGenParameters.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()); m_ImageGenParameters.m_FiberModelList.push_back(&m_ZeppelinModel2); m_ImageGenParameters.m_SignalModelString += "Zeppelin"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); break; case 3: m_TensorModel2.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_TensorModel2.SetBvalue(m_ImageGenParameters.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()); m_ImageGenParameters.m_FiberModelList.push_back(&m_TensorModel2); m_ImageGenParameters.m_SignalModelString += "Tensor"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); m_ImageGenParameters.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(m_ImageGenParameters.m_GradientDirections); m_BallModel1.SetBvalue(m_ImageGenParameters.m_Bvalue); m_BallModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); m_BallModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); m_BallModel1.SetWeight(m_ImageGenParameters.m_Comp3Weight); m_ImageGenParameters.m_NonFiberModelList.push_back(&m_BallModel1); m_ImageGenParameters.m_SignalModelString += "Ball"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_BallModel1.GetT2()) ); break; case 1: m_AstrosticksModel1.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_AstrosticksModel1.SetBvalue(m_ImageGenParameters.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()); m_AstrosticksModel1.SetWeight(m_ImageGenParameters.m_Comp3Weight); m_ImageGenParameters.m_NonFiberModelList.push_back(&m_AstrosticksModel1); m_ImageGenParameters.m_SignalModelString += "Astrosticks"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_AstrosticksModel1.GetT2()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: m_DotModel1.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_DotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); m_DotModel1.SetWeight(m_ImageGenParameters.m_Comp3Weight); m_ImageGenParameters.m_NonFiberModelList.push_back(&m_DotModel1); m_ImageGenParameters.m_SignalModelString += "Dot"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_DotModel1.GetT2()) ); break; } // compartment 4 switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: m_BallModel2.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_BallModel2.SetBvalue(m_ImageGenParameters.m_Bvalue); m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); m_BallModel2.SetWeight(m_ImageGenParameters.m_Comp4Weight); m_ImageGenParameters.m_NonFiberModelList.push_back(&m_BallModel2); m_ImageGenParameters.m_SignalModelString += "Ball"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) ); break; case 2: m_AstrosticksModel2.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_AstrosticksModel2.SetBvalue(m_ImageGenParameters.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()); m_AstrosticksModel2.SetWeight(m_ImageGenParameters.m_Comp4Weight); m_ImageGenParameters.m_NonFiberModelList.push_back(&m_AstrosticksModel2); m_ImageGenParameters.m_SignalModelString += "Astrosticks"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; case 3: m_DotModel2.SetGradientList(m_ImageGenParameters.m_GradientDirections); m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); m_DotModel2.SetWeight(m_ImageGenParameters.m_Comp4Weight); m_ImageGenParameters.m_NonFiberModelList.push_back(&m_DotModel2); m_ImageGenParameters.m_SignalModelString += "Dot"; m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) ); break; } m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.InterpolationShrink", IntProperty::New(m_ImageGenParameters.m_InterpolationShrink)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_ImageGenParameters.m_SignalScale)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_ImageGenParameters.m_AxonRadius)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(m_ImageGenParameters.m_tInhom)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(m_ImageGenParameters.m_tLine)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(m_ImageGenParameters.m_tEcho)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Repetitions", IntProperty::New(m_ImageGenParameters.m_Repetitions)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(m_ImageGenParameters.m_Bvalue)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(m_ImageGenParameters.m_DoDisablePartialVolume)); m_ImageGenParameters.