diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp index 7a58a8a5be..8b1fab2b28 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp @@ -1,336 +1,376 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkAddArtifactsToDwiImageFilter_txx #define __itkAddArtifactsToDwiImageFilter_txx #include #include #include #include "itkAddArtifactsToDwiImageFilter.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > AddArtifactsToDwiImageFilter< TPixelType > ::AddArtifactsToDwiImageFilter() : m_UseConstantRandSeed(false) { this->SetNumberOfRequiredInputs( 1 ); m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); m_RandGen->SetSeed(); } template< class TPixelType > void AddArtifactsToDwiImageFilter< TPixelType > ::GenerateData() { if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); m_StartTime = clock(); m_StatusText = "Starting simulation\n"; typename InputImageType::Pointer inputImage = static_cast< InputImageType* >( this->ProcessObject::GetInput(0) ); itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion(); typename itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage( inputImage ); duplicator->Update(); typename InputImageType::Pointer outputImage = duplicator->GetOutput(); // is input slize size even? int xMax=inputRegion.GetSize(0); int yMax=inputRegion.GetSize(1); if ( xMax%2 == 1 ) xMax += 1; if ( yMax%2 == 1 ) yMax += 1; // create slice object typename SliceType::Pointer slice = SliceType::New(); ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, xMax); sliceRegion.SetSize(1, yMax); slice->SetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->Allocate(); slice->FillBuffer(0.0); ImageRegion<2> upsampledSliceRegion; if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { upsampledSliceRegion.SetSize(0, xMax*2); upsampledSliceRegion.SetSize(1, yMax*2); } // frequency map slice typename SliceType::Pointer fMapSlice = NULL; if ( m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); fMapSlice->SetLargestPossibleRegion( sliceRegion ); fMapSlice->SetBufferedRegion( sliceRegion ); fMapSlice->SetRequestedRegion( sliceRegion ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } m_Parameters.m_SignalGen.m_SignalScale = 1; m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; if ( m_Parameters.m_SignalGen.m_Spikes>0 || m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() || m_Parameters.m_SignalGen.m_KspaceLineOffset>0.0 || m_Parameters.m_SignalGen.m_DoAddGibbsRinging || m_Parameters.m_SignalGen.m_EddyStrength>0 || m_Parameters.m_SignalGen.m_CroppingFactor<1.0) { ImageRegion<3> croppedRegion = inputRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)* m_Parameters.m_SignalGen.m_CroppingFactor); itk::Point shiftedOrigin = inputImage->GetOrigin(); shiftedOrigin[1] += (inputRegion.GetSize(1)-croppedRegion.GetSize(1))*inputImage->GetSpacing()[1]/2; outputImage = InputImageType::New(); outputImage->SetSpacing( inputImage->GetSpacing() ); outputImage->SetOrigin( shiftedOrigin ); outputImage->SetDirection( inputImage->GetDirection() ); outputImage->SetLargestPossibleRegion( croppedRegion ); outputImage->SetBufferedRegion( croppedRegion ); outputImage->SetRequestedRegion( croppedRegion ); outputImage->SetVectorLength( inputImage->GetVectorLength() ); outputImage->Allocate(); typename InputImageType::PixelType temp; temp.SetSize(inputImage->GetVectorLength()); temp.Fill(0.0); outputImage->FillBuffer(temp); int tempY=croppedRegion.GetSize(1); tempY += tempY%2; croppedRegion.SetSize(1, tempY); m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; if ( m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; if ( m_Parameters.m_SignalGen.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; if ( m_Parameters.m_SignalGen.m_Spikes>0) m_StatusText += "Simulating spikes\n"; if ( m_Parameters.m_SignalGen.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; if ( m_Parameters.m_SignalGen.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; std::vector< unsigned int > spikeVolume; for (unsigned int i=0; i< m_Parameters.m_SignalGen.m_Spikes; i++) spikeVolume.push_back(m_RandGen->GetIntegerVariate()%inputImage->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); FiberfoxParameters doubleParam = m_Parameters.CopyParameters(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(inputImage->GetVectorLength()*inputRegion.GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%inputImage->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } std::vector< SliceType::Pointer > compartmentSlices; // extract slice from channel g for (unsigned int y=0; yGetPixel(index3D)[g]; slice->SetPixel(index2D, pix2D); if (fMapSlice.IsNotNull()) fMapSlice->SetPixel(index2D, m_Parameters.m_SignalGen.m_FrequencyMap->GetPixel(index3D)); } if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(slice); resampler->SetOutputParametersFromImage(slice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(slice->GetSpacing()/2); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); typename SliceType::Pointer upslice = resampler->GetOutput(); compartmentSlices.push_back(upslice); if (fMapSlice.