diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index b8ec972e16..18faff8edc 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,1204 +1,1237 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkTractsToDWIImageFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk { template< class PixelType > TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter() : m_FiberBundle(NULL) , m_StatusText("") , m_UseConstantRandSeed(false) , m_RandGen(itk::Statistics::MersenneTwisterRandomVariateGenerator::New()) { m_RandGen->SetSeed(); } template< class PixelType > TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter() { } template< class PixelType > TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images ) { int numFiberCompartments = m_Parameters.m_FiberModelList.size(); // create slice object ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); Vector< double, 2 > sliceSpacing; sliceSpacing[0] = m_UpsampledSpacing[0]; sliceSpacing[1] = m_UpsampledSpacing[1]; // frequency map slice SliceType::Pointer fMapSlice = NULL; if (m_Parameters.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); fMapSlice->SetLargestPossibleRegion( region ); fMapSlice->SetBufferedRegion( region ); fMapSlice->SetRequestedRegion( region ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } DoubleDwiType::Pointer newImage = DoubleDwiType::New(); newImage->SetSpacing( m_Parameters.m_ImageSpacing ); newImage->SetOrigin( m_Parameters.m_ImageOrigin ); newImage->SetDirection( m_Parameters.m_ImageDirection ); newImage->SetLargestPossibleRegion( m_Parameters.m_ImageRegion ); newImage->SetBufferedRegion( m_Parameters.m_ImageRegion ); newImage->SetRequestedRegion( m_Parameters.m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); std::vector< unsigned int > spikeVolume; for (unsigned int i=0; iGetIntegerVariate()%images.at(0)->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (unsigned int i=0; i* signalModel; if (iSetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->SetSpacing(sliceSpacing); slice->Allocate(); slice->FillBuffer(0.0); // extract slice from channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]); if (fMapSlice.IsNotNull() && i==0) fMapSlice->SetPixel(index2D, m_Parameters.m_FrequencyMap->GetPixel(index3D)); } compartmentSlices.push_back(slice); t2Vector.push_back(signalModel->GetT2()); } if (this->GetAbortGenerateData()) return NULL; // create k-sapce (inverse fourier transform slices) itk::Size<2> outSize; outSize.SetElement(0, m_Parameters.m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_Parameters.m_ImageRegion.GetSize(1)); itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetT2(t2Vector); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(m_Parameters); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); idft->SetDiffusionGradientDirection(m_Parameters.GetGradientDirection(g)); idft->SetFrequencyMapSlice(fMapSlice); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; // fourier transform slice SliceType::Pointer newSlice; itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D); pix3D[g] = newSlice->GetPixel(index2D); newImage->SetPixel(index3D, pix3D); } ++disp; newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; return newImage; } template< class PixelType > void TractsToDWIImageFilter< PixelType >::GenerateData() { m_TimeProbe.Start(); m_StatusText = "Starting simulation\n"; // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); if (m_Parameters.m_FiberModelList.empty()) itkExceptionMacro("No diffusion model for fiber compartments defined!"); if (m_Parameters.m_NonFiberModelList.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); int baselineIndex = m_Parameters.GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); if (!m_Parameters.m_SimulateKspaceAcquisition) m_Parameters.m_DoAddGibbsRinging = false; if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); // initialize output dwi image ImageRegion<3> croppedRegion = m_Parameters.m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_CroppingFactor); itk::Point shiftedOrigin = m_Parameters.m_ImageOrigin; shiftedOrigin[1] += (m_Parameters.m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Parameters.m_ImageSpacing[1]/2; typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Parameters.m_ImageSpacing ); outImage->SetOrigin( shiftedOrigin ); outImage->SetDirection( m_Parameters.m_ImageDirection ); outImage->SetLargestPossibleRegion( croppedRegion ); outImage->SetBufferedRegion( croppedRegion ); outImage->SetRequestedRegion( croppedRegion ); outImage->SetVectorLength( m_Parameters.GetNumVolumes() ); outImage->Allocate(); typename OutputImageType::PixelType temp; temp.SetSize(m_Parameters.GetNumVolumes()); temp.Fill(0.0); outImage->FillBuffer(temp); // ADJUST GEOMETRY FOR FURTHER PROCESSING // is input slize size a power of two? unsigned int x=m_Parameters.m_ImageRegion.GetSize(0); unsigned int y=m_Parameters.m_ImageRegion.GetSize(1); ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0; m_Parameters.m_ImageRegion.SetSize(0, x+pad[0]); m_Parameters.m_ImageRegion.SetSize(1, y+pad[1]); if (m_Parameters.m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_FrequencyMap); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_FrequencyMap = zeroPadder->GetOutput(); } if (m_Parameters.m_MaskImage.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_MaskImage); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_MaskImage = zeroPadder->GetOutput(); } // Apply in-plane upsampling for Gibbs ringing artifact double upsampling = 1; if (m_Parameters.m_DoAddGibbsRinging) upsampling = 2; m_UpsampledSpacing = m_Parameters.m_ImageSpacing; m_UpsampledSpacing[0] /= upsampling; m_UpsampledSpacing[1] /= upsampling; m_UpsampledImageRegion = m_Parameters.m_ImageRegion; m_UpsampledImageRegion.SetSize(0, m_Parameters.m_ImageRegion.GetSize()[0]*upsampling); m_UpsampledImageRegion.SetSize(1, m_Parameters.m_ImageRegion.GetSize()[1]*upsampling); m_UpsampledOrigin = m_Parameters.m_ImageOrigin; m_UpsampledOrigin[0] -= m_Parameters.m_ImageSpacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; m_UpsampledOrigin[1] -= m_Parameters.m_ImageSpacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; m_UpsampledOrigin[2] -= m_Parameters.m_ImageSpacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; // generate double images to store the individual compartment signals m_CompartmentImages.clear(); int numFiberCompartments = m_Parameters.m_FiberModelList.size(); int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_UpsampledOrigin ); doubleDwi->SetDirection( m_Parameters.m_ImageDirection ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); doubleDwi->SetVectorLength( m_Parameters.GetNumVolumes() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; pix.SetSize(m_Parameters.GetNumVolumes()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); m_CompartmentImages.push_back(doubleDwi); } // initialize output volume fraction images m_VolumeFractions.clear(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleImg->SetOrigin( m_UpsampledOrigin ); doubleImg->SetDirection( m_Parameters.m_ImageDirection ); doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleImg->SetBufferedRegion( m_UpsampledImageRegion ); doubleImg->SetRequestedRegion( m_UpsampledImageRegion ); doubleImg->Allocate(); doubleImg->FillBuffer(0); m_VolumeFractions.push_back(doubleImg); } // get volume fraction images ItkDoubleImgType::Pointer sumImage = ItkDoubleImgType::New(); bool foundVolumeFractionImage = false; for (int i=0; iGetVolumeFractionImage().IsNotNull()) { foundVolumeFractionImage = true; itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(zeroPadder->GetOutput()); sumImage->SetSpacing( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetSpacing() ); sumImage->SetOrigin( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetOrigin() ); sumImage->SetDirection( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetDirection() ); sumImage->SetLargestPossibleRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetBufferedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetRequestedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->Allocate(); sumImage->FillBuffer(0); break; } } if (!foundVolumeFractionImage) { sumImage->SetSpacing( m_UpsampledSpacing ); sumImage->SetOrigin( m_UpsampledOrigin ); sumImage->SetDirection( m_Parameters.m_ImageDirection ); sumImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); sumImage->SetBufferedRegion( m_UpsampledImageRegion ); sumImage->SetRequestedRegion( m_UpsampledImageRegion ); sumImage->Allocate(); sumImage->FillBuffer(0.0); } for (int i=0; iGetVolumeFractionImage().IsNull()) { ItkDoubleImgType::Pointer doubleImg = ItkDoubleImgType::New(); doubleImg->SetSpacing( sumImage->GetSpacing() ); doubleImg->SetOrigin( sumImage->GetOrigin() ); doubleImg->SetDirection( sumImage->GetDirection() ); doubleImg->SetLargestPossibleRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetBufferedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetRequestedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->Allocate(); doubleImg->FillBuffer(1.0/numNonFiberCompartments); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(doubleImg); } ImageRegionIterator it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { sumImage->SetPixel(it.GetIndex(), sumImage->GetPixel(it.GetIndex())+it.Get()); ++it; } } for (int i=0; i it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (sumImage->GetPixel(it.GetIndex())>0) it.Set(it.Get()/sumImage->GetPixel(it.GetIndex())); ++it; } } // resample mask image and frequency map to fit upsampled geometry if (m_Parameters.m_DoAddGibbsRinging) { if (m_Parameters.m_MaskImage.IsNotNull()) { // rescale mask image (otherwise there are problems with the resampling) itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_Parameters.m_MaskImage); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); // resample mask image itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); resampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_MaskImage = resampler->GetOutput(); itk::ImageFileWriter::Pointer w = itk::ImageFileWriter::New(); w->SetFileName("/local/mask_ups.nrrd"); w->SetInput(m_Parameters.m_MaskImage); w->Update(); } // resample frequency map if (m_Parameters.m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(m_Parameters.m_FrequencyMap); resampler->SetOutputParametersFromImage(m_Parameters.m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_FrequencyMap = resampler->GetOutput(); } } // no input tissue mask is set -> create default bool maskImageSet = true; if (m_Parameters.m_MaskImage.IsNull()) { m_StatusText += "No tissue mask set\n"; MITK_INFO << "No tissue mask set"; m_Parameters.m_MaskImage = ItkUcharImgType::New(); m_Parameters.m_MaskImage->SetSpacing( m_UpsampledSpacing ); m_Parameters.m_MaskImage->SetOrigin( m_UpsampledOrigin ); m_Parameters.m_MaskImage->SetDirection( m_Parameters.m_ImageDirection ); m_Parameters.m_MaskImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->SetBufferedRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->SetRequestedRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->Allocate(); m_Parameters.m_MaskImage->FillBuffer(1); maskImageSet = false; } else { m_StatusText += "Using tissue mask\n"; MITK_INFO << "Using tissue mask"; } m_Parameters.m_ImageRegion = croppedRegion; x=m_Parameters.m_ImageRegion.GetSize(0); y=m_Parameters.m_ImageRegion.GetSize(1); if ( x%2 == 1 ) m_Parameters.m_ImageRegion.SetSize(0, x+1); if ( y%2 == 1 ) m_Parameters.m_ImageRegion.SetSize(1, y+1); // resample fiber bundle for sufficient voxel coverage m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n"; double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); double volumeAccuracy = 10; fiberBundle->ResampleFibers(minSpacing/volumeAccuracy); double mmRadius = m_Parameters.m_AxonRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/volumeAccuracy; double maxVolume = 0; double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; ofstream logFile; if (m_Parameters.m_DoAddMotion) { std::string fileName = "fiberfox_motion_0.log"; std::string filePath = mitk::IOUtil::GetTempPath(); if (m_Parameters.m_OutputPath.size()>0) filePath = m_Parameters.m_OutputPath; int c = 1; while (itksys::SystemTools::FileExists((filePath+fileName).c_str())) { fileName = "fiberfox_motion_"; fileName += boost::lexical_cast(c); fileName += ".log"; c++; } logFile.open((filePath+fileName).c_str()); logFile << "0 rotation: 0,0,0; translation: 0,0,0\n"; if (m_Parameters.m_DoRandomizeMotion) { m_StatusText += "Adding random motion artifacts:\n"; m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; } else { m_StatusText += "Adding linear motion artifacts:\n"; m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: " + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; } m_StatusText += "Motion logfile: " + (filePath+fileName) + "\n"; MITK_INFO << "Adding motion artifacts"; MITK_INFO << "Maximum rotation: " << m_Parameters.m_Rotation; MITK_INFO << "Maxmimum translation: " << m_Parameters.m_Translation; } maxVolume = 0; m_StatusText += "\n"+this->GetTime()+" > Generating " + boost::lexical_cast(numFiberCompartments+numNonFiberCompartments) + "-compartment diffusion-weighted signal.\n"; int numFibers = m_FiberBundle->GetNumFibers(); boost::progress_display disp(numFibers*m_Parameters.GetNumVolumes()); // get transform for motion artifacts FiberBundleType fiberBundleTransformed = fiberBundle; DoubleVectorType rotation = m_Parameters.m_Rotation/m_Parameters.GetNumVolumes(); DoubleVectorType translation = m_Parameters.m_Translation/m_Parameters.GetNumVolumes(); // creat image to hold transformed mask (motion artifact) ItkUcharImgType::Pointer tempTissueMask = ItkUcharImgType::New(); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_MaskImage); duplicator->Update(); tempTissueMask = duplicator->GetOutput(); // second upsampling needed for motion artifacts ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; DoubleVectorType upsampledSpacing = m_UpsampledSpacing; upsampledSpacing[0] /= 4; upsampledSpacing[1] /= 4; upsampledSpacing[2] /= 4; upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4); upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4); upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4); itk::Point upsampledOrigin = m_UpsampledOrigin; upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2; upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2; upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2; ItkUcharImgType::Pointer upsampledTissueMask = ItkUcharImgType::New(); itk::ResampleImageFilter::Pointer upsampler = itk::ResampleImageFilter::New(); upsampler->SetInput(m_Parameters.m_MaskImage); upsampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); upsampler->SetSize(upsampledImageRegion.GetSize()); upsampler->SetOutputSpacing(upsampledSpacing); upsampler->SetOutputOrigin(upsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); upsampler->SetInterpolator(nn_interpolator); upsampler->Update(); upsampledTissueMask = upsampler->GetOutput(); unsigned long lastTick = 0; switch (m_Parameters.m_DiffusionDirectionMode) { case(FiberfoxParameters<>::FIBER_TANGENT_DIRECTIONS): { m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; for (unsigned int g=0; gSetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); vtkPolyData* fiberPolyData = fiberBundleTransformed->GetFiberPolyData(); // generate fiber signal (if there are any fiber models present) if (!m_Parameters.m_FiberModelList.empty()) for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; for( int j=0; jGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } double* temp = points->GetPoint(j); itk::Point