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(m_ImageGenParameters.m_DoSimulateRelaxation)); m_ImageGenParameters.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); } void QmitkFiberfoxView::SaveParameters() { UpdateImageParameters(); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; if(!filename.endsWith(".ffp")) filename += ".ffp"; m_ParameterFile = filename; boost::property_tree::ptree parameters; // fiber generation parameters parameters.put("fiberfox.fibers.realtime", m_Controls->m_RealTimeFibers->isChecked()); parameters.put("fiberfox.fibers.showadvanced", m_Controls->m_AdvancedOptionsBox->isChecked()); parameters.put("fiberfox.fibers.distribution", m_Controls->m_DistributionBox->currentIndex()); parameters.put("fiberfox.fibers.variance", m_Controls->m_VarianceBox->value()); parameters.put("fiberfox.fibers.density", m_Controls->m_FiberDensityBox->value()); parameters.put("fiberfox.fibers.spline.sampling", m_Controls->m_FiberSamplingBox->value()); parameters.put("fiberfox.fibers.spline.tension", m_Controls->m_TensionBox->value()); parameters.put("fiberfox.fibers.spline.continuity", m_Controls->m_ContinuityBox->value()); parameters.put("fiberfox.fibers.spline.bias", m_Controls->m_BiasBox->value()); parameters.put("fiberfox.fibers.constantradius", m_Controls->m_ConstantRadiusBox->isChecked()); parameters.put("fiberfox.fibers.m_Rotation.x", m_Controls->m_XrotBox->value()); parameters.put("fiberfox.fibers.m_Rotation.y", m_Controls->m_YrotBox->value()); parameters.put("fiberfox.fibers.m_Rotation.z", m_Controls->m_ZrotBox->value()); parameters.put("fiberfox.fibers.m_Translation.x", m_Controls->m_XtransBox->value()); parameters.put("fiberfox.fibers.m_Translation.y", m_Controls->m_YtransBox->value()); parameters.put("fiberfox.fibers.m_Translation.z", m_Controls->m_ZtransBox->value()); parameters.put("fiberfox.fibers.scale.x", m_Controls->m_XscaleBox->value()); parameters.put("fiberfox.fibers.scale.y", m_Controls->m_YscaleBox->value()); parameters.put("fiberfox.fibers.scale.z", m_Controls->m_ZscaleBox->value()); parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); // image generation parameters parameters.put("fiberfox.image.basic.size.x", m_ImageGenParameters.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", m_ImageGenParameters.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", m_ImageGenParameters.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", m_ImageGenParameters.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", m_ImageGenParameters.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", m_ImageGenParameters.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.numgradients", m_ImageGenParameters.m_NumGradients); parameters.put("fiberfox.image.basic.bvalue", m_ImageGenParameters.m_Bvalue); parameters.put("fiberfox.image.showadvanced", m_Controls->m_AdvancedOptionsBox_2->isChecked()); parameters.put("fiberfox.image.repetitions", m_ImageGenParameters.m_Repetitions); parameters.put("fiberfox.image.signalScale", m_ImageGenParameters.m_SignalScale); parameters.put("fiberfox.image.tEcho", m_ImageGenParameters.m_tEcho); parameters.put("fiberfox.image.tLine", m_Controls->m_LineReadoutTimeBox->value()); parameters.put("fiberfox.image.tInhom", m_ImageGenParameters.m_tInhom); parameters.put("fiberfox.image.axonRadius", m_ImageGenParameters.m_AxonRadius); parameters.put("fiberfox.image.interpolationShrink", m_ImageGenParameters.m_InterpolationShrink); parameters.put("fiberfox.image.doSimulateRelaxation", m_ImageGenParameters.