diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.h b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.h index 11afc7b593..cdb43eec2e 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.h +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.h @@ -1,99 +1,100 @@ /*=================================================================== 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 __itkDwiNormilzationFilter_h_ #define __itkDwiNormilzationFilter_h_ #include "itkImageToImageFilter.h" #include "itkVectorImage.h" #include #include #include #include namespace itk{ /** \class DwiNormilzationFilter - * \brief Max-Normalizes the data vectors either using the global baseline maximum or the voxelwise baseline value. + * \brief Normalizes the data vectors either using the specified reference value or the voxelwise baseline value. */ template< class TInPixelType > class DwiNormilzationFilter : public ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > > { public: typedef DwiNormilzationFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > > Superclass; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self) itkCloneMacro(Self) /** Runtime information support. */ itkTypeMacro(DwiNormilzationFilter, ImageToImageFilter) typedef itk::Image< double, 3 > DoubleImageType; typedef itk::Image< unsigned char, 3 > UcharImageType; typedef itk::Image< unsigned short, 3 > BinImageType; typedef itk::Image< TInPixelType, 3 > TInPixelImageType; typedef typename Superclass::InputImageType InputImageType; typedef typename Superclass::OutputImageType OutputImageType; typedef typename Superclass::OutputImageRegionType OutputImageRegionType; typedef mitk::DiffusionImage< short >::GradientDirectionType GradientDirectionType; typedef mitk::DiffusionImage< short >::GradientDirectionContainerType::Pointer GradientContainerType; typedef itk::LabelStatisticsImageFilter< TInPixelImageType,BinImageType > StatisticsFilterType; typedef itk::Statistics::Histogram< typename TInPixelImageType::PixelType > HistogramType; typedef typename HistogramType::MeasurementType MeasurementType; typedef itk::ShiftScaleImageFilter ShiftScaleImageFilterType; itkSetMacro( GradientDirections, GradientContainerType ) - itkSetMacro( NewMax, TInPixelType ) - itkSetMacro( UseGlobalMax, bool ) + itkSetMacro( ScalingFactor, TInPixelType ) + itkSetMacro( UseGlobalReference, bool ) itkSetMacro( MaskImage, UcharImageType::Pointer ) + itkSetMacro( Reference, double ) protected: DwiNormilzationFilter(); ~DwiNormilzationFilter() {} void PrintSelf(std::ostream& os, Indent indent) const; void BeforeThreadedGenerateData(); void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType); UcharImageType::Pointer m_MaskImage; GradientContainerType m_GradientDirections; int m_B0Index; - TInPixelType m_NewMax; - bool m_UseGlobalMax; - double m_GlobalMax; + TInPixelType m_ScalingFactor; + bool m_UseGlobalReference; + double m_Reference; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkDwiNormilzationFilter.txx" #endif #endif //__itkDwiNormilzationFilter_h_ diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.txx b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.txx index ff11de92ab..59faf8479b 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.txx +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiNormilzationFilter.txx @@ -1,278 +1,127 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkDwiNormilzationFilter_txx #define __itkDwiNormilzationFilter_txx #include #include #include #define _USE_MATH_DEFINES #include #include "itkImageRegionConstIterator.h" #include "itkImageRegionConstIteratorWithIndex.h" #include "itkImageRegionIterator.h" #include namespace itk { template< class TInPixelType > DwiNormilzationFilter< TInPixelType>::DwiNormilzationFilter() :m_B0Index(-1) - ,m_NewMax(1000) - ,m_UseGlobalMax(false) + ,m_ScalingFactor(1000) + ,m_UseGlobalReference(false) { this->SetNumberOfRequiredInputs( 