vertex = GetItkPoint(temp); itk::Vector v = GetItkVector(temp); itk::Vector dir(3); if (jGetPoint(j+1))-v; else dir = v-GetItkVector(points->GetPoint(j-1)); if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2]) continue; itk::Index<3> idx; itk::ContinuousIndex contIndex; tempTissueMask->TransformPhysicalPointToIndex(vertex, idx); tempTissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!tempTissueMask->GetLargestPossibleRegion().IsInside(idx) || tempTissueMask->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment for (int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = m_CompartmentImages.at(k)->GetPixel(idx); pix[g] += segmentVolume*m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g); m_CompartmentImages.at(k)->SetPixel(idx, pix); } // update fiber volume image double vol = intraAxonalVolumeImage->GetPixel(idx) + segmentVolume; intraAxonalVolumeImage->SetPixel(idx, vol); if (g==0 && vol>maxVolume) maxVolume = vol; } // progress report ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } // generate non-fiber signal ImageRegionIterator it3(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); double fact = 1; if (m_Parameters.m_AxonRadius<0.0001 || maxVolume>voxelVolume) fact = voxelVolume/maxVolume; while(!it3.IsAtEnd()) { if (it3.Get()>0) { DoubleDwiType::IndexType index = it3.GetIndex(); // get fiber volume fraction double intraAxonalVolume = intraAxonalVolumeImage->GetPixel(index)*fact; for (int i=0; iGetPixel(index); pix[g] *= fact; m_CompartmentImages.at(i)->SetPixel(index, pix); } if (intraAxonalVolume>0.0001 && m_Parameters.m_DoDisablePartialVolume) // only fiber in voxel { DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index); pix[g] *= voxelVolume/intraAxonalVolume; m_CompartmentImages.at(0)->SetPixel(index, pix); m_VolumeFractions.at(0)->SetPixel(index, 1); for (int i=1; iGetPixel(index); pix[g] = 0; m_CompartmentImages.at(i)->SetPixel(index, pix); } } else { m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/voxelVolume); - double extraAxonalVolume = voxelVolume-intraAxonalVolume; // non-fiber volume - double interAxonalVolume = 0; - if (numFiberCompartments>1) - interAxonalVolume = extraAxonalVolume * intraAxonalVolume/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f - double other = extraAxonalVolume - interAxonalVolume; // rest of compartment - double singleinter = interAxonalVolume/(numFiberCompartments-1); - - // adjust non-fiber and intra-axonal signal - for (int i=1; iGetPixel(index); - if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment - pix[g] /= intraAxonalVolume; - pix[g] *= singleinter; - m_CompartmentImages.at(i)->SetPixel(index, pix); - m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume); - } - itk::Point point; tempTissueMask->TransformIndexToPhysicalPoint(index, point); if (m_Parameters.m_DoAddMotion) { if (m_Parameters.m_DoRandomizeMotion && g>0) 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,-rotation[1]*g,-rotation[2]*g,-translation[0]*g,-translation[1]*g,-translation[2]*g); } - for (int i=0; i1) + int maxVolumeIndex = 0; + double maxWeight = 0; + for (int i=0; iGetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); - if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) - continue; - weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); + double weight = 0; + if (numNonFiberCompartments>1) + { + DoubleDwiType::IndexType newIndex; + m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); + if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) + continue; + weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); + } + + if (weight>maxWeight) + { + maxWeight = weight; + maxVolumeIndex = i; + } } - - DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(i+numFiberCompartments); + DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(maxVolumeIndex+numFiberCompartments); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); - pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*weight; + pix[g] += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(g); doubleDwi->SetPixel(index, pix); - m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, other/voxelVolume*weight); + m_VolumeFractions.at(maxVolumeIndex+numFiberCompartments)->SetPixel(index, 1); + } + else + { + double extraAxonalVolume = voxelVolume-intraAxonalVolume; // non-fiber volume + double interAxonalVolume = 0; + if (numFiberCompartments>1) + interAxonalVolume = extraAxonalVolume * intraAxonalVolume/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f + double other = extraAxonalVolume - interAxonalVolume; // rest of compartment + double singleinter = interAxonalVolume/(numFiberCompartments-1); + + // adjust non-fiber and intra-axonal signal + for (int i=1; iGetPixel(index); + if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment + pix[g] /= intraAxonalVolume; + pix[g] *= singleinter; + m_CompartmentImages.at(i)->SetPixel(index, pix); + m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume); + } + + for (int i=0; i1) + { + DoubleDwiType::IndexType newIndex; + m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); + if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) + continue; + weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); + } + + DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(i+numFiberCompartments); + DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); + + pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*weight; + doubleDwi->SetPixel(index, pix); + m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, other/voxelVolume*weight); + } } } } ++it3; } // move fibers if (m_Parameters.m_DoAddMotion && gGetDeepCopy(); rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[0]*2)-m_Parameters.m_Rotation[0]; rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[1]*2)-m_Parameters.m_Rotation[1]; rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[2]*2)-m_Parameters.m_Rotation[2]; translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[0]*2)-m_Parameters.m_Translation[0]; translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[1]*2)-m_Parameters.m_Translation[1]; translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[2]*2)-m_Parameters.m_Translation[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_Parameters.m_DoRandomizeMotion) 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 if (logFile.is_open()) { 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]); } } break; } case (FiberfoxParameters<>::MAIN_FIBER_DIRECTIONS): { typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(fiberBundle); fOdfFilter->SetMaskImage(tempTissueMask); fOdfFilter->SetAngularThreshold(cos(45*M_PI/180)); fOdfFilter->SetNormalizeVectors(false); fOdfFilter->SetUseWorkingCopy(false); fOdfFilter->SetSizeThreshold(0); fOdfFilter->SetMaxNumDirections(3); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); { ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); writer->SetFileName("/local/NumDirections.nrrd"); writer->SetInput(numDirImage); writer->Update(); } ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); itk::TractDensityImageFilter< ItkDoubleImgType >::Pointer generator = itk::TractDensityImageFilter< ItkDoubleImgType >::New(); generator->SetFiberBundle(fiberBundle); generator->SetBinaryOutput(false); generator->SetOutputAbsoluteValues(false); generator->SetInputImage(intraAxonalVolumeImage); generator->SetUseImageGeometry(true); generator->Update(); intraAxonalVolumeImage = generator->GetOutput(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); ImageRegionIterator< ItkUcharImgType > it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } if (it.Get()>0) { int count = 0; DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); for (unsigned int i=0; iSize(); i++) { itk::Vector< float, 3> dir = directionImageContainer->GetElement(i)->GetPixel(it.GetIndex()); double norm = dir.GetNorm(); if (norm>0.0001) { int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_FiberModelList.size()-1); m_Parameters.m_FiberModelList.at(modelIndex)->SetFiberDirection(dir); pix += m_Parameters.m_FiberModelList.at(modelIndex)->SimulateMeasurement()*norm; count++; } } if (count>0) pix /= count; pix *= intraAxonalVolumeImage->GetPixel(it.GetIndex()); // GM/CSF { int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); pix += (1-intraAxonalVolumeImage->GetPixel(it.GetIndex()))*m_Parameters.m_NonFiberModelList.at(modelIndex)->SimulateMeasurement(); } m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); } ++it; } break; } case (FiberfoxParameters<>::RANDOM_DIRECTIONS): { ItkUcharImgType::Pointer numDirectionsImage = ItkUcharImgType::New(); numDirectionsImage->SetSpacing( m_UpsampledSpacing ); numDirectionsImage->SetOrigin( m_UpsampledOrigin ); numDirectionsImage->SetDirection( m_Parameters.m_ImageDirection ); numDirectionsImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); numDirectionsImage->SetBufferedRegion( m_UpsampledImageRegion ); numDirectionsImage->SetRequestedRegion( m_UpsampledImageRegion ); numDirectionsImage->Allocate(); numDirectionsImage->FillBuffer(0); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); ImageRegionIterator it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } if (it.Get()>0) { int numFibs = m_RandGen->GetIntegerVariate(2)+1; DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); double volume = m_RandGen->GetVariateWithClosedRange(0.3); double sum = 0; std::vector< double > fractions; for (int i=0; iGetVariateWithClosedRange(0.5)); sum += fractions.at(i); } for (int i=0; i > directions; for (int i=0; iGetVariateWithClosedRange(2)-1.0; fib[1] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib[2] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib.Normalize(); double min = 0; for (unsigned int d=0; dmin) min = angle; } if (min<0.5) { m_Parameters.m_FiberModelList.at(0)->SetFiberDirection(fib); pix += m_Parameters.m_FiberModelList.at(0)->SimulateMeasurement()*fractions[i]; directions.push_back(fib); } else i--; } pix *= (1-volume); // CSF/GM { -// int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); + // int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); pix += volume*m_Parameters.m_NonFiberModelList.at(0)->SimulateMeasurement(); } m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); numDirectionsImage->SetPixel(it.GetIndex(), numFibs); } ++it; } itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); wr->SetInput(numDirectionsImage); wr->SetFileName("/local/NumDirections.nrrd"); wr->Update(); } } if (logFile.is_open()) { logFile << "DONE"; 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_Parameters.m_SimulateKspaceAcquisition ) { m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; MITK_INFO << "Adjusting complex signal:"; if (m_Parameters.m_DoSimulateRelaxation) m_StatusText += "Simulating signal relaxation\n"; if (m_Parameters.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; if (m_Parameters.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; if (m_Parameters.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; if (m_Parameters.m_Spikes>0) m_StatusText += "Simulating spikes\n"; if (m_Parameters.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; if (m_Parameters.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; doubleOutImage = DoKspaceStuff(m_CompartmentImages); m_Parameters.m_SignalScale = 1; // already scaled in DoKspaceStuff } else { m_StatusText += this->GetTime()+" > Summing compartments\n"; MITK_INFO << "Summing compartments"; doubleOutImage = m_CompartmentImages.at(0); for (unsigned int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); adder->SetInput2(m_CompartmentImages.at(i)); adder->Update(); doubleOutImage = adder->GetOutput(); } } if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } m_StatusText += this->GetTime()+" > Finalizing image\n"; MITK_INFO << "Finalizing image"; if (m_Parameters.m_SignalScale>1) m_StatusText += " Scaling signal\n"; if (m_Parameters.m_NoiseModel!=NULL) m_StatusText += " Adding noise\n"; unsigned int window = 0; unsigned int min = itk::NumericTraits::max(); ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.GetNumVolumes()); boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; lastTick = 0; while(!it4.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp2; unsigned long newTick = 50*disp2.count()/disp2.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename OutputImageType::IndexType index = it4.GetIndex(); signal = doubleOutImage->GetPixel(index)*m_Parameters.m_SignalScale; if (m_Parameters.m_NoiseModel!=NULL) m_Parameters.m_NoiseModel->AddNoise(signal); for (unsigned int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); if ( (!m_Parameters.IsBaselineIndex(i) || signal.Size()==1) && signal[i]>window) window = signal[i]; if ( (!m_Parameters.IsBaselineIndex(i) || signal.Size()==1) && signal[i]SetNthOutput(0, outImage); m_StatusText += "\n\n"; m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); m_TimeProbe.Stop(); } template< class PixelType > itk::Point TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > itk::Vector TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } template< class PixelType > double TractsToDWIImageFilter< PixelType >::RoundToNearest(double num) { return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5); } template< class PixelType > std::string TractsToDWIImageFilter< PixelType >::GetTime() { m_TimeProbe.Stop(); unsigned long total = RoundToNearest(m_TimeProbe.GetTotal()); unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); m_TimeProbe.Start(); return out; } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp index 5f9327f551..5c8a4ad42b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2543 +1,2549 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ switch (m_FilterType) { case 0: m_View->m_TractsToDwiFilter->Update(); break; case 1: m_View->m_ArtifactsToDwiFilter->Update(); break; } } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; switch (m_Worker.m_FilterType) { case 0: m_TractsToDwiFilter->SetAbortGenerateData(true); break; case 1: m_ArtifactsToDwiFilter->SetAbortGenerateData(true); break; } m_Controls->m_AbortSimulationButton->setEnabled(false); m_Controls->m_AbortSimulationButton->setText("Aborting simulation ..."); } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_AbortSimulationButton->setEnabled(true); m_Controls->m_AbortSimulationButton->setText("Abort simulation"); m_Controls->m_GenerateImageButton->setVisible(true); m_ThreadIsRunning = false; QString statusText; FiberfoxParameters parameters; mitk::DiffusionImage::Pointer mitkImage = mitk::DiffusionImage::New(); switch (m_Worker.m_FilterType) { case 0: { statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage->SetVectorImage( m_TractsToDwiFilter->GetOutput() ); mitkImage->SetReferenceBValue(parameters.m_Bvalue); mitkImage->SetDirections(parameters.GetGradientDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_ResultNode->SetData( mitkImage ); parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName() +"_D"+QString::number(parameters.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(parameters.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(parameters.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(parameters.m_ImageSpacing[0]).toStdString() +"-"+QString::number(parameters.m_ImageSpacing[1]).toStdString() +"-"+QString::number(parameters.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(parameters.m_Bvalue).toStdString() +"_"+parameters.m_SignalModelString +parameters.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); parameters.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(parameters.