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", m_ImageGenParameters.m_DoDisablePartialVolume); parameters.put("fiberfox.image.outputvolumefractions", m_Controls->m_VolumeFractionsBox->isChecked()); parameters.put("fiberfox.image.artifacts.addnoise", m_Controls->m_AddNoise->isChecked()); parameters.put("fiberfox.image.artifacts.noisedistribution", m_Controls->m_NoiseDistributionBox->currentIndex()); parameters.put("fiberfox.image.artifacts.noisevariance", m_Controls->m_NoiseLevel->value()); parameters.put("fiberfox.image.artifacts.addghost", m_Controls->m_AddGhosts->isChecked()); parameters.put("fiberfox.image.artifacts.m_KspaceLineOffset", m_Controls->m_kOffsetBox->value()); parameters.put("fiberfox.image.artifacts.distortions", m_Controls->m_AddDistortions->isChecked()); parameters.put("fiberfox.image.artifacts.addeddy", m_Controls->m_AddEddy->isChecked()); parameters.put("fiberfox.image.artifacts.m_EddyStrength", m_Controls->m_EddyGradientStrength->value()); parameters.put("fiberfox.image.artifacts.addringing", m_Controls->m_AddGibbsRinging->isChecked()); parameters.put("fiberfox.image.artifacts.addspikes", m_Controls->m_AddSpikes->isChecked()); parameters.put("fiberfox.image.artifacts.m_Spikesnum", m_Controls->m_SpikeNumBox->value()); parameters.put("fiberfox.image.artifacts.m_Spikesscale", m_Controls->m_SpikeScaleBox->value()); parameters.put("fiberfox.image.artifacts.addaliasing", m_Controls->m_AddAliasing->isChecked()); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_Controls->m_WrapBox->value()); parameters.put("fiberfox.image.artifacts.m_DoAddMotion", m_Controls->m_AddMotion->isChecked()); parameters.put("fiberfox.image.artifacts.m_RandomMotion", m_Controls->m_RandomMotion->isChecked()); parameters.put("fiberfox.image.artifacts.m_Translation0", m_Controls->m_MaxTranslationBoxX->value()); parameters.put("fiberfox.image.artifacts.m_Translation1", m_Controls->m_MaxTranslationBoxY->value()); parameters.put("fiberfox.image.artifacts.m_Translation2", m_Controls->m_MaxTranslationBoxZ->value()); parameters.put("fiberfox.image.artifacts.m_Rotation0", m_Controls->m_MaxRotationBoxX->value()); parameters.put("fiberfox.image.artifacts.m_Rotation1", m_Controls->m_MaxRotationBoxY->value()); parameters.put("fiberfox.image.artifacts.m_Rotation2", m_Controls->m_MaxRotationBoxZ->value()); parameters.put("fiberfox.image.compartment1.index", m_Controls->m_Compartment1Box->currentIndex()); parameters.put("fiberfox.image.compartment2.index", m_Controls->m_Compartment2Box->currentIndex()); parameters.put("fiberfox.image.compartment3.index", m_Controls->m_Compartment3Box->currentIndex()); parameters.put("fiberfox.image.compartment4.index", m_Controls->m_Compartment4Box->currentIndex()); parameters.put("fiberfox.image.compartment1.stick.d", m_Controls->m_StickWidget1->GetD()); parameters.put("fiberfox.image.compartment1.stick.t2", m_Controls->m_StickWidget1->GetT2()); parameters.put("fiberfox.image.compartment1.zeppelin.d1", m_Controls->m_ZeppelinWidget1->GetD1()); parameters.put("fiberfox.image.compartment1.zeppelin.d2", m_Controls->m_ZeppelinWidget1->GetD2()); parameters.put("fiberfox.image.compartment1.zeppelin.t2", m_Controls->m_ZeppelinWidget1->GetT2()); parameters.put("fiberfox.image.compartment1.tensor.d1", m_Controls->m_TensorWidget1->GetD1()); parameters.put("fiberfox.image.compartment1.tensor.d2", m_Controls->m_TensorWidget1->GetD2()); parameters.put("fiberfox.image.compartment1.tensor.d3", m_Controls->m_TensorWidget1->GetD3()); parameters.put("fiberfox.image.compartment1.tensor.t2", m_Controls->m_TensorWidget1->GetT2()); parameters.put("fiberfox.image.compartment2.stick.d", m_Controls->m_StickWidget2->GetD()); parameters.put("fiberfox.image.compartment2.stick.t2", m_Controls->m_StickWidget2->GetT2()); parameters.put("fiberfox.image.compartment2.zeppelin.d1", m_Controls->m_ZeppelinWidget2->GetD1()); parameters.put("fiberfox.image.compartment2.zeppelin.d2", m_Controls->m_ZeppelinWidget2->GetD2()); parameters.put("fiberfox.image.compartment2.zeppelin.t2", m_Controls->m_ZeppelinWidget2->GetT2()); parameters.put("fiberfox.image.compartment2.tensor.d1", m_Controls->m_TensorWidget2->GetD1()); parameters.put("fiberfox.image.compartment2.tensor.d2", m_Controls->m_TensorWidget2->GetD2()); parameters.put("fiberfox.image.compartment2.tensor.d3", m_Controls->m_TensorWidget2->GetD3()); parameters.put("fiberfox.image.compartment2.tensor.t2", m_Controls->m_TensorWidget2->GetT2()); parameters.put("fiberfox.image.compartment3.ball.d", m_Controls->m_BallWidget1->GetD()); parameters.put("fiberfox.image.compartment3.ball.t2", m_Controls->m_BallWidget1->GetT2()); parameters.put("fiberfox.image.compartment3.astrosticks.d", m_Controls->m_AstrosticksWidget1->GetD()); parameters.put("fiberfox.image.compartment3.astrosticks.t2", m_Controls->m_AstrosticksWidget1->GetT2()); parameters.put("fiberfox.image.compartment3.astrosticks.randomize", m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); parameters.put("fiberfox.image.compartment3.dot.t2", m_Controls->m_DotWidget1->GetT2()); parameters.put("fiberfox.image.compartment4.ball.d", m_Controls->m_BallWidget2->GetD()); parameters.put("fiberfox.image.compartment4.ball.t2", m_Controls->m_BallWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.astrosticks.d", m_Controls->m_AstrosticksWidget2->GetD()); parameters.put("fiberfox.image.compartment4.astrosticks.t2", m_Controls->m_AstrosticksWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.astrosticks.randomize", m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); parameters.put("fiberfox.image.compartment4.dot.t2", m_Controls->m_DotWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.weight", m_Controls->m_Comp4FractionBox->value()); boost::property_tree::xml_parser::write_xml(filename.toStdString(), parameters); } 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; boost::property_tree::ptree parameters; boost::property_tree::xml_parser::read_xml(filename.toStdString(), parameters); BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_Controls->m_RealTimeFibers->setChecked(v1.second.get("realtime")); m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get("showadvanced")); m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get("distribution")); m_Controls->m_VarianceBox->setValue(v1.second.get("variance")); m_Controls->m_FiberDensityBox->setValue(v1.second.get("density")); m_Controls->m_IncludeFiducials->setChecked(v1.second.get("includeFiducials")); m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get("constantradius")); BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second ) { if( v2.first == "spline" ) { m_Controls->m_FiberSamplingBox->setValue(v2.second.get("sampling")); m_Controls->m_TensionBox->setValue(v2.second.get("tension")); m_Controls->m_ContinuityBox->setValue(v2.second.get("continuity")); m_Controls->m_BiasBox->setValue(v2.second.get("bias")); } if( v2.first == "rotation" ) { m_Controls->m_XrotBox->setValue(v2.second.get("x")); m_Controls->m_YrotBox->setValue(v2.second.get("y")); m_Controls->m_ZrotBox->setValue(v2.second.get("z")); } if( v2.first == "translation" ) { m_Controls->m_XtransBox->setValue(v2.second.get("x")); m_Controls->m_YtransBox->setValue(v2.second.get("y")); m_Controls->m_ZtransBox->setValue(v2.second.get("z")); } if( v2.first == "scale" ) { m_Controls->m_XscaleBox->setValue(v2.second.get("x")); m_Controls->m_YscaleBox->setValue(v2.second.get("y")); m_Controls->m_ZscaleBox->setValue(v2.second.get("z")); } } } if( v1.first == "image" ) { m_Controls->m_SizeX->setValue(v1.second.get("basic.size.x")); m_Controls->m_SizeY->setValue(v1.second.get("basic.size.y")); m_Controls->m_SizeZ->setValue(v1.second.get("basic.size.z")); m_Controls->m_SpacingX->setValue(v1.second.get("basic.spacing.x")); m_Controls->m_SpacingY->setValue(v1.second.get("basic.spacing.y")); m_Controls->m_SpacingZ->setValue(v1.second.get("basic.spacing.z")); m_Controls->m_NumGradientsBox->setValue(v1.second.get("basic.numgradients")); m_Controls->m_BvalueBox->setValue(v1.second.get("basic.bvalue")); m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get("showadvanced")); m_Controls->m_RepetitionsBox->setValue(v1.second.get("repetitions")); m_Controls->m_SignalScaleBox->setValue(v1.second.get("signalScale")); m_Controls->m_TEbox->setValue(v1.second.get("tEcho")); m_Controls->m_LineReadoutTimeBox->setValue(v1.second.get("tLine")); m_Controls->m_T2starBox->setValue(v1.second.get("tInhom")); m_Controls->m_FiberRadius->setValue(v1.second.get("axonRadius")); m_Controls->m_InterpolationShrink->setValue(v1.second.get("interpolationShrink")); m_Controls->m_RelaxationBox->setChecked(v1.second.get("doSimulateRelaxation")); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(v1.second