diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp index 3404b7c1f2..8ad4dee7c7 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp @@ -1,273 +1,266 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkAddArtifactsToDwiImageFilter_txx #define __itkAddArtifactsToDwiImageFilter_txx #include #include #include #include "itkAddArtifactsToDwiImageFilter.h" #include #include #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > AddArtifactsToDwiImageFilter< TPixelType > ::AddArtifactsToDwiImageFilter() : m_NoiseModel(NULL) - , m_RingingModel(NULL) , m_FrequencyMap(NULL) , m_kOffset(0) , m_tLine(1) , m_EddyGradientStrength(0.001) , m_SimulateEddyCurrents(false) , m_TE(100) + , m_Upsampling(1) { this->SetNumberOfRequiredInputs( 1 ); } template< class TPixelType > AddArtifactsToDwiImageFilter< TPixelType >::ComplexSliceType::Pointer AddArtifactsToDwiImageFilter< TPixelType >::RearrangeSlice(ComplexSliceType::Pointer slice) { ImageRegion<2> region = slice->GetLargestPossibleRegion(); typename ComplexSliceType::Pointer rearrangedSlice = ComplexSliceType::New(); rearrangedSlice->SetLargestPossibleRegion( region ); rearrangedSlice->SetBufferedRegion( region ); rearrangedSlice->SetRequestedRegion( region ); rearrangedSlice->Allocate(); int xHalf = region.GetSize(0)/2; int yHalf = region.GetSize(1)/2; for (int y=0; y pix = slice->GetPixel(idx); if( idx[0] < xHalf ) idx[0] = idx[0] + xHalf; else idx[0] = idx[0] - xHalf; if( idx[1] < yHalf ) idx[1] = idx[1] + yHalf; else idx[1] = idx[1] - yHalf; rearrangedSlice->SetPixel(idx, pix); } return rearrangedSlice; } template< class TPixelType > void AddArtifactsToDwiImageFilter< TPixelType > ::GenerateData() { typename DiffusionImageType::Pointer inputImage = static_cast< DiffusionImageType * >( this->ProcessObject::GetInput(0) ); itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion(); typename itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage( inputImage ); duplicator->Update(); typename DiffusionImageType::Pointer outputImage = duplicator->GetOutput(); // is input slize size even? int x=inputRegion.GetSize(0); int y=inputRegion.GetSize(1); if ( x%2 == 1 ) x += 1; if ( y%2 == 1 ) y += 1; // create slice object typename SliceType::Pointer slice = SliceType::New(); ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, x); sliceRegion.SetSize(1, y); slice->SetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->Allocate(); slice->FillBuffer(0.0); ImageRegion<2> upsampledSliceRegion; - unsigned int upsampling = 1; - if (m_RingingModel!=NULL) + if (m_Upsampling>1.00001) { - upsampling = m_RingingModel->GetKspaceCropping(); - upsampledSliceRegion.SetSize(0, x*upsampling); - upsampledSliceRegion.SetSize(1, y*upsampling); + upsampledSliceRegion.SetSize(0, x*m_Upsampling); + upsampledSliceRegion.SetSize(1, y*m_Upsampling); } // frequency map slice typename SliceType::Pointer fMap = NULL; if (m_FrequencyMap.IsNotNull()) { fMap = SliceType::New(); fMap->SetLargestPossibleRegion( sliceRegion ); fMap->SetBufferedRegion( sliceRegion ); fMap->SetRequestedRegion( sliceRegion ); fMap->Allocate(); fMap->FillBuffer(0.0); } - if ( m_FrequencyMap.IsNotNull() || m_kOffset>0.0 || m_RingingModel!=NULL || m_SimulateEddyCurrents) + if ( m_FrequencyMap.IsNotNull() || m_kOffset>0.0 || m_Upsampling>1.00001 || m_SimulateEddyCurrents) { MatrixType transform = inputImage->GetDirection(); for (int i=0; i<3; i++) for (int j=0; j<3; j++) transform[i][j] *= inputImage->GetSpacing()[j]; MITK_INFO << "Adjusting complex signal"; MITK_INFO << "line readout time: " << m_tLine; MITK_INFO << "line offset: " << m_kOffset; if (m_FrequencyMap.IsNotNull()) MITK_INFO << "frequency map is set"; else MITK_INFO << "no frequency map set"; - if (m_RingingModel!=NULL) + if (m_Upsampling>1.00001) MITK_INFO << "Gibbs ringing enabled"; else MITK_INFO << "Gibbs ringing disabled"; if (m_SimulateEddyCurrents) MITK_INFO << "Simulating eddy currents"; boost::progress_display disp(inputImage->GetVectorLength()*inputRegion.GetSize(2)); for (int g=0; gGetVectorLength(); g++) for (int z=0; z compartmentSlices; // extract slice from channel g for (int y=0; yGetPixel(index3D)[g]; slice->SetPixel(index2D, pix2D); if (fMap.IsNotNull()) fMap->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D)); } - if (upsampling>1) + if (m_Upsampling>1.00001) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(slice); resampler->SetOutputParametersFromImage(slice); resampler->SetSize(upsampledSliceRegion.GetSize()); - resampler->SetOutputSpacing(slice->GetSpacing()/upsampling); + resampler->SetOutputSpacing(slice->GetSpacing()/m_Upsampling); resampler->Update(); typename SliceType::Pointer upslice = resampler->GetOutput(); compartmentSlices.push_back(upslice); } else compartmentSlices.push_back(slice); // fourier transform slice typename ComplexSliceType::Pointer fSlice; - typename itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); + itk::Size<2> outSize; outSize.SetElement(0, x); outSize.SetElement(1, y); + typename itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetkOffset(m_kOffset); idft->SettLine(m_tLine); idft->SetSimulateRelaxation(false); idft->SetFrequencyMap(fMap); idft->SetDiffusionGradientDirection(m_GradientList.at(g)); idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents); idft->SetEddyGradientMagnitude(m_EddyGradientStrength); idft->SetTE(m_TE); idft->SetZ((double)z-(double)inputRegion.GetSize(2)/2.0); idft->SetDirectionMatrix(transform); + idft->SetOutSize(outSize); idft->Update(); - fSlice = idft->GetOutput(); - if (m_RingingModel!=NULL) - { - fSlice = RearrangeSlice(fSlice); - fSlice = m_RingingModel->AddArtifact(fSlice); - } - // inverse fourier transform slice typename SliceType::Pointer newSlice; typename itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (int y=0; yGetPixel(index3D); typename SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; double signal = newSlice->GetPixel(index2D); if (signal>0) signal = floor(signal+0.5); else signal = ceil(signal-0.5); pix3D[g] = signal; outputImage->SetPixel(index3D, pix3D); } + + ++disp; } } if (m_NoiseModel!=NULL) { ImageRegionIterator it1 (outputImage, inputRegion); boost::progress_display disp2(inputRegion.GetNumberOfPixels()); while(!it1.IsAtEnd()) { ++disp2; typename DiffusionImageType::PixelType signal = it1.Get(); m_NoiseModel->AddNoise(signal); it1.Set(signal); ++it1; } } this->SetNthOutput(0, outputImage); } } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h index 8beccd5648..7a467447ba 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h @@ -1,99 +1,97 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkAddArtifactsToDwiImageFilter_h_ #define __itkAddArtifactsToDwiImageFilter_h_ #include "FiberTrackingExports.h" #include #include #include #include #include -#include #include namespace itk{ /** * \brief Adds several artifacts to the input DWI. */ template< class TPixelType > class AddArtifactsToDwiImageFilter : public ImageToImageFilter< VectorImage< TPixelType, 3 >, VectorImage< TPixelType, 3 > > { public: typedef AddArtifactsToDwiImageFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageToImageFilter< VectorImage< TPixelType, 3 >, VectorImage< TPixelType, 3 > > Superclass; /** Method for creation through the object factory. */ itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(AddArtifactsToDwiImageFilter, ImageToImageFilter) typedef typename Superclass::InputImageType DiffusionImageType; typedef mitk::DiffusionNoiseModel NoiseModelType; - typedef mitk::GibbsRingingArtifact GibbsRingingType; typedef itk::Image< double, 2 > SliceType; typedef typename itk::KspaceImageFilter< double >::OutputImageType ComplexSliceType; typedef itk::Image ItkDoubleImgType; typedef itk::Matrix MatrixType; - void SetRingingModel(GibbsRingingType* ringingModel){ m_RingingModel = ringingModel; } void SetNoiseModel(NoiseModelType* noiseModel){ m_NoiseModel = noiseModel; } itkSetMacro( FrequencyMap, ItkDoubleImgType::Pointer ) itkSetMacro( kOffset, double ) itkSetMacro( tLine, double ) itkSetMacro( SimulateEddyCurrents, bool ) itkSetMacro( EddyGradientStrength, double ) void SetGradientList(mitk::DiffusionSignalModel::GradientListType list) { m_GradientList=list; } itkSetMacro( TE, double ) + itkSetMacro( Upsampling, double ) protected: AddArtifactsToDwiImageFilter(); ~AddArtifactsToDwiImageFilter() {} typename ComplexSliceType::Pointer RearrangeSlice(typename ComplexSliceType::Pointer slice); void GenerateData(); - GibbsRingingType* m_RingingModel; NoiseModelType* m_NoiseModel; ItkDoubleImgType::Pointer m_FrequencyMap; double m_kOffset; double m_tLine; bool m_SimulateEddyCurrents; double m_EddyGradientStrength; mitk::DiffusionSignalModel::GradientListType m_GradientList; double m_TE; + double m_Upsampling; ///< causes ringing artifacts private: }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkAddArtifactsToDwiImageFilter.cpp" #endif #endif //__itkAddArtifactsToDwiImageFilter_h_ diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp index f61bfab819..80faef1148 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp @@ -1,213 +1,236 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkKspaceImageFilter_txx #define __itkKspaceImageFilter_txx #include #include #include #include "itkKspaceImageFilter.h" #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > KspaceImageFilter< TPixelType > ::KspaceImageFilter() : m_tLine(1) , m_kOffset(0) , m_FrequencyMap(NULL) , m_SimulateRelaxation(true) , m_SimulateEddyCurrents(false) , m_Tau(70) , m_EddyGradientMagnitude(30) , m_IsBaseline(true) , m_SignalScale(1) { m_DiffusionGradientDirection.Fill(0.0); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::BeforeThreadedGenerateData() { typename OutputImageType::Pointer outputImage = OutputImageType::New(); outputImage->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); outputImage->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); outputImage->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); - outputImage->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); - outputImage->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); - outputImage->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); + itk::ImageRegion<2> region; region.SetSize(0, m_OutSize[0]); region.SetSize(1, m_OutSize[1]); + outputImage->SetLargestPossibleRegion( region ); + outputImage->SetBufferedRegion( region ); + outputImage->SetRequestedRegion( region ); outputImage->Allocate(); - typename InputImageType::Pointer tempImage = InputImageType::New(); - tempImage->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); - tempImage->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); - tempImage->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); - tempImage->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); - tempImage->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); - tempImage->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); - tempImage->Allocate(); + m_TEMPIMAGE = InputImageType::New(); + m_TEMPIMAGE->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); + m_TEMPIMAGE->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); + m_TEMPIMAGE->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); + m_TEMPIMAGE->SetLargestPossibleRegion( region ); + m_TEMPIMAGE->SetBufferedRegion( region ); + m_TEMPIMAGE->SetRequestedRegion( region ); + m_TEMPIMAGE->Allocate(); m_SimulateDistortions = true; if (m_FrequencyMap.IsNull()) { m_SimulateDistortions = false; m_FrequencyMap = InputImageType::New(); - m_FrequencyMap->SetSpacing( outputImage->GetSpacing() ); - m_FrequencyMap->SetOrigin( outputImage->GetOrigin() ); - m_FrequencyMap->SetDirection( outputImage->GetDirection() ); - m_FrequencyMap->SetLargestPossibleRegion( outputImage->GetLargestPossibleRegion() ); - m_FrequencyMap->SetBufferedRegion( outputImage->GetLargestPossibleRegion() ); - m_FrequencyMap->SetRequestedRegion( outputImage->GetLargestPossibleRegion() ); + m_FrequencyMap->SetSpacing( m_CompartmentImages.at(0)->GetSpacing() ); + m_FrequencyMap->SetOrigin( m_CompartmentImages.at(0)->GetOrigin() ); + m_FrequencyMap->SetDirection( m_CompartmentImages.at(0)->GetDirection() ); + m_FrequencyMap->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); + m_FrequencyMap->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); + m_FrequencyMap->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); m_FrequencyMap->Allocate(); m_FrequencyMap->FillBuffer(0); } double gamma = 42576000; // Gyromagnetic ratio in Hz/T if (m_DiffusionGradientDirection.GetNorm()>0.001) { m_DiffusionGradientDirection.Normalize(); m_EddyGradientMagnitude /= 1000; // eddy gradient magnitude in T/m m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_EddyGradientMagnitude * gamma; m_IsBaseline = false; } else m_EddyGradientMagnitude = gamma*m_EddyGradientMagnitude/1000; this->SetNthOutput(0, outputImage); - this->SetNthOutput(1, tempImage); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId) { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); - typename InputImageType::Pointer tempImage = static_cast< InputImageType * >(this->ProcessObject::GetOutput(1)); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); typedef ImageRegionConstIterator< InputImageType > InputIteratorType; double szx = outputImage->GetLargestPossibleRegion().GetSize(0); double szy = outputImage->GetLargestPossibleRegion().GetSize(1); double numPix = szx*szy; double dt = m_tLine/szx; double fromMaxEcho = - m_tLine*szy/2; + double in_szx = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); + double in_szy = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); + int xOffset = in_szx-szx; + int yOffset = in_szy-szy; + while( !oit.IsAtEnd() ) { itk::Index< 2 > kIdx; kIdx[0] = oit.GetIndex()[0]; kIdx[1] = oit.GetIndex()[1]; double t = fromMaxEcho + ((double)kIdx[1]*szx+(double)kIdx[0])*dt; // dephasing time // calculate eddy current decay factors double eddyDecay = 0; if (m_SimulateEddyCurrents) eddyDecay = exp(-(m_TE/2 + t)/m_Tau) * t/1000; // calcualte signal relaxation factors std::vector< double > relaxFactor; if (m_SimulateRelaxation) { for (int i=0; iSetPixel(kIdx, t ); + temp_kx += m_kOffset; // add gradient delay induced offset vcl_complex s(0,0); InputIteratorType it(m_CompartmentImages.at(0), m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { double x = it.GetIndex()[0]; double y = it.GetIndex()[1]; vcl_complex f(0, 0); // sum compartment signals and simulate relaxation for (int i=0; i( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * relaxFactor.at(i) * m_SignalScale, 0); else f += std::complex( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * m_SignalScale ); // simulate eddy currents and other distortions double omega_t = 0; if ( m_SimulateEddyCurrents ) { if (!m_IsBaseline) { itk::Vector< double, 3 > pos; pos[0] = x-szx/2; pos[1] = y-szy/2; pos[2] = m_Z; pos = m_DirectionMatrix*pos/1000; // vector from image center to current position (in meter) omega_t += (m_DiffusionGradientDirection[0]*pos[0]+m_DiffusionGradientDirection[1]*pos[1]+m_DiffusionGradientDirection[2]*pos[2])*eddyDecay; } else omega_t += m_EddyGradientMagnitude*eddyDecay; } if (m_SimulateDistortions) omega_t += m_FrequencyMap->GetPixel(it.GetIndex())*t/1000; + // add gibbs ringing offset (cropps k-space) + double tempOffsetX = 0; + if (temp_kx>=szx/2) + tempOffsetX = xOffset; + double temp_ky = kIdx[1]; + if (temp_ky>=szy/2) + temp_ky += yOffset; + // actual DFT term - s += f * exp( std::complex(0, 2 * M_PI * (temp_k*x/szx + (double)kIdx[1]*y/szy) + omega_t ) ); + s += f * exp( std::complex(0, 2 * M_PI * ((temp_kx+tempOffsetX)*x/in_szx + temp_ky*y/in_szy) + omega_t ) ); ++it; } s /= numPix; + + /* rearrange slice not needed + if( kIdx[0] < szx/2 ) + kIdx[0] = kIdx[0] + szx/2; + else + kIdx[0] = kIdx[0] - szx/2; + + if( kIdx[1] < szx/2 ) + kIdx[1] = kIdx[1] + szy/2; + else + kIdx[1] = kIdx[1] - szy/2;*/ + + m_TEMPIMAGE->SetPixel(kIdx, sqrt(s.real()*s.real()+s.imag()*s.imag())); outputImage->SetPixel(kIdx, s); ++oit; } // typedef itk::ImageFileWriter< InputImageType > WriterType; // typename WriterType::Pointer writer = WriterType::New(); -// writer->SetFileName("/local/dist.nrrd"); -// writer->SetInput(tempImage); +// writer->SetFileName("/local/kspace.nrrd"); +// writer->SetInput(m_TEMPIMAGE); // writer->Update(); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::AfterThreadedGenerateData() { } } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.h index 9da9b12400..01bdb7d9bb 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.h @@ -1,115 +1,118 @@ /*=================================================================== 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. ===================================================================*/ /*=================================================================== This file is based heavily on a corresponding ITK filter. ===================================================================*/ #ifndef __itkKspaceImageFilter_h_ #define __itkKspaceImageFilter_h_ #include "FiberTrackingExports.h" #include #include #include namespace itk{ /** * \brief Performes deterministic streamline tracking on the input tensor image. */ template< class TPixelType > class KspaceImageFilter : public ImageSource< Image< vcl_complex< TPixelType >, 2 > > { public: typedef KspaceImageFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageSource< Image< vcl_complex< TPixelType >, 2 > > Superclass; /** Method for creation through the object factory. */ - itkNewMacro(Self); + itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(KspaceImageFilter, ImageToImageFilter) typedef typename itk::Image< double, 2 > InputImageType; typedef typename InputImageType::Pointer InputImagePointerType; typedef typename Superclass::OutputImageType OutputImageType; typedef typename Superclass::OutputImageRegionType OutputImageRegionType; typedef itk::Matrix MatrixType; itkSetMacro( FrequencyMap, typename InputImageType::Pointer ) itkSetMacro( tLine, double ) itkSetMacro( kOffset, double ) itkSetMacro( TE, double) itkSetMacro( Tinhom, double) itkSetMacro( Tau, double) itkSetMacro( SimulateRelaxation, bool ) itkSetMacro( SimulateEddyCurrents, bool ) itkSetMacro( Z, double ) itkSetMacro( DirectionMatrix, MatrixType ) itkSetMacro( SignalScale, double ) + itkSetMacro( OutSize, itk::Size<2> ) void SetT2( std::vector< double > t2Vector ) { m_T2=t2Vector; } void SetCompartmentImages( std::vector< InputImagePointerType > cImgs ) { m_CompartmentImages=cImgs; } void SetDiffusionGradientDirection(itk::Vector g) { m_DiffusionGradientDirection=g; } void SetEddyGradientMagnitude(double g_mag) { m_EddyGradientMagnitude=g_mag; } ///< in T/m protected: KspaceImageFilter(); ~KspaceImageFilter() {} void BeforeThreadedGenerateData(); void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId); void AfterThreadedGenerateData(); bool m_SimulateRelaxation; bool m_SimulateDistortions; bool m_SimulateEddyCurrents; + typename InputImageType::Pointer m_TEMPIMAGE; typename InputImageType::Pointer m_FrequencyMap; double m_tLine; double m_kOffset; double m_Tinhom; double m_TE; std::vector< double > m_T2; std::vector< InputImagePointerType > m_CompartmentImages; itk::Vector m_DiffusionGradientDirection; double m_Tau; ///< eddy current decay constant double m_EddyGradientMagnitude; ///< in T/m double m_Z; MatrixType m_DirectionMatrix; bool m_IsBaseline; double m_SignalScale; + itk::Size<2> m_OutSize; private: }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkKspaceImageFilter.cpp" #endif #endif //__itkKspaceImageFilter_h_ diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index 3c7ec39bc5..a432420dcb 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,702 +1,699 @@ /*=================================================================== 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 namespace itk { TractsToDWIImageFilter::TractsToDWIImageFilter() : m_CircleDummy(false) , m_VolumeAccuracy(10) , m_Upsampling(1) , m_NumberOfRepetitions(1) , m_EnforcePureFiberVoxels(false) , m_InterpolationShrink(1000) , m_FiberRadius(0) , m_SignalScale(25) , m_kOffset(0) , m_tLine(1) , m_UseInterpolation(false) , m_SimulateRelaxation(true) , m_tInhom(50) , m_TE(100) , m_FrequencyMap(NULL) , m_EddyGradientStrength(0.001) , m_SimulateEddyCurrents(false) { m_Spacing.Fill(2.5); m_Origin.Fill(0.0); m_DirectionMatrix.SetIdentity(); m_ImageRegion.SetSize(0, 