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_ParentNode); } } m_TractsToDwiFilter = NULL; break; } case 1: { statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); if (m_ArtifactsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_ArtifactsToDwiFilter->GetParameters().CopyParameters(); mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(parameters.m_ParentNode->GetData()); mitkImage = mitk::DiffusionImage::New(); mitkImage->SetVectorImage( m_ArtifactsToDwiFilter->GetOutput() ); mitkImage->SetReferenceBValue(diffImg->GetReferenceBValue()); mitkImage->SetDirections(diffImg->GetDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_ResultNode->SetData( mitkImage ); parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName()+parameters.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); m_ArtifactsToDwiFilter = NULL; break; } } mitk::BaseData::Pointer basedata = parameters.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_OutputPath.empty()) { try{ QString outputFileName(parameters.m_OutputPath.c_str()); outputFileName += parameters.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::SaveBaseData(mitkImage, outputFileName.toStdString()); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_FrequencyMap = NULL; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText; switch (m_Worker.m_FilterType) { case 0: statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); break; case 1: statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); break; } if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); statusText = "
"+statusText+"
"; m_Controls->m_SimulationStatusText->setText(statusText); QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); m_Controls->m_PrototypeWidget2->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_PrototypeWidget3->SetMinFa(0.0); m_Controls->m_PrototypeWidget3->SetMaxFa(0.15); m_Controls->m_PrototypeWidget4->SetMinFa(0.0); m_Controls->m_PrototypeWidget4->SetMaxFa(0.15); m_Controls->m_PrototypeWidget3->SetMinAdc(0.0); m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001); m_Controls->m_PrototypeWidget4->SetMinAdc(0.003); m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetPredicate(finalPredicate); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); } } template< class ScalarType > FiberfoxParameters< ScalarType > QmitkFiberfoxView::UpdateImageParameters() { FiberfoxParameters< ScalarType > parameters; parameters.m_OutputPath = ""; string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { parameters.m_OutputPath = outputPath; parameters.m_OutputPath += "/"; } if (m_MaskImageNode.IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_MaskImageNode->GetData()); mitk::CastToItkImage(mitkMaskImage, parameters.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(parameters.m_MaskImage); duplicator->Update(); parameters.m_MaskImage = duplicator->GetOutput(); } if (m_SelectedDWI.IsNotNull()) // use parameters of selected DWI { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); parameters.m_ImageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_ImageSpacing = dwi->GetVectorImage()->GetSpacing(); parameters.m_ImageOrigin = dwi->GetVectorImage()->GetOrigin(); parameters.m_ImageDirection = dwi->GetVectorImage()->GetDirection(); parameters.m_Bvalue = dwi->GetReferenceBValue(); parameters.SetGradienDirections(dwi->GetDirections()); } else if (m_SelectedImage.IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); parameters.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_ImageDirection = itkImg->GetDirection(); parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); } else // use GUI parameters { parameters.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); parameters.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); parameters.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); parameters.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); parameters.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); parameters.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); parameters.m_ImageOrigin[0] = parameters.m_ImageSpacing[0]/2; parameters.m_ImageOrigin[1] = parameters.m_ImageSpacing[1]/2; parameters.m_ImageOrigin[2] = parameters.m_ImageSpacing[2]/2; parameters.m_ImageDirection.SetIdentity(); parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); parameters.GenerateGradientHalfShell(); } // signal relaxation parameters.m_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); parameters.m_SimulateKspaceAcquisition = parameters.m_DoSimulateRelaxation; if (parameters.m_DoSimulateRelaxation && m_SelectedBundles.size()>0 ) parameters.m_ArtifactModelString += "_RELAX"; // N/2 ghosts if (m_Controls->m_AddGhosts->isChecked()) { parameters.m_SimulateKspaceAcquisition = true; parameters.m_ArtifactModelString += "_GHOST"; parameters.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); parameters.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(parameters.m_KspaceLineOffset)); } else parameters.m_KspaceLineOffset = 0; // Aliasing if (m_Controls->m_AddAliasing->isChecked()) { parameters.m_SimulateKspaceAcquisition = true; parameters.m_ArtifactModelString += "_ALIASING"; parameters.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; parameters.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Spikes if (m_Controls->m_AddSpikes->isChecked()) { parameters.m_SimulateKspaceAcquisition = true; parameters.m_Spikes = m_Controls->m_SpikeNumBox->value(); parameters.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); parameters.m_ArtifactModelString += "_SPIKES"; parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_Spikes)); parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SpikeAmplitude)); } // gibbs ringing parameters.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { parameters.m_SimulateKspaceAcquisition = true; parameters.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); parameters.m_ArtifactModelString += "_RINGING"; } // 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 (parameters.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && parameters.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && parameters.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { parameters.m_SimulateKspaceAcquisition = true; itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(itkImg); duplicator->Update(); parameters.m_FrequencyMap = duplicator->GetOutput(); parameters.m_ArtifactModelString += "_DISTORTED"; parameters.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } } parameters.m_EddyStrength = 0; if (m_Controls->m_AddEddy->isChecked()) { parameters.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); parameters.m_ArtifactModelString += "_EDDY"; parameters.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_EddyStrength)); } // Motion parameters.m_DoAddMotion = m_Controls->m_AddMotion->isChecked(); parameters.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); parameters.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); parameters.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); parameters.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); parameters.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); parameters.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); parameters.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); if ( m_Controls->m_AddMotion->isChecked() && m_SelectedBundles.size()>0 ) { parameters.m_ArtifactModelString += "_MOTION"; parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(parameters.m_DoRandomizeMotion)); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(parameters.m_Translation[0])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(parameters.m_Translation[1])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(parameters.m_Translation[2])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(parameters.m_Rotation[0])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(parameters.m_Rotation[1])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(parameters.m_Rotation[2])); } // other imaging parameters parameters.