.get("doDisablePartialVolume")); m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get("outputvolumefractions")); m_Controls->m_AddNoise->setChecked(v1.second.get("artifacts.addnoise")); m_Controls->m_NoiseDistributionBox->setCurrentIndex(v1.second.get("artifacts.noisedistribution")); m_Controls->m_NoiseLevel->setValue(v1.second.get("artifacts.noisevariance")); m_Controls->m_AddGhosts->setChecked(v1.second.get("artifacts.addghost")); m_Controls->m_kOffsetBox->setValue(v1.second.get("artifacts.m_KspaceLineOffset")); m_Controls->m_AddAliasing->setChecked(v1.second.get("artifacts.addaliasing")); m_Controls->m_WrapBox->setValue(v1.second.get("artifacts.aliasingfactor")); m_Controls->m_AddDistortions->setChecked(v1.second.get("artifacts.distortions")); m_Controls->m_AddSpikes->setChecked(v1.second.get("artifacts.addspikes")); m_Controls->m_SpikeNumBox->setValue(v1.second.get("artifacts.m_Spikesnum")); m_Controls->m_SpikeScaleBox->setValue(v1.second.get("artifacts.m_Spikesscale")); m_Controls->m_AddEddy->setChecked(v1.second.get("artifacts.addeddy")); m_Controls->m_EddyGradientStrength->setValue(v1.second.get("artifacts.m_EddyStrength")); m_Controls->m_AddGibbsRinging->setChecked(v1.second.get("artifacts.addringing")); m_Controls->m_AddMotion->setChecked(v1.second.get("artifacts.m_DoAddMotion")); m_Controls->m_RandomMotion->setChecked(v1.second.get("artifacts.m_RandomMotion")); m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get("artifacts.m_Translation0")); m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get("artifacts.m_Translation1")); m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get("artifacts.m_Translation2")); m_Controls->m_MaxRotationBoxX->setValue(v1.second.get("artifacts.m_Rotation0")); m_Controls->m_MaxRotationBoxY->setValue(v1.second.get("artifacts.m_Rotation1")); m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get("artifacts.m_Rotation2")); m_Controls->m_Compartment1Box->setCurrentIndex(v1.second.get("compartment1.index")); m_Controls->m_Compartment2Box->setCurrentIndex(v1.second.get("compartment2.index")); m_Controls->m_Compartment3Box->setCurrentIndex(v1.second.get("compartment3.index")); m_Controls->m_Compartment4Box->setCurrentIndex(v1.second.get("compartment4.index")); m_Controls->m_StickWidget1->SetD(v1.second.get("compartment1.stick.d")); m_Controls->m_StickWidget1->SetT2(v1.second.get("compartment1.stick.t2")); m_Controls->m_ZeppelinWidget1->SetD1(v1.second.get("compartment1.zeppelin.d1")); m_Controls->m_ZeppelinWidget1->SetD2(v1.second.get("compartment1.zeppelin.d2")); m_Controls->m_ZeppelinWidget1->SetT2(v1.second.get("compartment1.zeppelin.t2")); m_Controls->m_TensorWidget1->SetD1(v1.second.get("compartment1.tensor.d1")); m_Controls->m_TensorWidget1->SetD2(v1.second.get("compartment1.tensor.d2")); m_Controls->m_TensorWidget1->SetD3(v1.second.get("compartment1.tensor.d3")); m_Controls->m_TensorWidget1->SetT2(v1.second.get("compartment1.tensor.t2")); m_Controls->m_StickWidget2->SetD(v1.second.get("compartment2.stick.d")); m_Controls->m_StickWidget2->SetT2(v1.second.get("compartment2.stick.t2")); m_Controls->m_ZeppelinWidget2->SetD1(v1.second.get("compartment2.zeppelin.d1")); m_Controls->m_ZeppelinWidget2->SetD2(v1.second.get("compartment2.zeppelin.d2")); m_Controls->m_ZeppelinWidget2->SetT2(v1.second.get("compartment2.zeppelin.t2")); m_Controls->m_TensorWidget2->SetD1(v1.second.get("compartment2.tensor.d1")); m_Controls->m_TensorWidget2->SetD2(v1.second.get("compartment2.tensor.d2")); m_Controls->m_TensorWidget2->SetD3(v1.second.get("compartment2.tensor.d3")); m_Controls->m_TensorWidget2->SetT2(v1.second.get("compartment2.tensor.t2")); m_Controls->m_BallWidget1->SetD(v1.second.get("compartment3.ball.d")); m_Controls->m_BallWidget1->SetT2(v1.second.get("compartment3.ball.t2")); m_Controls->m_AstrosticksWidget1->SetD(v1.second.get("compartment3.astrosticks.d")); m_Controls->m_AstrosticksWidget1->SetT2(v1.second.get("compartment3.astrosticks.t2")); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); m_Controls->m_DotWidget1->SetT2(v1.second.get("compartment3.dot.t2")); m_Controls->m_BallWidget2->SetD(v1.second.get("compartment4.ball.d")); m_Controls->m_BallWidget2->SetT2(v1.second.get("compartment4.ball.t2")); m_Controls->m_AstrosticksWidget2->SetD(v1.second.get("compartment4.astrosticks.d")); m_Controls->m_AstrosticksWidget2->SetT2(v1.second.get("compartment4.astrosticks.t2")); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); m_Controls->m_DotWidget2->SetT2(v1.second.get("compartment4.dot.t2")); m_Controls->m_Comp4FractionBox->setValue(v1.second.get("compartment4.weight")); } } UpdateImageParameters(); } 