10); m_ImageRegion.SetSize(1, 10); m_ImageRegion.SetSize(2, 10); } TractsToDWIImageFilter::~TractsToDWIImageFilter() { } TractsToDWIImageFilter::DoubleDwiType::Pointer TractsToDWIImageFilter::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images ) { // create slice object ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); // frequency map slice SliceType::Pointer fMap = NULL; if (m_FrequencyMap.IsNotNull()) { fMap = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); fMap->SetLargestPossibleRegion( region ); fMap->SetBufferedRegion( region ); fMap->SetRequestedRegion( region ); fMap->Allocate(); } DoubleDwiType::Pointer newImage = DoubleDwiType::New(); newImage->SetSpacing( m_Spacing ); newImage->SetOrigin( m_Origin ); newImage->SetDirection( m_DirectionMatrix ); newImage->SetLargestPossibleRegion( m_ImageRegion ); newImage->SetBufferedRegion( m_ImageRegion ); newImage->SetRequestedRegion( m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); MatrixType transform = m_DirectionMatrix; for (int i=0; i<3; i++) for (int j=0; j<3; j++) { if (j<2) transform[i][j] *= m_UpsampledSpacing[j]; else transform[i][j] *= m_Spacing[j]; } boost::progress_display disp(images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2)); for (int g=0; gGetVectorLength(); g++) for (int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { - ++disp; std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (int i=0; i* signalModel; if (iSetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->Allocate(); slice->FillBuffer(0.0); // extract slice from channel g for (int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (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 (fMap.IsNotNull() && i==0) fMap->SetPixel(index2D, m_FrequencyMap->GetPixel(index3D)); } compartmentSlices.push_back(slice); t2Vector.push_back(signalModel->GetT2()); } // create k-sapce (inverse fourier transform slices) + itk::Size<2> outSize; outSize.SetElement(0, m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_ImageRegion.GetSize(1)); + MITK_INFO << outSize; itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetT2(t2Vector); idft->SetkOffset(m_kOffset); idft->SettLine(m_tLine); idft->SetTE(m_TE); idft->SetTinhom(m_tInhom); idft->SetSimulateRelaxation(m_SimulateRelaxation); idft->SetSimulateEddyCurrents(m_SimulateEddyCurrents); idft->SetEddyGradientMagnitude(m_EddyGradientStrength); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); idft->SetDirectionMatrix(transform); idft->SetDiffusionGradientDirection(m_FiberModels.at(0)->GetGradientDirection(g)); idft->SetFrequencyMap(fMap); idft->SetSignalScale(m_SignalScale); + idft->SetOutSize(outSize); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); - fSlice = RearrangeSlice(fSlice); - // add artifacts - for (int a=0; aAddArtifact(fSlice); + for (int i=0; iAddArtifact(fSlice); // 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 (int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (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; } return newImage; } TractsToDWIImageFilter::ComplexSliceType::Pointer TractsToDWIImageFilter::RearrangeSlice(ComplexSliceType::Pointer slice) { ImageRegion<2> region = slice->GetLargestPossibleRegion(); ComplexSliceType::Pointer rearrangedSlice = ComplexSliceType::New(); rearrangedSlice->SetLargestPossibleRegion( region ); rearrangedSlice->SetBufferedRegion( region ); rearrangedSlice->SetRequestedRegion( region ); rearrangedSlice->Allocate(); int xHalf = region.GetSize(0)/2; int yHalf = region.GetSize(1)/2; for (int y=0; y pix = slice->GetPixel(idx); if( idx[0] < xHalf ) idx[0] = idx[0] + xHalf; else idx[0] = idx[0] - xHalf; if( idx[1] < yHalf ) idx[1] = idx[1] + yHalf; else idx[1] = idx[1] - yHalf; rearrangedSlice->SetPixel(idx, pix); } return rearrangedSlice; } void TractsToDWIImageFilter::GenerateData() { // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); int numFibers = m_FiberBundle->GetNumFibers(); if (numFibers<=0) itkExceptionMacro("Input fiber bundle contains no fibers!"); if (m_FiberModels.empty()) itkExceptionMacro("No diffusion model for fiber compartments defined!"); if (m_NonFiberModels.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); int baselineIndex = m_FiberModels[0]->GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); - // determine k-space undersampling - for (int i=0; i*>(m_KspaceArtifacts.at(i)) ) - m_Upsampling = dynamic_cast*>(m_KspaceArtifacts.at(i))->GetKspaceCropping(); + // check k-space undersampling if (m_Upsampling<1) m_Upsampling = 1; if (m_TissueMask.IsNotNull()) { // use input tissue mask m_Spacing = m_TissueMask->GetSpacing(); m_Origin = m_TissueMask->GetOrigin(); m_DirectionMatrix = m_TissueMask->GetDirection(); m_ImageRegion = m_TissueMask->GetLargestPossibleRegion(); if (m_Upsampling>1.00001) { + MITK_INFO << "Adding ringing artifacts. Image upsampling factor: " << m_Upsampling; ImageRegion<3> region = m_ImageRegion; region.SetSize(0, m_ImageRegion.GetSize(0)*m_Upsampling); region.SetSize(1, m_ImageRegion.GetSize(1)*m_Upsampling); itk::Vector spacing = m_Spacing; spacing[0] /= m_Upsampling; spacing[1] /= m_Upsampling; itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_TissueMask); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); resampler->SetOutputParametersFromImage(m_TissueMask); resampler->SetSize(region.GetSize()); resampler->SetOutputSpacing(spacing); resampler->Update(); m_TissueMask = resampler->GetOutput(); } MITK_INFO << "Using tissue mask"; } // initialize output dwi image OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Spacing ); outImage->SetOrigin( m_Origin ); outImage->SetDirection( m_DirectionMatrix ); outImage->SetLargestPossibleRegion( m_ImageRegion ); outImage->SetBufferedRegion( m_ImageRegion ); outImage->SetRequestedRegion( m_ImageRegion ); outImage->SetVectorLength( m_FiberModels[0]->GetNumGradients() ); outImage->Allocate(); OutputImageType::PixelType temp; temp.SetSize(m_FiberModels[0]->GetNumGradients()); temp.Fill(0.0); outImage->FillBuffer(temp); // is input slize size a power of two? int x=m_ImageRegion.GetSize(0); int y=m_ImageRegion.GetSize(1); if ( x%2 == 1 ) x += 1; if ( y%2 == 1 ) y += 1; // if not, adjust size and dimension (needed for FFT); zero-padding if (x!=m_ImageRegion.GetSize(0)) m_ImageRegion.SetSize(0, x); if (y!=m_ImageRegion.GetSize(1)) m_ImageRegion.SetSize(1, y); // apply undersampling to image parameters m_UpsampledSpacing = m_Spacing; m_UpsampledImageRegion = m_ImageRegion; m_UpsampledSpacing[0] /= m_Upsampling; m_UpsampledSpacing[1] /= m_Upsampling; m_UpsampledImageRegion.SetSize(0, m_ImageRegion.GetSize()[0]*m_Upsampling); m_UpsampledImageRegion.SetSize(1, m_ImageRegion.GetSize()[1]*m_Upsampling); // everything from here on is using the upsampled image parameters!!! if (m_TissueMask.IsNull()) { m_TissueMask = ItkUcharImgType::New(); m_TissueMask->SetSpacing( m_UpsampledSpacing ); m_TissueMask->SetOrigin( m_Origin ); m_TissueMask->SetDirection( m_DirectionMatrix ); m_TissueMask->SetLargestPossibleRegion( m_UpsampledImageRegion ); m_TissueMask->SetBufferedRegion( m_UpsampledImageRegion ); m_TissueMask->SetRequestedRegion( m_UpsampledImageRegion ); m_TissueMask->Allocate(); m_TissueMask->FillBuffer(1); } // resample frequency map if (m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(m_FrequencyMap); resampler->SetOutputParametersFromImage(m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->Update(); m_FrequencyMap = resampler->GetOutput(); } // initialize volume fraction images m_VolumeFractions.clear(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); tempimg->SetOrigin( m_Origin ); tempimg->SetDirection( m_DirectionMatrix ); tempimg->SetLargestPossibleRegion( m_UpsampledImageRegion ); tempimg->SetBufferedRegion( m_UpsampledImageRegion ); tempimg->SetRequestedRegion( m_UpsampledImageRegion ); tempimg->Allocate(); tempimg->FillBuffer(0); m_VolumeFractions.push_back(tempimg); } // resample fiber bundle for sufficient voxel coverage double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); fiberBundle->ResampleFibers(minSpacing/m_VolumeAccuracy); double mmRadius = m_FiberRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/m_VolumeAccuracy; // generate double images to work with because we don't want to lose precision // we use a separate image for each compartment model std::vector< DoubleDwiType::Pointer > compartments; for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_Origin ); doubleDwi->SetDirection( m_DirectionMatrix ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); doubleDwi->SetVectorLength( m_FiberModels[0]->GetNumGradients() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; pix.SetSize(m_FiberModels[0]->GetNumGradients()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); compartments.push_back(doubleDwi); } double interpFact = 2*atan(-0.5*m_InterpolationShrink); double maxVolume = 0; MITK_INFO << "Generating signal of " << m_FiberModels.size() << " fiber compartments"; vtkSmartPointer fiberPolyData = fiberBundle->GetFiberPolyData(); boost::progress_display disp(numFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; for( int j=0; jGetPoint(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)); itk::Index<3> idx; itk::ContinuousIndex contIndex; m_TissueMask->TransformPhysicalPointToIndex(vertex, idx); m_TissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!m_UseInterpolation) // use nearest neighbour interpolation { if (!m_TissueMask->GetLargestPossibleRegion().IsInside(idx) || m_TissueMask->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment for (int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(idx); pix += segmentVolume*m_FiberModels[k]->SimulateMeasurement(); doubleDwi->SetPixel(idx, pix ); if (pix[baselineIndex]>maxVolume) maxVolume = pix[baselineIndex]; } continue; } double frac_x = contIndex[0] - idx[0]; double frac_y = contIndex[1] - idx[1]; double frac_z = contIndex[2] - idx[2]; if (frac_x<0) { idx[0] -= 1; frac_x += 1; } if (frac_y<0) { idx[1] -= 1; frac_y += 1; } if (frac_z<0) { idx[2] -= 1; frac_z += 1; } frac_x = atan((0.5-frac_x)*m_InterpolationShrink)/interpFact + 0.5; frac_y = atan((0.5-frac_y)*m_InterpolationShrink)/interpFact + 0.5; frac_z = atan((0.5-frac_z)*m_InterpolationShrink)/interpFact + 0.5; // use trilinear interpolation itk::Index<3> newIdx; for (int x=0; x<2; x++) { frac_x = 1-frac_x; for (int y=0; y<2; y++) { frac_y = 1-frac_y; for (int z=0; z<2; z++) { frac_z = 1-frac_z; newIdx[0] = idx[0]+x; newIdx[1] = idx[1]+y; newIdx[2] = idx[2]+z; double frac = frac_x*frac_y*frac_z; // is position valid? if (!m_TissueMask->GetLargestPossibleRegion().IsInside(newIdx) || m_TissueMask->GetPixel(newIdx)<=0) continue; // generate signal for each fiber compartment for (int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(newIdx); pix += segmentVolume*frac*m_FiberModels[k]->SimulateMeasurement(); doubleDwi->SetPixel(newIdx, pix ); if (pix[baselineIndex]>maxVolume) maxVolume = pix[baselineIndex]; } } } } } + ++disp; } MITK_INFO << "Generating signal of " << m_NonFiberModels.size() << " non-fiber compartments"; ImageRegionIterator it3(m_TissueMask, m_TissueMask->GetLargestPossibleRegion()); boost::progress_display disp3(m_TissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; double fact = 1; if (m_FiberRadius<0.0001) fact = voxelVolume/maxVolume; while(!it3.IsAtEnd()) { - ++disp3; DoubleDwiType::IndexType index = it3.GetIndex(); if (it3.Get()>0) { // get fiber volume fraction DoubleDwiType::Pointer fiberDwi = compartments.at(0); DoubleDwiType::PixelType fiberPix = fiberDwi->GetPixel(index); // intra axonal compartment if (fact>1) // auto scale intra-axonal if no fiber radius is specified { fiberPix *= fact; fiberDwi->SetPixel(index, fiberPix); } double f = fiberPix[baselineIndex]; if (f>voxelVolume || f>0 && m_EnforcePureFiberVoxels) // more fiber than space in voxel? { fiberDwi->SetPixel(index, fiberPix*voxelVolume/f); for (int i=1; iSetPixel(index, pix); m_VolumeFractions.at(i)->SetPixel(index, 1); } } else { m_VolumeFractions.at(0)->SetPixel(index, f); double nonf = voxelVolume-f; // non-fiber volume double inter = 0; if (m_FiberModels.size()>1) inter = nonf * f/voxelVolume; // intra-axonal fraction of non fiber compartment scales linearly with f double other = nonf - inter; // rest of compartment double singleinter = inter/(m_FiberModels.size()-1); // adjust non-fiber and intra-axonal signal for (int i=1; iGetPixel(index); if (pix[baselineIndex]>0) pix /= pix[baselineIndex]; pix *= singleinter; doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume); } for (int i=0; iGetPixel(index) + m_NonFiberModels[i]->SimulateMeasurement()*other*m_NonFiberModels[i]->GetWeight(); doubleDwi->SetPixel(index, pix); m_VolumeFractions.at(i+m_FiberModels.size())->SetPixel(index, other/voxelVolume*m_NonFiberModels[i]->GetWeight()); } } } ++it3; + ++disp3; } // do k-space stuff DoubleDwiType::Pointer doubleOutImage; - if (m_FrequencyMap.IsNotNull() || !m_KspaceArtifacts.empty() || m_kOffset>0 || m_SimulateRelaxation || m_SimulateEddyCurrents) + if (m_FrequencyMap.IsNotNull() || !m_KspaceArtifacts.empty() || m_kOffset>0 || m_SimulateRelaxation || m_SimulateEddyCurrents || m_Upsampling>1.00001) { MITK_INFO << "Adjusting complex signal"; doubleOutImage = DoKspaceStuff(compartments); m_SignalScale = 1; } else { MITK_INFO << "Summing compartments"; doubleOutImage = compartments.at(0); for (int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); adder->SetInput2(compartments.at(i)); adder->Update(); doubleOutImage = adder->GetOutput(); } } MITK_INFO << "Finalizing image"; unsigned int window = 0; unsigned int min = itk::NumericTraits::max(); ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); DoubleDwiType::PixelType signal; signal.SetSize(m_FiberModels[0]->GetNumGradients()); boost::progress_display disp4(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); while(!it4.IsAtEnd()) { ++disp4; DWIImageType::IndexType index = it4.GetIndex(); signal = doubleOutImage->GetPixel(index)*m_SignalScale; if (m_NoiseModel->GetNoiseVariance() > 0) { DoubleDwiType::PixelType accu = signal; accu.Fill(0.0); for (int i=0; iAddNoise(temp); accu += temp; } signal = accu/m_NumberOfRepetitions; } for (int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]>window) window = signal[i]; if (!m_FiberModels.at(0)->IsBaselineIndex(i) && signal[i]SetNthOutput(0, outImage); } itk::Point TractsToDWIImageFilter::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } itk::Vector TractsToDWIImageFilter::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } vnl_vector_fixed TractsToDWIImageFilter::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } vnl_vector_fixed TractsToDWIImageFilter::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h index 18dbccc23b..c09dfbc671 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h @@ -1,151 +1,151 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkTractsToDWIImageFilter_h__ #define __itkTractsToDWIImageFilter_h__ // MITK #include #include #include #include -#include // ITK #include #include #include #include #include #include typedef itk::VectorImage< short, 3 > DWIImageType; namespace itk { /** * \brief Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. */ class TractsToDWIImageFilter : public ImageSource< DWIImageType > { public: typedef TractsToDWIImageFilter Self; typedef ImageSource< DWIImageType > Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkFloatImgType; typedef itk::Image ItkUcharImgType; typedef mitk::FiberBundleX::Pointer FiberBundleType; typedef itk::VectorImage< double, 3 > DoubleDwiType; typedef std::vector< mitk::KspaceArtifact* > KspaceArtifactList; typedef std::vector< mitk::DiffusionSignalModel* > DiffusionModelList; typedef itk::Matrix MatrixType; typedef mitk::DiffusionNoiseModel NoiseModelType; typedef itk::Image< double, 2 > SliceType; typedef itk::VnlForwardFFTImageFilter::OutputImageType ComplexSliceType; itkNewMacro(Self) itkTypeMacro( TractsToDWIImageFilter, ImageToImageFilter ) // input itkSetMacro( SignalScale, double ) itkSetMacro( FiberRadius, double ) itkSetMacro( InterpolationShrink, double ) ///< large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation) itkSetMacro( VolumeAccuracy, unsigned int ) ///< determines fiber sampling density and thereby the accuracy of the fiber volume fraction itkSetMacro( FiberBundle, FiberBundleType ) ///< input fiber bundle itkSetMacro( Spacing, mitk::Vector3D ) ///< output image spacing itkSetMacro( Origin, mitk::Point3D ) ///< output image origin itkSetMacro( DirectionMatrix, MatrixType ) ///< output image rotation itkSetMacro( EnforcePureFiberVoxels, bool ) ///< treat all voxels containing at least one fiber as fiber-only (actually disable non-fiber compartments for this voxel). itkSetMacro( ImageRegion, ImageRegion<3> ) ///< output image size itkSetMacro( NumberOfRepetitions, unsigned int ) ///< number of acquisition repetitions to reduce noise (default is no additional repetition) itkSetMacro( TissueMask, ItkUcharImgType::Pointer ) ///< voxels outside of this binary mask contain only noise (are treated as air) void SetNoiseModel(NoiseModelType* noiseModel){ m_NoiseModel = noiseModel; } ///< generates the noise added to the image values void SetFiberModels(DiffusionModelList modelList){ m_FiberModels = modelList; } ///< generate signal of fiber compartments void SetNonFiberModels(DiffusionModelList modelList){ m_NonFiberModels = modelList; } ///< generate signal of non-fiber compartments void SetKspaceArtifacts(KspaceArtifactList artifactList){ m_KspaceArtifacts = artifactList; } mitk::LevelWindow GetLevelWindow(){ return m_LevelWindow; } itkSetMacro( FrequencyMap, ItkDoubleImgType::Pointer ) itkSetMacro( kOffset, double ) itkSetMacro( tLine, double ) itkSetMacro( tInhom, double ) itkSetMacro( TE, double ) itkSetMacro( UseInterpolation, bool ) itkSetMacro( SimulateEddyCurrents, bool ) itkSetMacro( SimulateRelaxation, bool ) itkSetMacro( EddyGradientStrength, double ) + itkSetMacro( Upsampling, double ) // output std::vector< ItkDoubleImgType::Pointer > GetVolumeFractions(){ return m_VolumeFractions; } void GenerateData(); protected: TractsToDWIImageFilter(); virtual ~TractsToDWIImageFilter(); itk::Point GetItkPoint(double point[3]); itk::Vector GetItkVector(double point[3]); vnl_vector_fixed GetVnlVector(double point[3]); vnl_vector_fixed GetVnlVector(Vector< float, 3 >& vector); /** Transform generated image compartment by compartment, channel by channel and slice by slice using FFT and add k-space artifacts. */ DoubleDwiType::Pointer DoKspaceStuff(std::vector< DoubleDwiType::Pointer >& images); /** Rearrange FFT output to shift low frequencies to the iamge center (correct itk). */ TractsToDWIImageFilter::ComplexSliceType::Pointer RearrangeSlice(ComplexSliceType::Pointer slice); itk::Vector m_Spacing; ///< output image spacing itk::Vector m_UpsampledSpacing; mitk::Point3D m_Origin; ///< output image origin MatrixType m_DirectionMatrix; ///< output image rotation ImageRegion<3> m_ImageRegion; ///< output image size ImageRegion<3> m_UpsampledImageRegion; ItkUcharImgType::Pointer m_TissueMask; ///< voxels outside of this binary mask contain only noise (are treated as air) ItkDoubleImgType::Pointer m_FrequencyMap; ///< map of the B0 inhomogeneities double m_kOffset; double m_tLine; double m_TE; double m_tInhom; FiberBundleType m_FiberBundle; ///< input fiber bundle DiffusionModelList m_FiberModels; ///< generate signal of fiber compartments DiffusionModelList m_NonFiberModels; ///< generate signal of non-fiber compartments KspaceArtifactList m_KspaceArtifacts; NoiseModelType* m_NoiseModel; ///< generates the noise added to the image values bool m_CircleDummy; unsigned int m_VolumeAccuracy; - double m_Upsampling; + double m_Upsampling; ///< causes ringing artifacts unsigned int m_NumberOfRepetitions; bool m_EnforcePureFiberVoxels; double m_InterpolationShrink; double m_FiberRadius; double m_SignalScale; mitk::LevelWindow m_LevelWindow; bool m_UseInterpolation; std::vector< ItkDoubleImgType::Pointer > m_VolumeFractions; ///< one double image for each compartment containing the corresponding volume fraction per voxel bool m_SimulateRelaxation; bool m_SimulateEddyCurrents; double m_EddyGradientStrength; }; } #include "itkTractsToDWIImageFilter.