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); parameters.m_tInhom = m_Controls->m_T2starBox->value(); parameters.m_tEcho = m_Controls->m_TEbox->value(); parameters.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); parameters.m_AxonRadius = m_Controls->m_FiberRadius->value(); parameters.m_SignalScale = m_Controls->m_SignalScaleBox->value(); // adjust echo time if needed if ( parameters.m_tEcho < parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ) { this->m_Controls->m_TEbox->setValue( parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ); parameters.m_tEcho = m_Controls->m_TEbox->value(); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(parameters.m_tEcho)+" ms"); } // Noise if (m_Controls->m_AddNoise->isChecked()) { double noiseVariance = m_Controls->m_NoiseLevel->value(); { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_ArtifactModelString += "_RICIAN-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); break; } case 1: { parameters.m_NoiseModel = new mitk::ChiSquareNoiseModel(); parameters.m_ArtifactModelString += "_CHISQUARED-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); break; } default: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_ArtifactModelString += "_RICIAN-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); } } } parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); parameters.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } // adjusting line readout time to the adapted image size needed for the DFT unsigned int y = parameters.m_ImageRegion.GetSize(1); y += y%2; if ( y>parameters.m_ImageRegion.GetSize(1) ) parameters.m_tLine *= (double)parameters.m_ImageRegion.GetSize(1)/y; // signal models m_PrototypeModel1.Clear(); m_PrototypeModel3.Clear(); m_PrototypeModel4.Clear(); // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: m_StickModel1.SetGradientList(parameters.GetGradientDirections()); m_StickModel1.SetBvalue(parameters.m_Bvalue); m_StickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); m_StickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_StickModel1); parameters.m_SignalModelString += "Stick"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_StickModel1.GetT2()) ); break; case 1: m_ZeppelinModel1.SetGradientList(parameters.GetGradientDirections()); m_ZeppelinModel1.SetBvalue(parameters.m_Bvalue); m_ZeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); m_ZeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); m_ZeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); m_ZeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_ZeppelinModel1); parameters.m_SignalModelString += "Zeppelin"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; case 2: m_TensorModel1.SetGradientList(parameters.GetGradientDirections()); m_TensorModel1.SetBvalue(parameters.m_Bvalue); m_TensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); m_TensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); m_TensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); m_TensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_TensorModel1); parameters.m_SignalModelString += "Tensor"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; case 3: parameters.m_SimulateKspaceAcquisition = false; m_PrototypeModel1.SetGradientList(parameters.GetGradientDirections()); m_PrototypeModel1.SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); m_PrototypeModel1.SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); m_PrototypeModel1.SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); parameters.m_FiberModelList.push_back(&m_PrototypeModel1); parameters.m_SignalModelString += "Prototype"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: m_StickModel2.SetGradientList(parameters.GetGradientDirections()); m_StickModel2.SetBvalue(parameters.m_Bvalue); m_StickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); m_StickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_StickModel2); parameters.m_SignalModelString += "Stick"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_StickModel2.GetT2()) ); break; case 2: m_ZeppelinModel2.SetGradientList(parameters.GetGradientDirections()); m_ZeppelinModel2.SetBvalue(parameters.m_Bvalue); m_ZeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); m_ZeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); m_ZeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); m_ZeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_ZeppelinModel2); parameters.m_SignalModelString += "Zeppelin"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); break; case 3: m_TensorModel2.SetGradientList(parameters.GetGradientDirections()); m_TensorModel2.SetBvalue(parameters.m_Bvalue); m_TensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); m_TensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); m_TensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); m_TensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_TensorModel2); parameters.m_SignalModelString += "Tensor"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); break; } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: m_BallModel1.SetGradientList(parameters.GetGradientDirections()); m_BallModel1.SetBvalue(parameters.m_Bvalue); m_BallModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); m_BallModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); parameters.m_NonFiberModelList.push_back(&m_BallModel1); parameters.m_SignalModelString += "Ball"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_BallModel1.GetT2()) ); break; case 1: m_AstrosticksModel1.SetGradientList(parameters.GetGradientDirections()); m_AstrosticksModel1.SetBvalue(parameters.m_Bvalue); m_AstrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); m_AstrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); m_AstrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel1); parameters.m_SignalModelString += "Astrosticks"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_AstrosticksModel1.GetT2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: m_DotModel1.SetGradientList(parameters.GetGradientDirections()); m_DotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); parameters.m_NonFiberModelList.push_back(&m_DotModel1); parameters.m_SignalModelString += "Dot"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_DotModel1.GetT2()) ); break; case 3: parameters.m_SimulateKspaceAcquisition = false; m_PrototypeModel3.SetGradientList(parameters.GetGradientDirections()); m_PrototypeModel3.SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); m_PrototypeModel3.SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); m_PrototypeModel3.SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); parameters.m_NonFiberModelList.push_back(&m_PrototypeModel3); parameters.m_SignalModelString += "Prototype"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); break; } // compartment 4 ItkDoubleImgType::Pointer comp4VolumeImage = NULL; ItkDoubleImgType::Pointer comp3VolumeImage = NULL; if (m_Controls->m_Compartment4Box->currentIndex()>0) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); if (volumeNode.IsNull()) { MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; } else { MITK_INFO << "Rescaling volume fraction image..."; comp4VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp4VolumeImage); double max = itk::NumericTraits::min(); double min = itk::NumericTraits::max(); itk::ImageRegionIterator< ItkDoubleImgType > it(comp4VolumeImage, comp4VolumeImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) { it.Set(0.0); ++it; continue; } if (it.Get()>max) max = it.Get(); if (it.Get()::Pointer scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); scaler->SetInput(comp4VolumeImage); scaler->SetShift(-min); scaler->SetScale(1/(max-min)); scaler->Update(); comp4VolumeImage = scaler->GetOutput(); itk::ImageFileWriter< ItkDoubleImgType >::Pointer wr = itk::ImageFileWriter< ItkDoubleImgType >::New(); wr->SetInput(comp4VolumeImage); wr->SetFileName("/local/comp4.nrrd"); wr->Update(); // if (max>1 || min<0) // are volume fractions between 0 and 1? // { // itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); // rescaler->SetInput(0, comp4VolumeImage); // rescaler->SetOutputMaximum(1); // rescaler->SetOutputMinimum(0); // rescaler->Update(); // comp4VolumeImage = rescaler->GetOutput(); // } itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); inverter->SetMaximum(1.0); inverter->SetInput(comp4VolumeImage); inverter->Update(); comp3VolumeImage = inverter->GetOutput(); } } if (comp4VolumeImage.IsNotNull()) switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: { m_BallModel2.SetGradientList(parameters.GetGradientDirections()); m_BallModel2.SetBvalue(parameters.m_Bvalue); m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); m_BallModel2.SetVolumeFractionImage(comp4VolumeImage); parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); parameters.m_NonFiberModelList.push_back(&m_BallModel2); parameters.m_SignalModelString += "Ball"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) ); break; } case 2: { m_AstrosticksModel2.SetGradientList(parameters.GetGradientDirections()); m_AstrosticksModel2.SetBvalue(parameters.m_Bvalue); m_AstrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); m_AstrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); m_AstrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); m_AstrosticksModel2.SetVolumeFractionImage(comp4VolumeImage); parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel2); parameters.m_SignalModelString += "Astrosticks"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; } case 3: { m_DotModel2.SetGradientList(parameters.GetGradientDirections()); m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); m_DotModel2.SetVolumeFractionImage(comp4VolumeImage); parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); parameters.m_NonFiberModelList.push_back(&m_DotModel2); parameters.m_SignalModelString += "Dot"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) ); break; } case 4: { parameters.m_SimulateKspaceAcquisition = false; m_PrototypeModel4.SetGradientList(parameters.GetGradientDirections()); m_PrototypeModel4.SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); m_PrototypeModel4.SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); m_PrototypeModel4.SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); m_PrototypeModel4.SetVolumeFractionImage(comp4VolumeImage); parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); parameters.m_NonFiberModelList.push_back(&m_PrototypeModel4); parameters.m_SignalModelString += "Prototype"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); break; } } parameters.m_DiffusionDirectionMode = FiberfoxParameters::FIBER_TANGENT_DIRECTIONS; parameters.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(parameters.m_SignalScale)); parameters.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(parameters.m_AxonRadius)); parameters.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(parameters.m_tInhom)); parameters.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(parameters.m_tLine)); parameters.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(parameters.m_tEcho)); parameters.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(parameters.m_Bvalue)); parameters.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(parameters.m_DoDisablePartialVolume)); parameters.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(parameters.m_DoSimulateRelaxation)); parameters.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); return parameters; } void QmitkFiberfoxView::SaveParameters() { FiberfoxParameters ffParamaters = 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.rotation.x", m_Controls->m_XrotBox->value()); parameters.put("fiberfox.fibers.rotation.y", m_Controls->m_YrotBox->value()); parameters.put("fiberfox.fibers.rotation.z", m_Controls->m_ZrotBox->value()); parameters.put("fiberfox.fibers.translation.x", m_Controls->m_XtransBox->value()); parameters.put("fiberfox.fibers.translation.y", m_Controls->m_YtransBox->value()); parameters.put("fiberfox.fibers.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", ffParamaters.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", ffParamaters.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", ffParamaters.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", ffParamaters.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", ffParamaters.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", ffParamaters.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.numgradients", ffParamaters.GetNumWeightedVolumes()); parameters.put("fiberfox.image.basic.bvalue", ffParamaters.m_Bvalue); parameters.put("fiberfox.image.showadvanced", m_Controls->m_AdvancedOptionsBox_2->isChecked()); parameters.put("fiberfox.image.signalScale", ffParamaters.m_SignalScale); parameters.put("fiberfox.image.tEcho", ffParamaters.m_tEcho); parameters.put("fiberfox.image.tLine", m_Controls->m_LineReadoutTimeBox->value()); parameters.put("fiberfox.image.tInhom", ffParamaters.m_tInhom); parameters.put("fiberfox.image.axonRadius", ffParamaters.m_AxonRadius); parameters.put("fiberfox.image.doSimulateRelaxation", ffParamaters.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", ffParamaters.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.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.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.spikesnum", m_Controls->m_SpikeNumBox->value()); parameters.put("fiberfox.image.artifacts.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.doAddMotion", m_Controls->m_AddMotion->isChecked()); parameters.put("fiberfox.image.artifacts.randomMotion", m_Controls->m_RandomMotion->isChecked()); parameters.put("fiberfox.image.artifacts.translation0", m_Controls->m_MaxTranslationBoxX->value()); parameters.put("fiberfox.image.artifacts.translation1", m_Controls->m_MaxTranslationBoxY->value()); parameters.put("fiberfox.image.artifacts.translation2", m_Controls->m_MaxTranslationBoxZ->value()); parameters.put("fiberfox.image.artifacts.rotation0", m_Controls->m_MaxRotationBoxX->value()); parameters.put("fiberfox.image.artifacts.rotation1", m_Controls->m_MaxRotationBoxY->value()); parameters.put("fiberfox.image.artifacts.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()); 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_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_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.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.spikesnum")); m_Controls->m_SpikeScaleBox->setValue(v1.second.get("artifacts.spikesscale")); m_Controls->m_AddEddy->setChecked(v1.second.get("artifacts.addeddy")); m_Controls->m_EddyGradientStrength->setValue(v1.second.get("artifacts.eddyStrength")); m_Controls->m_AddGibbsRinging->setChecked(v1.second.get("artifacts.addringing")); m_Controls->m_AddMotion->setChecked(v1.second.get("artifacts.doAddMotion")); m_Controls->m_RandomMotion->setChecked(v1.second.get("artifacts.randomMotion")); m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get("artifacts.translation0")); m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get("artifacts.translation1")); m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get("artifacts.translation2")); m_Controls->m_MaxRotationBoxX->setValue(v1.second.get("artifacts.rotation0")); m_Controls->m_MaxRotationBoxY->setValue(v1.second.get("artifacts.rotation1")); m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get("artifacts.