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); 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; } } 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); 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; } } 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_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; } } 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 value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (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::Geometry3D::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( 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::Geometry3D::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( 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::Geometry3D::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 ); 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( "PlanarFigure" ); 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 (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::Geometry3D* geom = image->GetGeometry(); geom->SetOrigin(m_ImageGenParameters.m_ImageOrigin); 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->GetTimeSlicedGeometry(), 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; UpdateImageParameters(); + if (m_ImageGenParameters.m_NoiseModel==NULL && + m_ImageGenParameters.m_Spikes==0 && + m_ImageGenParameters.m_FrequencyMap.IsNull() && + m_ImageGenParameters.m_KspaceLineOffset<=0.000001 && + !m_ImageGenParameters.m_AddGibbsRinging && + !m_ImageGenParameters.m_DoSimulateEddyCurrents && + m_ImageGenParameters.m_Wrap>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()); m_ArtifactsToDwiFilter->SettLine(m_ImageGenParameters.m_tLine); m_ArtifactsToDwiFilter->SetkOffset(m_ImageGenParameters.m_KspaceLineOffset); m_ArtifactsToDwiFilter->SetNoiseModel(m_ImageGenParameters.m_NoiseModelShort); m_ArtifactsToDwiFilter->SetGradientList(m_ImageGenParameters.m_GradientDirections); m_ArtifactsToDwiFilter->SetTE(m_ImageGenParameters.m_tEcho); m_ArtifactsToDwiFilter->SetSimulateEddyCurrents(m_ImageGenParameters.m_DoSimulateEddyCurrents); m_ArtifactsToDwiFilter->SetEddyGradientStrength(m_ImageGenParameters.m_EddyStrength); m_ArtifactsToDwiFilter->SetAddGibbsRinging(m_ImageGenParameters.m_AddGibbsRinging); m_ArtifactsToDwiFilter->SetFrequencyMap(m_ImageGenParameters.m_FrequencyMap); m_ArtifactsToDwiFilter->SetSpikeAmplitude(m_ImageGenParameters.m_SpikeAmplitude); m_ArtifactsToDwiFilter->SetSpikes(m_ImageGenParameters.m_Spikes); m_ArtifactsToDwiFilter->SetWrap(m_ImageGenParameters.m_Wrap); m_ImageGenParameters.m_ParentNode = imageNode; 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; UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); m_TractsToDwiFilter->SetSimulateEddyCurrents(m_ImageGenParameters.m_DoSimulateEddyCurrents); m_TractsToDwiFilter->SetEddyGradientStrength(m_ImageGenParameters.m_EddyStrength); m_TractsToDwiFilter->SetAddGibbsRinging(m_ImageGenParameters.m_AddGibbsRinging); m_TractsToDwiFilter->SetSimulateRelaxation(m_ImageGenParameters.m_DoSimulateRelaxation); m_TractsToDwiFilter->SetImageRegion(m_ImageGenParameters.m_ImageRegion); m_TractsToDwiFilter->SetSpacing(m_ImageGenParameters.m_ImageSpacing); m_TractsToDwiFilter->SetOrigin(m_ImageGenParameters.m_ImageOrigin); m_TractsToDwiFilter->SetDirectionMatrix(m_ImageGenParameters.m_ImageDirection); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_TractsToDwiFilter->SetFiberModels(m_ImageGenParameters.m_FiberModelList); m_TractsToDwiFilter->SetNonFiberModels(m_ImageGenParameters.m_NonFiberModelList); m_TractsToDwiFilter->SetNoiseModel(m_ImageGenParameters.m_NoiseModel); m_TractsToDwiFilter->SetkOffset(m_ImageGenParameters.m_KspaceLineOffset); m_TractsToDwiFilter->SettLine(m_ImageGenParameters.m_tLine); m_TractsToDwiFilter->SettInhom(m_ImageGenParameters.m_tInhom); m_TractsToDwiFilter->SetTE(m_ImageGenParameters.m_tEcho); m_TractsToDwiFilter->SetNumberOfRepetitions(m_ImageGenParameters.m_Repetitions); m_TractsToDwiFilter->SetEnforcePureFiberVoxels(m_ImageGenParameters.m_DoDisablePartialVolume); m_TractsToDwiFilter->SetInterpolationShrink(m_ImageGenParameters.m_InterpolationShrink); m_TractsToDwiFilter->SetFiberRadius(m_ImageGenParameters.m_AxonRadius); m_TractsToDwiFilter->SetSignalScale(m_ImageGenParameters.m_SignalScale); if (m_ImageGenParameters.m_InterpolationShrink>0) m_TractsToDwiFilter->SetUseInterpolation(true); m_TractsToDwiFilter->SetTissueMask(m_ImageGenParameters.m_MaskImage); m_TractsToDwiFilter->SetFrequencyMap(m_ImageGenParameters.m_FrequencyMap); m_TractsToDwiFilter->SetSpikeAmplitude(m_ImageGenParameters.m_SpikeAmplitude); m_TractsToDwiFilter->SetSpikes(m_ImageGenParameters.m_Spikes); m_TractsToDwiFilter->SetWrap(m_ImageGenParameters.m_Wrap); m_TractsToDwiFilter->SetAddMotionArtifact(m_ImageGenParameters.m_DoAddMotion); m_TractsToDwiFilter->SetMaxTranslation(m_ImageGenParameters.m_Translation); m_TractsToDwiFilter->SetMaxRotation(m_ImageGenParameters.m_Rotation); m_TractsToDwiFilter->SetRandomMotion(m_ImageGenParameters.m_RandomMotion); m_ImageGenParameters.m_ParentNode = fiberNode; m_Worker.m_FilterType = 0; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for( 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()) { std::vector::const_iterator it = selectedBundles.begin(); for (it; 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::Geometry3D* 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); } } } } } else { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Geometry3D* 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()); } 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; } std::vector::const_iterator it = m_SelectedBundles.begin(); for (it; 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()); 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; 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_ImageGenParameters.m_MaskImage.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_ImageGenParameters.m_MaskImage = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = 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; mitk::Image::Pointer image = dynamic_cast(node->GetData()); bool isbinary = false; node->GetPropertyValue("binary", isbinary); if (isbinary) { mitk::CastToItkImage(image, m_ImageGenParameters.m_MaskImage); m_Controls->m_TissueMaskLabel->setText(node->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( "PlanarFigure" ); 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 m_OutputPath = QFileDialog::getExistingDirectory(NULL, "Save images to...", QString(m_OutputPath.c_str())).toStdString(); if (m_OutputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { m_OutputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(m_OutputPath.c_str())); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui index a706b5e9f1..ebc46cd06a 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,3065 +1,3065 @@ QmitkFiberfoxViewControls 0 0 435 2274 Form Load Parameters :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Operations false Join Bundles :/QmitkDiffusionImaging/general_icons/plus.ico:/QmitkDiffusionImaging/general_icons/plus.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Copy Bundles :/QmitkDiffusionImaging/general_icons/copy2.ico:/QmitkDiffusionImaging/general_icons/copy2.ico false Transform Selection :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Distance of fiber sampling points (in mm) 1 0.100000000000000 0.100000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation Data Tissue Mask: false <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Save path: false QFrame::NoFrame QFrame::Raised 0 0 0 0 0 - ... Noise and other Artifacts Qt::Horizontal Add Noise false Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Shrink FOV (%): false Shrink FOV by this percentage. 