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt index 833650d9e1..0b885f1b05 100644 --- a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt @@ -1,44 +1,45 @@ MITK_CHECK_MODULE(_missing_deps DiffusionCore MitkGraphAlgorithms) if(NOT _missing_deps) set(lut_url http://mitk.org/download/data/FibertrackingLUT.tar.gz) set(lut_tarball ${CMAKE_CURRENT_BINARY_DIR}/FibertrackingLUT.tar.gz) message("Downloading FiberTracking LUT ${lut_url}...") file(DOWNLOAD ${lut_url} ${lut_tarball} EXPECTED_MD5 38ecb6d4a826c9ebb0f4965eb9aeee44 TIMEOUT 20 STATUS status SHOW_PROGRESS ) list(GET status 0 status_code) list(GET status 1 status_msg) if(NOT status_code EQUAL 0) message(SEND_ERROR "${status_msg} (error code ${status_code})") else() message("done.") endif() file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources) message("Unpacking FiberTracking LUT tarball...") execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ../FibertrackingLUT.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources RESULT_VARIABLE result ERROR_VARIABLE err_msg) if(result) message(SEND_ERROR "Unpacking FibertrackingLUT.tar.gz failed: ${err_msg}") else() message("done.") endif() endif() MITK_CREATE_MODULE( FiberTracking SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms Algorithms/GibbsTracking Algorithms/StochasticTracking IODataStructures IODataStructures/FiberBundleX IODataStructures/PlanarFigureComposite Interactions SignalModels Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS DiffusionCore MitkGraphAlgorithms ) if(MODULE_IS_ENABLED) add_subdirectory(Testing) + add_subdirectory(MiniApps) endif() diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/MiniApps/CMakeLists.txt new file mode 100755 index 0000000000..860206a99f --- /dev/null +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/CMakeLists.txt @@ -0,0 +1,47 @@ +OPTION(BUILD_FiberTrackingMiniApps "Build commandline tools for fiber tracking" OFF) + +IF(BUILD_FiberTrackingMiniApps) + + # include necessary modules here MitkExt QmitkExt + MITK_CHECK_MODULE(_RESULT DiffusionCore FiberTracking ) + IF(_RESULT) + MESSAGE("Warning: FiberTrackingMiniApps is missing ${_RESULT}") + ELSE(_RESULT) + MITK_USE_MODULE( DiffusionCore FiberTracking ) + + # needed include directories + INCLUDE_DIRECTORIES( + ${CMAKE_CURRENT_SOURCE_DIR} + ${CMAKE_CURRENT_BINARY_DIR} + ${ALL_INCLUDE_DIRECTORIES}) + + PROJECT( mitkFiberTrackingMiniApps ) + + # fill in the standalone executables here + SET(FIBERTRACKINGMINIAPPS + mitkFiberTrackingMiniApps + ) + + # set additional files here + SET(FIBERTRACKING_ADDITIONAL_FILES + MiniAppManager.cpp + GibbsTracking.cpp + ) + + # create an executable foreach tool (only one at the moment) + FOREACH(tool ${FIBERTRACKINGMINIAPPS}) + ADD_EXECUTABLE( + ${tool} + ${tool}.cpp + ${FIBERTRACKING_ADDITIONAL_FILES} + ) + + TARGET_LINK_LIBRARIES( + ${tool} + ${ALL_LIBRARIES} ) + ENDFOREACH(tool) + ENDIF() + + MITK_INSTALL_TARGETS(EXECUTABLES mitkFiberTrackingMiniApps ) + +ENDIF(BUILD_FiberTrackingMiniApps) diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/GibbsTracking.cpp b/Modules/DiffusionImaging/FiberTracking/MiniApps/GibbsTracking.cpp new file mode 100755 index 0000000000..c527d8367d --- /dev/null +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/GibbsTracking.cpp @@ -0,0 +1,219 @@ +/*=================================================================== + +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 "MiniAppManager.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +template +typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit) +{ + typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType; + typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(mitkImg); + caster->Update(); + + typename FilterType::Pointer filter = FilterType::New(); + + switch (toolkit) + { + case 0: + filter->SetToolkit(FilterType::FSL); + break; + case 1: + filter->SetToolkit(FilterType::MRTRIX); + break; + default: + filter->SetToolkit(FilterType::FSL); + } + + filter->SetInputImage(caster->GetOutput()); + filter->GenerateData(); + return filter->GetQballImage(); +} + +int GibbsTracking(int argc, char* argv[]) +{ + if (argc<6) + { + std::cout << std::endl; + std::cout << "Performes Gibbs Tracking" << std::endl; + std::cout << std::endl; + std::cout << "usage: " << argv[0] << " " << std::endl; + std::cout << std::endl; + return EXIT_FAILURE; + } + + try + { + RegisterDiffusionCoreObjectFactory(); + RegisterFiberTrackingObjectFactory(); + + std::cout << "input: " << argv[1] << std::endl; + std::cout << "param: " << argv[2] << std::endl; + std::cout << "output: " << argv[3] << std::endl; + + // instantiate gibbs tracker + typedef itk::Vector OdfVectorType; + typedef itk::Image ItkQballImageType; + typedef itk::GibbsTrackingFilter GibbsTrackingFilterType; + GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); + + // load input image + const std::string s1="", s2=""; + std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[1], s1, s2, false ); + + // try to cast to qball image + QString inImageName(argv[1]); + if( inImageName.endsWith(".qbi") ) + { + MITK_INFO << "Loading qball image ..."; + mitk::QBallImage::Pointer mitkQballImage = dynamic_cast(infile.at(0).GetPointer()); + ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); + mitk::CastToItkImage(mitkQballImage, itk_qbi); + gibbsTracker->SetQBallImage(itk_qbi.GetPointer()); + } + else if( inImageName.endsWith(".dti") ) + { + MITK_INFO << "Loading tensor image ..."; + typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; + mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); + ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); + mitk::CastToItkImage(mitkTensorImage, itk_dti); + gibbsTracker->SetTensorImage(itk_dti); + } + else if ( inImageName.endsWith(".nii") ) + { + MITK_INFO << "Loading sh-coefficient image ..."; + mitk::Image::Pointer mitkImage = dynamic_cast(infile.at(0).GetPointer()); + + int nrCoeffs = mitkImage->GetLargestPossibleRegion().GetSize()[3]; + int c=3, d=2-2*nrCoeffs; + double D = c*c-4*d; + int shOrder; + if (D>0) + { + shOrder = (-c+sqrt(D))/2.0; + if (shOrder<0) + shOrder = (-c-sqrt(D))/2.0; + } + else if (D==0) + shOrder = -c/2.0; + + MITK_INFO << "using SH-order " << shOrder; + + int toolkitConvention = 0; + if(argc==6) + { + QString convention(argv[5]); + if ( convention.compare("MRtrix", Qt::CaseInsensitive)==0 ) + { + toolkitConvention = 1; + MITK_INFO << "Using MRtrix style sh-coefficient convention"; + } + else + MITK_INFO << "Using FSL style sh-coefficient convention"; + } + else + MITK_INFO << "Using FSL style sh-coefficient convention"; + + switch (shOrder) + { + case 4: + gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention)); + break; + case 6: + gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention)); + break; + case 8: + gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention)); + break; + case 10: + gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention)); + break; + case 12: + gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention)); + break; + default: + MITK_INFO << "SH-order " << shOrder << " not supported"; + } + } + else + return EXIT_FAILURE; + + // global tracking + if(argc>=5) + { + typedef itk::Image MaskImgType; + std::cout << "mask: " << argv[4]<< std::endl; + infile = mitk::BaseDataIO::LoadBaseDataFromFile( argv[4], s1, s2, false ); + mitk::Image::Pointer mitkMaskImage = dynamic_cast(infile.at(0).GetPointer()); + MaskImgType::Pointer itk_mask = MaskImgType::New(); + mitk::CastToItkImage(mitkMaskImage, itk_mask); + gibbsTracker->SetMaskImage(itk_mask); + } + else{ + std::cout << "perform tracking without mask" << std::endl; + } + + gibbsTracker->SetDuplicateImage(false); + gibbsTracker->SetLoadParameterFile( argv[2] ); +// gibbsTracker->SetLutPath( "" ); + gibbsTracker->Update(); + + mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); + + std::string outfilename = argv[3]; + MITK_INFO << "searching writer"; + mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); + for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) + { + if ( (*it)->CanWriteBaseDataType(mitkFiberBundle.GetPointer()) ) { + (*it)->SetFileName( outfilename.c_str() ); + (*it)->DoWrite( mitkFiberBundle.GetPointer() ); + } + } + } + catch (itk::ExceptionObject e) + { + MITK_INFO << e; + return EXIT_FAILURE; + } + catch (std::exception e) + { + MITK_INFO << e.what(); + return EXIT_FAILURE; + } + catch (...) + { + MITK_INFO << "ERROR!?!"; + return EXIT_FAILURE; + } + MITK_INFO << "DONE"; + return EXIT_SUCCESS; +} +RegisterFiberTrackingMiniApp(GibbsTracking); diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/MiniAppManager.cpp b/Modules/DiffusionImaging/FiberTracking/MiniApps/MiniAppManager.cpp new file mode 100755 index 0000000000..a27128840b --- /dev/null +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/MiniAppManager.cpp @@ -0,0 +1,91 @@ +/*=================================================================== + +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 "MiniAppManager.h" + +MiniAppManager* MiniAppManager::GetInstance() +{ + static MiniAppManager instance; + return &instance; +} + +// Attention: Name of the miniApp must be the last argument!!! +// it will be cut off from the rest of the arguments and then +// the app will be run +int MiniAppManager::RunMiniApp(int argc, char* argv[]) +{ + try + { + std::string nameOfMiniApp; + std::map< std::string, MiniAppFunction >::iterator it = m_Functions.begin(); + + if( argc < 2) + { + std::cout << "Please choose the mini app to execute: " << std::endl; + + for(int i=0; it != m_Functions.end(); ++i,++it) + { + std::cout << "(" << i << ")" << " " << it->first << std::endl; + } + std::cout << "Please select: "; + int choose; + std::cin >> choose; + + it = m_Functions.begin(); + std::advance(it, choose); + if( it != m_Functions.end() ) + nameOfMiniApp = it->first; + } + else + { + nameOfMiniApp = argv[argc-1]; + --argc; + } + + it = m_Functions.find(nameOfMiniApp); + if(it == m_Functions.end()) + { + std::ostringstream s; s << "MiniApp (" << nameOfMiniApp << ") not found!"; + throw std::invalid_argument(s.str().c_str()); + } + + MITK_INFO << "Start " << nameOfMiniApp << " .."; + MiniAppFunction func = it->second; + return func( argc, argv ); + } + + catch(std::exception& e) + { + MITK_ERROR << e.what(); + } + + catch(...) + { + MITK_ERROR << "Unknown error occurred"; + } + + return EXIT_FAILURE; +} + +///////////////////// +// MiniAppFunction // +///////////////////// +MiniAppManager::MiniAppFunction +MiniAppManager::AddFunction(const std::string& name, MiniAppFunction func) +{ + m_Functions.insert( std::pair(name, func) ); + return func; +} diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/MiniAppManager.h b/Modules/DiffusionImaging/FiberTracking/MiniApps/MiniAppManager.h new file mode 100755 index 0000000000..989baad3cc --- /dev/null +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/MiniAppManager.h @@ -0,0 +1,38 @@ +#ifndef MiniAppManager_h +#define MiniAppManager_h + +#include + +struct MiniAppManager +{ + +public: + + typedef int (*MiniAppFunction)(int argc, char* argv[]); + +public: + + static MiniAppManager* GetInstance(); + + // Attention: Name of the miniApp must be the last argument!!! + // it will be cut off from the rest of the arguments and then + // the app will be run + int RunMiniApp(int argc, char* argv[]); + + // + // Add miniApp + // + MiniAppFunction AddFunction(const std::string& name, MiniAppFunction func); + +protected: + + std::map< std::string, MiniAppFunction > m_Functions; +}; + +// +// Register miniApps +// +#define RegisterFiberTrackingMiniApp(functionName) \ + static MiniAppManager::MiniAppFunction MiniApp##functionName = \ + MiniAppManager::GetInstance()->AddFunction(#functionName, &functionName) +#endif diff --git a/Modules/DiffusionImaging/FiberTracking/MiniApps/mitkFiberTrackingMiniApps.cpp b/Modules/DiffusionImaging/FiberTracking/MiniApps/mitkFiberTrackingMiniApps.cpp new file mode 100755 index 0000000000..c7d6ac601a --- /dev/null +++ b/Modules/DiffusionImaging/FiberTracking/MiniApps/mitkFiberTrackingMiniApps.cpp @@ -0,0 +1,22 @@ +/*=================================================================== + +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 + +int main(int argc, char* argv[]) +{ + return MiniAppManager::GetInstance()->RunMiniApp(argc, argv); +} diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkGibbsRingingArtifact.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkGibbsRingingArtifact.cpp deleted file mode 100755 index b9f16f14ce..0000000000 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkGibbsRingingArtifact.cpp +++ /dev/null @@ -1,62 +0,0 @@ -/*=================================================================== - -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 - -template< class ScalarType > -GibbsRingingArtifact< ScalarType >::GibbsRingingArtifact() - : m_KspaceCropping(1.1) -{ - -} - -template< class ScalarType > -GibbsRingingArtifact< ScalarType >::~GibbsRingingArtifact() -{ - -} - -template< class ScalarType > -typename GibbsRingingArtifact< ScalarType >::ComplexSliceType::Pointer GibbsRingingArtifact< ScalarType >::AddArtifact(typename ComplexSliceType::Pointer slice) -{ - itk::ImageRegion<2> region = slice->GetLargestPossibleRegion(); - - int x = region.GetSize()[0]/m_KspaceCropping; - int y = region.GetSize()[1]/m_KspaceCropping; - - typename ComplexSliceType::Pointer newSlice = ComplexSliceType::New(); - itk::ImageRegion<2> newRegion; - newRegion.SetSize(0, x); - newRegion.SetSize(1, y); - - newSlice->SetLargestPossibleRegion( newRegion ); - newSlice->SetBufferedRegion( newRegion ); - newSlice->SetRequestedRegion( newRegion ); - newSlice->Allocate(); - - itk::ImageRegionIterator it(newSlice, newRegion); - while(!it.IsAtEnd()) - { - typename ComplexSliceType::IndexType idx; - idx[0] = region.GetSize()[0]/2-x/2+it.GetIndex()[0]; - idx[1] = region.GetSize()[1]/2-y/2+it.GetIndex()[1]; - - it.Set(slice->GetPixel(idx)); - - ++it; - } - return newSlice; -} diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkGibbsRingingArtifact.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkGibbsRingingArtifact.h deleted file mode 100755 index f418a9d16a..0000000000 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkGibbsRingingArtifact.h +++ /dev/null @@ -1,58 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef _MITK_GibbsRingingArtifact_H -#define _MITK_GibbsRingingArtifact_H - -#include -#include -#include -#include - -namespace mitk { - -/** - * \brief Class to add gibbs ringing artifact to input complex slice - * - */ -template< class ScalarType > -class GibbsRingingArtifact : public KspaceArtifact< ScalarType > -{ -public: - - GibbsRingingArtifact(); - ~GibbsRingingArtifact(); - - typedef typename KspaceArtifact< ScalarType >::ComplexSliceType ComplexSliceType; - - /** Adds Gibbs ringing to the input slice (by zero padding). **/ - typename ComplexSliceType::Pointer AddArtifact(typename ComplexSliceType::Pointer slice); - - void SetKspaceCropping(double factor){ m_KspaceCropping=factor; } - double GetKspaceCropping(){ return m_KspaceCropping; } - -protected: - - double m_KspaceCropping; - -}; - -#include "mitkGibbsRingingArtifact.cpp" - -} - -#endif - diff --git a/Modules/DiffusionImaging/FiberTracking/files.cmake b/Modules/DiffusionImaging/FiberTracking/files.cmake index c793736569..6b4fa49bff 100644 --- a/Modules/DiffusionImaging/FiberTracking/files.cmake +++ b/Modules/DiffusionImaging/FiberTracking/files.cmake @@ -1,103 +1,102 @@ set(CPP_FILES # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.cpp # DataStructures -> PlanarFigureComposite IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp # DataStructures IODataStructures/mitkFiberTrackingObjectFactory.cpp # Rendering Rendering/mitkFiberBundleXMapper2D.cpp Rendering/mitkFiberBundleXMapper3D.cpp Rendering/mitkFiberBundleXThreadMonitorMapper3D.cpp #Rendering/mitkPlanarFigureMapper3D.cpp # Interactions Interactions/mitkFiberBundleInteractor.cpp # Algorithms Algorithms/mitkTractAnalyzer.cpp # Tractography Algorithms/GibbsTracking/mitkParticleGrid.cpp Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp Algorithms/GibbsTracking/mitkEnergyComputer.cpp Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp Algorithms/GibbsTracking/mitkFiberBuilder.cpp Algorithms/GibbsTracking/mitkSphereInterpolator.cpp ) set(H_FILES # Rendering Rendering/mitkFiberBundleXMapper3D.h Rendering/mitkFiberBundleXMapper2D.h Rendering/mitkFiberBundleXThreadMonitorMapper3D.h #Rendering/mitkPlanarFigureMapper3D.h # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.h IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h IODataStructures/FiberBundleX/mitkFiberBundleXReader.h IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.h IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.h IODataStructures/mitkFiberTrackingObjectFactory.h # Algorithms Algorithms/itkTractDensityImageFilter.h Algorithms/itkTractsToFiberEndingsImageFilter.h Algorithms/itkTractsToRgbaImageFilter.h Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h Algorithms/itkFibersFromPlanarFiguresFilter.h Algorithms/itkTractsToDWIImageFilter.h Algorithms/itkTractsToVectorImageFilter.h Algorithms/itkKspaceImageFilter.h Algorithms/itkDftImageFilter.h Algorithms/itkAddArtifactsToDwiImageFilter.h Algorithms/itkFieldmapGeneratorFilter.h # (old) Tractography Algorithms/itkGibbsTrackingFilter.h Algorithms/itkStochasticTractographyFilter.h Algorithms/itkStreamlineTrackingFilter.h Algorithms/GibbsTracking/mitkParticle.h Algorithms/GibbsTracking/mitkParticleGrid.h Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h Algorithms/GibbsTracking/mitkSimpSamp.h Algorithms/GibbsTracking/mitkEnergyComputer.h Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h Algorithms/GibbsTracking/mitkSphereInterpolator.h Algorithms/GibbsTracking/mitkFiberBuilder.h # Signal Models SignalModels/mitkDiffusionSignalModel.h SignalModels/mitkTensorModel.h SignalModels/mitkBallModel.h SignalModels/mitkDotModel.h SignalModels/mitkAstroStickModel.h SignalModels/mitkStickModel.h SignalModels/mitkDiffusionNoiseModel.h SignalModels/mitkRicianNoiseModel.h SignalModels/mitkKspaceArtifact.h - SignalModels/mitkGibbsRingingArtifact.h ) set(RESOURCE_FILES # Binary directory resources FiberTrackingLUTBaryCoords.bin FiberTrackingLUTIndices.bin # Shaders Shaders/mitkShaderFiberClipping.xml ) 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 340e871f4c..ff0bd67487 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,1794 +1,1789 @@ /*=================================================================== 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 #include #include #include #include #define _USE_MATH_DEFINES #include const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) { } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_GibbsRingingFrame->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_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); connect((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(int)), (QObject*) this, SLOT(OnFiberSamplingChanged(int))); 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_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGibbsRinging(int))); 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_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))); } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::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::OnAddGibbsRinging(int value) { if (value>0) m_Controls->m_GibbsRingingFrame->setVisible(true); else m_Controls->m_GibbsRingingFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for( int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for( int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); UpdateGui(); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (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() { itk::ImageRegion<3> imageRegion; imageRegion.SetSize(0, m_Controls->m_SizeX->value()); imageRegion.SetSize(1, m_Controls->m_SizeY->value()); imageRegion.SetSize(2, m_Controls->m_SizeZ->value()); mitk::Vector3D spacing; spacing[0] = m_Controls->m_SpacingX->value(); spacing[1] = m_Controls->m_SpacingY->value(); spacing[2] = m_Controls->m_SpacingZ->value(); mitk::Point3D origin; origin[0] = spacing[0]/2; origin[1] = spacing[1]/2; origin[2] = spacing[2]/2; itk::Matrix directionMatrix; directionMatrix.SetIdentity(); if (m_SelectedImage.IsNotNull()) { mitk::Image* img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); imageRegion = itkImg->GetLargestPossibleRegion(); spacing = itkImg->GetSpacing(); origin = itkImg->GetOrigin(); directionMatrix = itkImg->GetDirection(); } DiffusionSignalModel::GradientListType gradientList; double bVal = 1000; if (m_SelectedDWI.IsNull()) { gradientList = GenerateHalfShell(m_Controls->m_NumGradientsBox->value());; bVal = m_Controls->m_BvalueBox->value(); } else { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); imageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); spacing = dwi->GetVectorImage()->GetSpacing(); origin = dwi->GetVectorImage()->GetOrigin(); directionMatrix = dwi->GetVectorImage()->GetDirection(); bVal = dwi->GetB_Value(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections(); for (int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; gradientList.push_back(g); } } if (m_SelectedBundles.empty()) { if (m_SelectedDWI.IsNotNull()) // add artifacts to existing diffusion weighted image { for (int i=0; i*>(m_SelectedImages.at(i)->GetData())) continue; mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedImages.at(i)->GetData()); double noiseVariance = 0; if (m_Controls->m_AddNoise->isChecked()) { noiseVariance = m_Controls->m_NoiseLevel->value(); artifactModelString += "_NOISE"; artifactModelString += QString::number(noiseVariance); } mitk::RicianNoiseModel noiseModel; noiseModel.SetNoiseVariance(noiseVariance); if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } double lineReadoutTime = m_Controls->m_LineReadoutTimeBox->value(); // add N/2 ghosting double kOffset = 0; if (m_Controls->m_AddGhosts->isChecked()) { artifactModelString += "_GHOST"; kOffset = m_Controls->m_kOffsetBox->value(); } if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } itk::AddArtifactsToDwiImageFilter< short >::Pointer filter = itk::AddArtifactsToDwiImageFilter< short >::New(); filter->SetInput(diffImg->GetVectorImage()); filter->SettLine(lineReadoutTime); filter->SetkOffset(kOffset); filter->SetNoiseModel(&noiseModel); filter->SetGradientList(gradientList); filter->SetTE(this->m_Controls->m_TEbox->value()); if (m_Controls->m_AddEddy->isChecked()) { filter->SetSimulateEddyCurrents(true); filter->SetEddyGradientStrength(m_Controls->m_EddyGradientStrength->value()); artifactModelString += "_EDDY"; } - mitk::GibbsRingingArtifact gibbsModel; if (m_Controls->m_AddGibbsRinging->isChecked()) { - resultNode->AddProperty("Fiberfox.k-Space-Undersampling", DoubleProperty::New(m_Controls->m_KspaceUndersamplingBox->value())); - gibbsModel.SetKspaceCropping(m_Controls->m_KspaceUndersamplingBox->value()); - filter->SetRingingModel(&gibbsModel); + resultNode->AddProperty("Fiberfox.kRinging-Upsampling", DoubleProperty::New(m_Controls->m_ImageUpsamplingBox->value())); + filter->SetUpsampling(m_Controls->m_ImageUpsamplingBox->value()); } 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 (imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { filter->SetFrequencyMap(itkImg); artifactModelString += "_DISTORTED"; } } filter->Update(); resultNode->AddProperty("Fiberfox.Line-Offset", DoubleProperty::New(kOffset)); resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); resultNode->AddProperty("Fiberfox.Tinhom", IntProperty::New(m_Controls->m_T2starBox->value())); resultNode->AddProperty("binary", BoolProperty::New(false)); mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(diffImg->GetB_Value()); image->SetDirections(diffImg->GetDirections()); image->InitializeFromVectorImage(); resultNode->SetData( image ); resultNode->SetName(m_SelectedImages.at(i)->GetName()+artifactModelString.toStdString()); GetDataStorage()->Add(resultNode); } return; } mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::Geometry3D* geom = image->GetGeometry(); geom->SetOrigin(origin); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); return; } for (int i=0; im_Compartment4Box->currentIndex()>0) { comp4Weight = m_Controls->m_Comp4FractionBox->value(); comp3Weight -= comp4Weight; } mitk::StickModel stickModel1; mitk::StickModel stickModel2; mitk::TensorModel zeppelinModel1; mitk::TensorModel zeppelinModel2; mitk::TensorModel tensorModel1; mitk::TensorModel tensorModel2; mitk::BallModel ballModel1; mitk::BallModel ballModel2; mitk::AstroStickModel astrosticksModel1; mitk::AstroStickModel astrosticksModel2; mitk::DotModel dotModel1; mitk::DotModel dotModel2; // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: MITK_INFO << "Using stick model"; stickModel1.SetGradientList(gradientList); stickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); stickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); fiberModelList.push_back(&stickModel1); signalModelString += "Stick"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); resultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(stickModel1.GetT2()) ); break; case 1: MITK_INFO << "Using zeppelin model"; zeppelinModel1.SetGradientList(gradientList); zeppelinModel1.SetBvalue(bVal); zeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); zeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); fiberModelList.push_back(&zeppelinModel1); signalModelString += "Zeppelin"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; case 2: MITK_INFO << "Using tensor model"; tensorModel1.SetGradientList(gradientList); tensorModel1.SetBvalue(bVal); tensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); tensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); tensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); tensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); fiberModelList.push_back(&tensorModel1); signalModelString += "Tensor"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: stickModel2.SetGradientList(gradientList); stickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); stickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); fiberModelList.push_back(&stickModel2); signalModelString += "Stick"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); resultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(stickModel2.GetT2()) ); break; case 2: zeppelinModel2.SetGradientList(gradientList); zeppelinModel2.SetBvalue(bVal); zeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); zeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); fiberModelList.push_back(&zeppelinModel2); signalModelString += "Zeppelin"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; case 3: tensorModel2.SetGradientList(gradientList); tensorModel2.SetBvalue(bVal); tensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); tensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); tensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); tensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); fiberModelList.push_back(&tensorModel2); signalModelString += "Tensor"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: ballModel1.SetGradientList(gradientList); ballModel1.SetBvalue(bVal); ballModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); ballModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); ballModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&ballModel1); signalModelString += "Ball"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(ballModel1.GetT2()) ); break; case 1: astrosticksModel1.SetGradientList(gradientList); astrosticksModel1.SetBvalue(bVal); astrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); astrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); astrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); astrosticksModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&astrosticksModel1); signalModelString += "Astrosticks"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(astrosticksModel1.GetT2()) ); resultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: dotModel1.SetGradientList(gradientList); dotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); dotModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&dotModel1); signalModelString += "Dot"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(dotModel1.GetT2()) ); break; } // compartment 4 switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: ballModel2.SetGradientList(gradientList); ballModel2.SetBvalue(bVal); ballModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); ballModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); ballModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&ballModel2); signalModelString += "Ball"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(ballModel2.GetT2()) ); break; case 2: astrosticksModel2.SetGradientList(gradientList); astrosticksModel2.SetBvalue(bVal); astrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); astrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); astrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); astrosticksModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&astrosticksModel2); signalModelString += "Astrosticks"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(astrosticksModel2.GetT2()) ); resultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; case 3: dotModel2.SetGradientList(gradientList); dotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); dotModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&dotModel2); signalModelString += "Dot"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(dotModel2.GetT2()) ); break; } itk::TractsToDWIImageFilter::KspaceArtifactList artifactList; // artifact models QString artifactModelString(""); double noiseVariance = 0; if (m_Controls->m_AddNoise->isChecked()) { noiseVariance = m_Controls->m_NoiseLevel->value(); artifactModelString += "_NOISE"; artifactModelString += QString::number(noiseVariance); resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } mitk::RicianNoiseModel noiseModel; noiseModel.SetNoiseVariance(noiseVariance); - mitk::GibbsRingingArtifact gibbsModel; if (m_Controls->m_AddGibbsRinging->isChecked()) { artifactModelString += "_RINGING"; - resultNode->AddProperty("Fiberfox.k-Space-Undersampling", DoubleProperty::New(m_Controls->m_KspaceUndersamplingBox->value())); - gibbsModel.SetKspaceCropping(m_Controls->m_KspaceUndersamplingBox->value()); - artifactList.push_back(&gibbsModel); + resultNode->AddProperty("Fiberfox.Ringing-Upsampling", DoubleProperty::New(m_Controls->m_ImageUpsamplingBox->value())); + tractsToDwiFilter->SetUpsampling(m_Controls->m_ImageUpsamplingBox->value()); } if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } double lineReadoutTime = m_Controls->m_LineReadoutTimeBox->value(); // adjusting line readout time to the adapted image size needed for the DFT int y = imageRegion.GetSize(1); if ( y%2 == 1 ) y += 1; if ( y>imageRegion.GetSize(1) ) lineReadoutTime *= (double)imageRegion.GetSize(1)/y; // add N/2 ghosting double kOffset = 0; if (m_Controls->m_AddGhosts->isChecked()) { artifactModelString += "_GHOST"; kOffset = m_Controls->m_kOffsetBox->value(); resultNode->AddProperty("Fiberfox.Line-Offset", DoubleProperty::New(kOffset)); } // 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 (imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { tractsToDwiFilter->SetFrequencyMap(itkImg); artifactModelString += "_DISTORTED"; } } if (m_Controls->m_AddEddy->isChecked()) { tractsToDwiFilter->SetSimulateEddyCurrents(true); tractsToDwiFilter->SetEddyGradientStrength(m_Controls->m_EddyGradientStrength->value()); artifactModelString += "_EDDY"; } mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(m_SelectedBundles.at(i)->GetData()); if (fiberBundle->GetNumFibers()<=0) continue; if (m_Controls->m_RelaxationBox->isChecked()) artifactModelString += "_RELAX"; tractsToDwiFilter->SetSimulateRelaxation(m_Controls->m_RelaxationBox->isChecked()); tractsToDwiFilter->SetImageRegion(imageRegion); tractsToDwiFilter->SetSpacing(spacing); tractsToDwiFilter->SetOrigin(origin); tractsToDwiFilter->SetDirectionMatrix(directionMatrix); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->SetFiberModels(fiberModelList); tractsToDwiFilter->SetNonFiberModels(nonFiberModelList); tractsToDwiFilter->SetNoiseModel(&noiseModel); tractsToDwiFilter->SetKspaceArtifacts(artifactList); tractsToDwiFilter->SetkOffset(kOffset); tractsToDwiFilter->SettLine(m_Controls->m_LineReadoutTimeBox->value()); tractsToDwiFilter->SettInhom(this->m_Controls->m_T2starBox->value()); tractsToDwiFilter->SetTE(this->m_Controls->m_TEbox->value()); tractsToDwiFilter->SetNumberOfRepetitions(m_Controls->m_RepetitionsBox->value()); tractsToDwiFilter->SetEnforcePureFiberVoxels(m_Controls->m_EnforcePureFiberVoxelsBox->isChecked()); tractsToDwiFilter->SetInterpolationShrink(m_Controls->m_InterpolationShrink->value()); tractsToDwiFilter->SetFiberRadius(m_Controls->m_FiberRadius->value()); tractsToDwiFilter->SetSignalScale(m_Controls->m_SignalScaleBox->value()); if (m_Controls->m_InterpolationShrink->value()<1000) tractsToDwiFilter->SetUseInterpolation(true); if (m_TissueMask.IsNotNull()) { ItkUcharImgType::Pointer mask = ItkUcharImgType::New(); mitk::CastToItkImage(m_TissueMask, mask); tractsToDwiFilter->SetTissueMask(mask); } tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( tractsToDwiFilter->GetOutput() ); image->SetB_Value(bVal); image->SetDirections(gradientList); image->InitializeFromVectorImage(); resultNode->SetData( image ); resultNode->SetName(m_SelectedBundles.at(i)->GetName() +"_D"+QString::number(imageRegion.GetSize(0)).toStdString() +"-"+QString::number(imageRegion.GetSize(1)).toStdString() +"-"+QString::number(imageRegion.GetSize(2)).toStdString() +"_S"+QString::number(spacing[0]).toStdString() +"-"+QString::number(spacing[1]).toStdString() +"-"+QString::number(spacing[2]).toStdString() +"_b"+QString::number(bVal).toStdString() +"_"+signalModelString.toStdString() +artifactModelString.toStdString()); GetDataStorage()->Add(resultNode, m_SelectedBundles.at(i)); resultNode->AddProperty("Fiberfox.InterpolationShrink", IntProperty::New(m_Controls->m_InterpolationShrink->value())); resultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_Controls->m_SignalScaleBox->value())); resultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_Controls->m_FiberRadius->value())); resultNode->AddProperty("Fiberfox.Tinhom", IntProperty::New(m_Controls->m_T2starBox->value())); resultNode->AddProperty("Fiberfox.Repetitions", IntProperty::New(m_Controls->m_RepetitionsBox->value())); resultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(bVal)); resultNode->AddProperty("Fiberfox.Model", StringProperty::New(signalModelString.toStdString())); resultNode->AddProperty("Fiberfox.PureFiberVoxels", BoolProperty::New(m_Controls->m_EnforcePureFiberVoxelsBox->isChecked())); resultNode->AddProperty("binary", BoolProperty::New(false)); resultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(tractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter::ItkDoubleImgType::Pointer > volumeFractions = tractsToDwiFilter->GetVolumeFractions(); for (int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(m_SelectedBundles.at(i)->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, m_SelectedBundles.at(i)); } } mitk::BaseData::Pointer basedata = resultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for( int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { std::vector::const_iterator it = selectedBundles.begin(); for (it; it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 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< float, 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< float, 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< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); } } } } } else { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 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< float, 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< float, 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< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); for (it; it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (it; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_TissueMask.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_TissueMask = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_TissueMask = dynamic_cast(node->GetData()); m_Controls->m_TissueMaskLabel->setText(node->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if( 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->GetInteractor()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", nonConstNode); } else { // just to be sure that the interactor is not added twice mitk::GlobalInteraction::GetInstance()->RemoveInteractor(figureInteractor); } MITK_DEBUG << "adding interactor to globalinteraction"; mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); 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(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui index d8fbe2ec33..63972bd20f 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,2198 +1,2204 @@ QmitkFiberfoxViewControls 0 0 493 1565 Form 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid Operations false Copy Bundles false Transform Selection QFrame::NoFrame QFrame::Raised 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Join Bundles If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Fiber sampling points (per cm) 1 100 1 10 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 QFrame::NoFrame QFrame::Raised 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers QFrame::NoFrame QFrame::Raised 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model Data Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Tissue Mask: false <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Extra-axonal Compartments Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 Weighting factor between the two extra-axonal compartments. 1.000000000000000 0.100000000000000 0.300000000000000 Compartment Fraction: true Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. Generate Image Image Settings QFrame::NoFrame QFrame::Raised 0 6 <html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html> Simulate Signal Relaxation true Repetitions: T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 Fiber Radius: Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 TE in milliseconds 1 10000 1 100 Interpolation Shrink: Line Readout Time: false <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Output one image per compartment containing the corresponding volume fractions per voxel. Output Volume Fractions false <html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html> false Number of signal averages. Increase to reduce noise. 1 100 1 1 Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 TE in milliseconds 1 10000 1 100 <html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html> 1 1000 1000 Signal Scale: color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 QFrame::NoFrame QFrame::Raised 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 b-Value: false b-value in mm/s² 0 10000 100 1000 Advanced Options Qt::Vertical 20 40 Noise and other Artifacts Add N/2 Ghosts false true QFrame::NoFrame QFrame::Raised 6 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 Variance: Variance of Rician noise model. 4 0.000000000000000 100000.000000000000000 0.001000000000000 25.000000000000000 + + Add ringing artifacts occuring at strong edges in the image. + Add Gibbs Ringing false Add Rician Noise false true QFrame::NoFrame QFrame::Raised 6 0 - k-Space Undersampling: + Upsampling: false - + - A larger offset increases the inensity of the ghost image. + Larger values increase the ringing range. Beware of performance issues! 2 1.000000000000000 - 4.000000000000000 + 10.000000000000000 0.100000000000000 - 1.100000000000000 + 2.000000000000000 Add Distortions false true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 Gradient Strength: false A larger offset increases the inensity of the ghost image. 5 1000.000000000000000 0.001000000000000 - 0.015000000000000 + 0.001000000000000 true QFrame::NoFrame QFrame::Raised 6 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). + + !!!EXPERIMENTAL!!! + Add Eddy Current Effects false Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_RepetitionsBox m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_InterpolationShrink m_EnforcePureFiberVoxelsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_Comp4FractionBox m_AddNoise m_NoiseLevel m_AddGhosts m_kOffsetBox m_AddDistortions m_FrequencyMapBox m_AddGibbsRinging tabWidget