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(fMapSlice); resampler->SetOutputParametersFromImage(fMapSlice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(fMapSlice->GetSpacing()/2); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); fMapSlice = resampler->GetOutput(); } } else compartmentSlices.push_back(slice); // fourier transform slice typename ComplexSliceType::Pointer fSlice; itk::Size<2> outSize; outSize.SetElement(0, xMax); outSize.SetElement(1, croppedRegion.GetSize()[1]); typename itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(doubleParam); idft->SetCompartmentImages(compartmentSlices); idft->SetFrequencyMapSlice(fMapSlice); idft->SetDiffusionGradientDirection( m_Parameters.m_SignalGen.GetGradientDirection(g)); idft->SetZ((double)z-(double)inputRegion.GetSize(2)/2.0); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); fSlice = idft->GetOutput(); // inverse fourier transform slice typename SliceType::Pointer newSlice; typename itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { typename InputImageType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; typename InputImageType::PixelType pix3D = outputImage->GetPixel(index3D); typename SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; double signal = newSlice->GetPixel(index2D); if (signal>0) signal = floor(signal+0.5); else signal = ceil(signal-0.5); pix3D[g] = signal; outputImage->SetPixel(index3D, pix3D); } ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; } if ( m_Parameters.m_NoiseModel!=NULL) { m_StatusText += this->GetTime()+" > Adding noise\n"; m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; ImageRegionIterator it1 (outputImage, outputImage->GetLargestPossibleRegion()); boost::progress_display disp(outputImage->GetLargestPossibleRegion().GetNumberOfPixels()); while(!it1.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename InputImageType::PixelType signal = it1.Get(); m_Parameters.m_NoiseModel->AddNoise(signal); it1.Set(signal); ++it1; } m_StatusText += "\n\n"; } this->SetNthOutput(0, outputImage); m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); } template< class TPixelType > std::string AddArtifactsToDwiImageFilter< TPixelType >::GetTime() { unsigned long total = (double)(clock() - m_StartTime)/CLOCKS_PER_SEC; unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); return out; } +template< class TPixelType > +void AddArtifactsToDwiImageFilter< TPixelType >::UpdateOutputInformation() +{ + // Calls to superclass updateoutputinformation + Superclass::UpdateOutputInformation(); + + typename InputImageType::Pointer inputImage = static_cast< InputImageType* >( this->ProcessObject::GetInput(0) ); + itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion(); + + typename itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); + duplicator->SetInputImage( inputImage ); + duplicator->Update(); + typename InputImageType::Pointer outputImage = duplicator->GetOutput(); + + if ( m_Parameters.m_SignalGen.m_CroppingFactor<1.0) + { + ImageRegion<3> croppedRegion = inputRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)* m_Parameters.m_SignalGen.m_CroppingFactor); + itk::Point shiftedOrigin = inputImage->GetOrigin(); shiftedOrigin[1] += (inputRegion.GetSize(1)-croppedRegion.GetSize(1))*inputImage->GetSpacing()[1]/2; + + outputImage = InputImageType::New(); + outputImage->SetSpacing( inputImage->GetSpacing() ); + outputImage->SetOrigin( shiftedOrigin ); + outputImage->SetDirection( inputImage->GetDirection() ); + outputImage->SetLargestPossibleRegion( croppedRegion ); + outputImage->SetBufferedRegion( croppedRegion ); + outputImage->SetRequestedRegion( croppedRegion ); + outputImage->SetVectorLength( inputImage->GetVectorLength() ); + outputImage->Allocate(); + typename InputImageType::PixelType temp; + temp.SetSize(inputImage->GetVectorLength()); + temp.Fill(0.0); + outputImage->FillBuffer(temp); + } + + this->GetOutput()->SetOrigin( outputImage->GetOrigin() ); + this->GetOutput()->SetLargestPossibleRegion( outputImage->GetLargestPossibleRegion() ); + this->GetOutput()->SetBufferedRegion( outputImage->GetLargestPossibleRegion() ); + this->GetOutput()->SetRequestedRegion( outputImage->GetLargestPossibleRegion() ); +} + } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h index 312f3d40db..3a9d3d348f 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.h @@ -1,90 +1,92 @@ /*=================================================================== 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 #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. */ itkFactorylessNewMacro(Self) itkCloneMacro(Self) /** Runtime information support. */ itkTypeMacro(AddArtifactsToDwiImageFilter, ImageToImageFilter) typedef VectorImage< TPixelType, 3 > InputImageType; typedef itk::Image< double, 2 > SliceType; typedef typename itk::KspaceImageFilter< double >::OutputImageType ComplexSliceType; typedef itk::Image ItkDoubleImgType; typedef itk::Matrix MatrixType; itkGetMacro( StatusText, std::string ) itkSetMacro( UseConstantRandSeed, bool ) void SetParameters( FiberfoxParameters param ){ m_Parameters = param; } FiberfoxParameters GetParameters(){ return m_Parameters; } + virtual void UpdateOutputInformation(); + protected: AddArtifactsToDwiImageFilter(); ~AddArtifactsToDwiImageFilter() {} std::string GetTime(); void GenerateData(); FiberfoxParameters m_Parameters; std::string m_StatusText; time_t m_StartTime; itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen; bool m_UseConstantRandSeed; private: }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkAddArtifactsToDwiImageFilter.cpp" #endif #endif //__itkAddArtifactsToDwiImageFilter_h_