1 0.000000000000000 90.000000000000000 0.100000000000000 25.000000000000000 Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Spikes: The number of randomly occurring signal spikes. 1 Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. 0.100000000000000 0.100000000000000 Scale: !!!EXPERIMENTAL!!! Add Eddy Current Effects false Add Spikes false QFrame::NoFrame QFrame::Raised 0 0 0 0 Variance: Variance of selected noise distribution. 4 0.000000000000000 - 100000.000000000000000 + 999999999.000000000000000 0.001000000000000 50.000000000000000 Distribution: Noise distribution Rician Chi-squared Add N/2 Ghosts false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). Qt::Horizontal Qt::Horizontal Qt::Horizontal true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 6 0 0 Toggle between random movement and linear movement. Randomize motion true Rotation 0 9 0 0 Degree: false x false Axis: false Maximum rotation around x-axis. 1 360.000000000000000 1.000000000000000 0.000000000000000 Maximum rotation around z-axis. 1 360.000000000000000 1.000000000000000 15.000000000000000 y false z false Maximum rotation around y-axis. 1 360.000000000000000 1.000000000000000 0.000000000000000 Translation 0 0 0 Distance: false x false y false Axis: false z false Maximum translation along x-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along y-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along z-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Add Motion Artifacts false Add Distortions false Add Aliasing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.250000000000000 true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Magnitude: false Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). 5 1000.000000000000000 0.001000000000000 0.005000000000000 color: rgb(255, 0, 0); Experimental! Qt::Horizontal Qt::Horizontal Image Settings QFrame::NoFrame QFrame::Raised 0 0 0 0 6 <html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html> Simulate Signal Relaxation true Repetitions: T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 Fiber Radius: Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 TE in milliseconds 1 10000 1 100 Interpolation Shrink: Line Readout Time: false <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Output one image per compartment containing the corresponding volume fractions per voxel. Output Volume Fractions false <html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html> false Number of signal averages. Increase to reduce noise. 1 100 1 1 Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 TE in milliseconds 1 10000 1 100 <html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html> 0 10000 0 Signal Scale: color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 1 10000 1 30 b-Value: false b-value in mm/s² 0 10000 100 1000 Advanced Options true - Start DWI generation from selected fiber bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. + <html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html> Start Simulation :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model true Stop current simulation. Abort Simulation :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico Extra-axonal Compartments Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Weighting factor between the two extra-axonal compartments. 1.000000000000000 0.100000000000000 0.300000000000000 Compartment Fraction: Qt::Vertical 20 40 Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model 8 true Save Parameters :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_RepetitionsBox m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_InterpolationShrink m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_Comp4FractionBox m_AddNoise m_NoiseLevel m_AddSpikes m_SpikeNumBox m_SpikeScaleBox m_AddGhosts m_kOffsetBox m_AddAliasing m_WrapBox m_AddDistortions m_FrequencyMapBox m_AddMotion m_RandomMotion m_MaxRotationBoxX m_MaxRotationBoxY m_MaxRotationBoxZ m_MaxTranslationBoxX m_MaxTranslationBoxY m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_SaveParametersButton m_LoadParametersButton tabWidget