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")); } } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget3->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 4: m_Controls->m_PrototypeWidget4->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for(unsigned int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for(unsigned int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); node->SetBoolProperty("planarfigure.3drendering", true); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( node ); } UpdateGui(); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (unsigned int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (unsigned int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { if (m_SelectedBundles.empty() && m_SelectedDWI.IsNull()) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); } else if (!m_SelectedBundles.empty()) SimulateImageFromFibers(m_SelectedBundles.at(0)); else if (m_SelectedDWI.IsNotNull()) SimulateForExistingDwi(m_SelectedDWI); } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { if (!dynamic_cast*>(imageNode->GetData())) return; FiberfoxParameters parameters = UpdateImageParameters(); if (parameters.m_NoiseModel==NULL && parameters.m_Spikes==0 && parameters.m_FrequencyMap.IsNull() && parameters.m_KspaceLineOffset<=0.000001 && !parameters.m_DoAddGibbsRinging && !(parameters.m_EddyStrength>0) && parameters.m_CroppingFactor>0.999) { QMessageBox::information( NULL, "Simulation cancelled", "No valid artifact enabled! Motion artifacts and relaxation effects can NOT be added to an existing diffusion weighted image."); return; } mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(imageNode->GetData()); m_ArtifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); m_ArtifactsToDwiFilter->SetInput(diffImg->GetVectorImage()); parameters.m_ParentNode = imageNode; m_ArtifactsToDwiFilter->SetParameters(parameters); m_Worker.m_FilterType = 1; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) return; FiberfoxParameters parameters = UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); parameters.m_ParentNode = fiberNode; if (m_SelectedDWI.IsNotNull()) { mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedDWI->GetData()); bool doSampling = false; for (unsigned int i=0; i* >(parameters.m_FiberModelList[i]) ) doSampling = true; for (unsigned int i=0; i* >(parameters.m_NonFiberModelList[i]) ) doSampling = true; // sample prototype signals if ( doSampling ) { - const int shOrder = 4; + const int shOrder = 2; typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); filter->SetBValue(diffImg->GetReferenceBValue()); filter->Update(); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = filter->GetOutput(); const int NumCoeffs = (shOrder*shOrder + shOrder + 2)/2 + shOrder; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; typename QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); qballfilter->SetBValue(diffImg->GetReferenceBValue()); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); QballFilterType::CoefficientImageType::Pointer itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput(diffImg->GetVectorImage()); adcFilter->SetGradientDirections(diffImg->GetDirections()); adcFilter->SetB_value(diffImg->GetReferenceBValue()); adcFilter->Update(); ItkDoubleImgType::Pointer adcImage = adcFilter->GetOutput(); int b0Index; for (unsigned int i=0; iGetDirectionsWithoutMeasurementFrame()->Size(); i++) if ( diffImg->GetDirectionsWithoutMeasurementFrame()->GetElement(i).magnitude()<0.001 ) { b0Index = i; break; } double max = 0; { itk::ImageRegionIterator< itk::VectorImage< short, 3 > > it(diffImg->GetVectorImage(), diffImg->GetVectorImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) { ++it; continue; } if (it.Get()[b0Index]>max) max = it.Get()[b0Index]; ++it; } } MITK_INFO << "Sampling signal kernels."; itk::ImageRegionIterator< itk::Image< itk::DiffusionTensor3D< double >, 3 > > it(tensorImage, tensorImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { + bool skipPixel = false; if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) { ++it; continue; } for (unsigned int i=0; iGetDirections()->Size(); i++) { - if (diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]<=0 || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]>diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]) + if (diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]!=diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i] || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]<=0 || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]>diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]) { - ++it; - continue; + skipPixel = true; + break; } } + if (skipPixel) + { + ++it; + continue; + } typedef itk::DiffusionTensor3D TensorType; TensorType::EigenValuesArrayType eigenvalues; TensorType::EigenVectorsMatrixType eigenvectors; TensorType tensor = it.Get(); double FA = tensor.GetFractionalAnisotropy(); double ADC = adcImage->GetPixel(it.GetIndex()); - itk::Vector< float, NumCoeffs > itkv = itkFeatureImage->GetPixel(it.GetIndex()); + QballFilterType::CoefficientImageType::PixelType itkv = itkFeatureImage->GetPixel(it.GetIndex()); vnl_vector_fixed< double, NumCoeffs > coeffs; for (unsigned int c=0; c* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) { tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); itk::Vector dir; dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); model->m_PrototypeMaxDirection.push_back(dir); MITK_INFO << "WM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } } } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) MITK_INFO << "CSF/GM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } } ++it; } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); if ( model && model->GetNumberOfKernels()<=0 ) { QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for fiber compartment "+QString::number(i)); return; } } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); if ( model && model->GetNumberOfKernels()<=0 ) { QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for non-fiber compartment "+QString::number(i)); return; } } } } else if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 || m_Controls->m_Compartment4Box->currentIndex()==4 ) { QMessageBox::information( NULL, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } m_TractsToDwiFilter->SetParameters(parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Worker.m_FilterType = 0; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for(unsigned int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { for (std::vector::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); pe->Modified(); } } } } } else { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); pe->Modified(); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } for (std::vector::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); newNode->SetBoolProperty("planarfigure.3drendering", true); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_MaskImageNode.IsNotNull() || m_SelectedImage.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (!m_SelectedBundles.empty()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = NULL; m_MaskImageNode = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isbinary = false; node->GetPropertyValue("binary", isbinary); if (isbinary) { m_MaskImageNode = node; m_Controls->m_TissueMaskLabel->setText(m_MaskImageNode->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(node->GetData())) m_SelectedImages.clear(); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( nonConstNode ); } MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG string outputPath = QFileDialog::getExistingDirectory(NULL, "Save images to...", QString(outputPath.c_str())).toStdString(); if (outputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { outputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str())); } }