1 ); } template< class TInPixelType > void DwiNormilzationFilter< TInPixelType>::BeforeThreadedGenerateData() { typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); m_B0Index = -1; for (unsigned int i=0; iGetVectorLength(); i++) { GradientDirectionType g = m_GradientDirections->GetElement(i); if (g.magnitude()<0.001) m_B0Index = i; } if (m_B0Index==-1) itkExceptionMacro(<< "DwiNormilzationFilter: No b-Zero indecies found!"); -// // cleanup -// itk::ImageRegionIterator inIt(inputImagePointer, inputImagePointer->GetLargestPossibleRegion()); -// while ( !inIt.IsAtEnd() ) -// { -// typename InputImageType::PixelType pix = inIt.Get(); -// for (unsigned int i=0; iGetVectorLength(); i++) -// { -// if (pix[i]<0) -// pix[i] = 0; -// else if(pix[i]>pix[m_B0Index]) -// pix[i] = pix[m_B0Index]; -// } -// inIt.Set(pix); -// ++inIt; -// } - -// if (m_MaskImage.IsNull()) -// { -// m_MaskImage = UcharImageType::New(); -// m_MaskImage->SetRegions(inputImagePointer->GetLargestPossibleRegion()); -// m_MaskImage->SetOrigin(inputImagePointer->GetOrigin()); -// m_MaskImage->SetSpacing(inputImagePointer->GetSpacing()); -// m_MaskImage->SetDirection(inputImagePointer->GetDirection()); -// m_MaskImage->Allocate(); -// m_MaskImage->FillBuffer(1); -// } - -// BinImageType::Pointer outputBinMaskImage = BinImageType::New(); -// outputBinMaskImage->SetRegions(m_MaskImage->GetLargestPossibleRegion()); -// outputBinMaskImage->SetOrigin(m_MaskImage->GetOrigin()); -// outputBinMaskImage->SetSpacing(m_MaskImage->GetSpacing()); -// outputBinMaskImage->SetDirection(m_MaskImage->GetDirection()); -// outputBinMaskImage->Allocate(); - -// typename TInPixelImageType::Pointer b0Image = TInPixelImageType::New(); -// b0Image->SetRegions(m_MaskImage->GetLargestPossibleRegion()); -// b0Image->SetOrigin(m_MaskImage->GetOrigin()); -// b0Image->SetSpacing(m_MaskImage->GetSpacing()); -// b0Image->SetDirection(m_MaskImage->GetDirection()); -// b0Image->Allocate(); -// b0Image->FillBuffer(0); - -// itk::ImageRegionIterator it(inputImagePointer, inputImagePointer->GetLargestPossibleRegion()); -// while( !it.IsAtEnd() ) -// { -// if (it.Get()[m_B0Index]>0) -// b0Image->SetPixel(it.GetIndex(), it.Get()[m_B0Index]); -// if( m_MaskImage->GetPixel(it.GetIndex()) > 0) -// outputBinMaskImage->SetPixel(it.GetIndex(), 1); -// else -// outputBinMaskImage->SetPixel(it.GetIndex(), 0); - -// ++it; -// } - -// typename StatisticsFilterType::Pointer statistics = StatisticsFilterType::New(); -// statistics->SetLabelInput( outputBinMaskImage ); -// statistics->SetInput( b0Image ); -// statistics->Update(); - -// typename HistogramType::Pointer histogram = HistogramType::New(); -// typename HistogramType::SizeType sz; -// typename HistogramType::MeasurementVectorType lowerBound; -// typename HistogramType::MeasurementVectorType upperBound; -// sz.SetSize(1); -// lowerBound.SetSize(1); -// upperBound.SetSize(1); -// histogram->SetMeasurementVectorSize(1); - -// // Numver of Bins -// sz[0] = 256; - -// lowerBound.Fill(statistics->GetMinimum(1)); -// upperBound.Fill(statistics->GetMaximum(1)); - -// histogram->Initialize(sz, lowerBound, upperBound); -// histogram->SetToZero(); - -// typename HistogramType::MeasurementVectorType measurement; -// measurement.SetSize(1); measurement[0] = 0; - -// itk::ImageRegionIterator b0It(b0Image, b0Image->GetLargestPossibleRegion()); -// while ( !b0It.IsAtEnd() ) -// { -// if (m_MaskImage->GetPixel(b0It.GetIndex()) > 0) -// { -// TInPixelType value = b0It.Value(); -// measurement[0] = value; -// histogram->IncreaseFrequencyOfMeasurement(measurement, 1); -// } -// ++b0It; -// } - -// // Find bin with max frequency -// double maxFreq =0 ; -// unsigned int index = 0; -// for (unsigned int ii =0 ; ii < sz[0];++ii) -// { -// if( maxFreq < histogram->GetFrequency(ii)) -// { -// maxFreq = histogram->GetFrequency(ii); -// index = ii; -// } -// } - -// typename StatisticsFilterType::Pointer statisticsImageFilter = StatisticsFilterType::New(); -// statisticsImageFilter->SetInput(b0Image); -// statisticsImageFilter->SetLabelInput(outputBinMaskImage); -// statisticsImageFilter->Update(); -// double variance = statisticsImageFilter->GetVariance(1); - -// typename ShiftScaleImageFilterType::Pointer shiftScaleImageFilter = ShiftScaleImageFilterType::New(); -// MITK_INFO << "******************* " << histogram->GetBinMax(0,index); -// m_GlobalMax = histogram->GetBinMax(0,index); -// m_UseGlobalMax = true; -// MITK_INFO << "******************* " << maxFreq; -// shiftScaleImageFilter->SetShift( 0 );//-histogram->GetBinMax(0,index)); -// shiftScaleImageFilter->SetScale( ( (double) 1 ) / std::sqrt(variance)); - -// for (unsigned int i=0; iGetVectorLength(); i++) -// { -// typename TInPixelImageType::Pointer channel = TInPixelImageType::New(); -// channel->SetSpacing( this->GetInput()->GetSpacing() ); -// channel->SetOrigin( this->GetInput()->GetOrigin() ); -// channel->SetDirection( this->GetInput()->GetDirection() ); -// channel->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion() ); -// channel->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() ); -// channel->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() ); -// channel->Allocate(); - -// ImageRegionIterator it(channel, channel->GetLargestPossibleRegion()); -// while(!it.IsAtEnd()) -// { -// typename InputImageType::PixelType pix = inputImagePointer->GetPixel(it.GetIndex()); -// it.Set(pix[i]); -// ++it; -// } - -// shiftScaleImageFilter->SetInput( channel ); -// shiftScaleImageFilter->Update(); -// DoubleImageType::Pointer normalized = shiftScaleImageFilter->GetOutput(); - -// ImageRegionIterator it2(normalized, normalized->GetLargestPossibleRegion()); -// while(!it2.IsAtEnd()) -// { -// typename InputImageType::PixelType pix = inputImagePointer->GetPixel(it2.GetIndex()); -// pix[i] = m_NewMax*it2.Get(); -// inputImagePointer->SetPixel(it2.GetIndex(), pix); -// ++it2; -// } -// } - + if (m_UseGlobalReference) + MITK_INFO << "Using global reference value: " << m_Reference; } template< class TInPixelType > void DwiNormilzationFilter< TInPixelType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType ) { - MITK_INFO << "8"; typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); oit.GoToBegin(); typedef ImageRegionConstIterator< InputImageType > InputIteratorType; typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); typename OutputImageType::PixelType nullPix; nullPix.SetSize(inputImagePointer->GetVectorLength()); nullPix.Fill(0); InputIteratorType git( inputImagePointer, outputRegionForThread ); git.GoToBegin(); while( !git.IsAtEnd() ) { typename InputImageType::PixelType pix = git.Get(); typename OutputImageType::PixelType outPix; outPix.SetSize(inputImagePointer->GetVectorLength()); double S0 = pix[m_B0Index]; - if (m_UseGlobalMax) - S0 = m_GlobalMax; + if (m_UseGlobalReference) + S0 = m_Reference; - if (S0>0.1) + if (S0>0.1 && pix[m_B0Index]>0) { for (unsigned int i=0; iGetVectorLength(); i++) { double val = (double)pix[i]; if (val!=val || val<0) val = 0; else { val /= S0; - val *= (double)m_NewMax; + val *= (double)m_ScalingFactor; } outPix[i] = (TInPixelType)val; } oit.Set(outPix); } else oit.Set(nullPix); ++oit; ++git; } std::cout << "One Thread finished calculation" << std::endl; } template< class TInPixelType > void DwiNormilzationFilter< TInPixelType> ::PrintSelf(std::ostream& os, Indent indent) const { Superclass::PrintSelf(os,indent); } } #endif // __itkDwiNormilzationFilter_txx diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.h b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.h new file mode 100644 index 0000000000..5db210b559 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.h @@ -0,0 +1,78 @@ +/*=================================================================== + +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 __itkExtractDwiChannelFilter_h_ +#define __itkExtractDwiChannelFilter_h_ + +#include "itkImageToImageFilter.h" +#include "itkVectorImage.h" +#include +#include +#include + +namespace itk{ +/** \class ExtractDwiChannelFilter + * \brief Remove spcified channels from diffusion-weighted image. + */ + +template< class TInPixelType > +class ExtractDwiChannelFilter : + public ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TInPixelType, 3 > > +{ + +public: + + typedef ExtractDwiChannelFilter Self; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TInPixelType, 3 > > Superclass; + + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /** Runtime information support. */ + itkTypeMacro(ExtractDwiChannelFilter, ImageToImageFilter) + + typedef typename Superclass::InputImageType InputImageType; + typedef typename Superclass::OutputImageType OutputImageType; + typedef typename Superclass::OutputImageRegionType OutputImageRegionType; + + itkSetMacro( ChannelIndex, unsigned int ) + + protected: + ExtractDwiChannelFilter(); + ~ExtractDwiChannelFilter() {} + + void BeforeThreadedGenerateData(); + void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType ); + + unsigned int m_ChannelIndex; +}; + +} + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkExtractDwiChannelFilter.txx" +#endif + +#endif //__itkExtractDwiChannelFilter_h_ + diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.txx b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.txx new file mode 100644 index 0000000000..b6a38a6076 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkExtractDwiChannelFilter.txx @@ -0,0 +1,73 @@ +/*=================================================================== + +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 __itkExtractDwiChannelFilter_txx +#define __itkExtractDwiChannelFilter_txx + +#include +#include +#include + +#define _USE_MATH_DEFINES +#include + +#include "itkImageRegionConstIterator.h" +#include "itkImageRegionConstIteratorWithIndex.h" +#include "itkImageRegionIterator.h" + +namespace itk { + + +template< class TInPixelType > +ExtractDwiChannelFilter< TInPixelType>::ExtractDwiChannelFilter() +{ + this->SetNumberOfRequiredInputs( 1 ); +} + +template< class TInPixelType > +void ExtractDwiChannelFilter< TInPixelType>::BeforeThreadedGenerateData() +{ + typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); + if ( inputImagePointer->GetVectorLength()<=m_ChannelIndex ) + itkExceptionMacro("Index out of bounds!"); +} + +template< class TInPixelType > +void ExtractDwiChannelFilter< TInPixelType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType ) +{ + typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); + + ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); + oit.GoToBegin(); + + typedef ImageRegionConstIterator< InputImageType > InputIteratorType; + typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); + + InputIteratorType git( inputImagePointer, outputRegionForThread ); + git.GoToBegin(); + while( !git.IsAtEnd() ) + { + oit.Set( git.Get()[m_ChannelIndex] ); + ++oit; + ++git; + } + + std::cout << "One Thread finished calculation" << std::endl; +} + +} + +#endif // __itkExtractDwiChannelFilter_txx diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.h b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.h new file mode 100644 index 0000000000..95a39eed95 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.h @@ -0,0 +1,85 @@ +/*=================================================================== + +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 __itkRemoveDwiChannelFilter_h_ +#define __itkRemoveDwiChannelFilter_h_ + +#include "itkImageToImageFilter.h" +#include "itkVectorImage.h" +#include +#include +#include + +namespace itk{ +/** \class RemoveDwiChannelFilter + * \brief Remove spcified channels from diffusion-weighted image. + */ + +template< class TInPixelType > +class RemoveDwiChannelFilter : + public ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > > +{ + +public: + + typedef RemoveDwiChannelFilter Self; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > > Superclass; + + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + /** Runtime information support. */ + itkTypeMacro(RemoveDwiChannelFilter, ImageToImageFilter) + + typedef typename Superclass::InputImageType InputImageType; + typedef typename Superclass::OutputImageType OutputImageType; + typedef typename Superclass::OutputImageRegionType OutputImageRegionType; + typedef typename mitk::DiffusionImage< TInPixelType >::GradientDirectionType DirectionType; + typedef typename mitk::DiffusionImage< TInPixelType >::GradientDirectionContainerType DirectionContainerType; + + itkSetMacro( ChannelIndices, std::vector< unsigned int > ) + void SetDirections( typename DirectionContainerType::Pointer directions ){ m_Directions = directions; } + typename DirectionContainerType::Pointer GetNewDirections(){ return m_NewDirections; } + + protected: + RemoveDwiChannelFilter(); + ~RemoveDwiChannelFilter() {} + void PrintSelf(std::ostream& os, Indent indent) const; + + void BeforeThreadedGenerateData(); + void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType id ); + + std::vector< unsigned int > m_ChannelIndices; + typename DirectionContainerType::Pointer m_Directions; + typename DirectionContainerType::Pointer m_NewDirections; +}; + +} + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkRemoveDwiChannelFilter.txx" +#endif + +#endif //__itkRemoveDwiChannelFilter_h_ + diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.txx b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.txx new file mode 100644 index 0000000000..cc87ff38dc --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkRemoveDwiChannelFilter.txx @@ -0,0 +1,133 @@ +/*=================================================================== + +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 __itkRemoveDwiChannelFilter_txx +#define __itkRemoveDwiChannelFilter_txx + +#include +#include +#include + +#define _USE_MATH_DEFINES +#include + +#include "itkImageRegionConstIterator.h" +#include "itkImageRegionConstIteratorWithIndex.h" +#include "itkImageRegionIterator.h" + +namespace itk { + + +template< class TInPixelType > +RemoveDwiChannelFilter< TInPixelType>::RemoveDwiChannelFilter() +{ + this->SetNumberOfRequiredInputs( 1 ); +} + +template< class TInPixelType > +void RemoveDwiChannelFilter< TInPixelType>::BeforeThreadedGenerateData() +{ + typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); + if ( inputImagePointer->GetVectorLength()-m_ChannelIndices.size()<=0 ) + itkExceptionMacro("No channels remaining!"); + + typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); + outputImage->SetSpacing( inputImagePointer->GetSpacing() ); + outputImage->SetOrigin( inputImagePointer->GetOrigin() ); + outputImage->SetDirection( inputImagePointer->GetDirection() ); + outputImage->SetLargestPossibleRegion( inputImagePointer->GetLargestPossibleRegion() ); + outputImage->SetBufferedRegion( inputImagePointer->GetLargestPossibleRegion() ); + outputImage->SetRequestedRegion( inputImagePointer->GetLargestPossibleRegion() ); + outputImage->Allocate(); + outputImage->SetVectorLength( inputImagePointer->GetVectorLength()-m_ChannelIndices.size() ); + typename OutputImageType::PixelType nullPix; + nullPix.SetSize(outputImage->GetVectorLength()); + nullPix.Fill(0); + outputImage->FillBuffer(nullPix); + this->SetNthOutput(0, outputImage); + + m_NewDirections = DirectionContainerType::New(); + + int chIdx = 0; + for (unsigned int i=0; iGetVectorLength(); i++) + { + bool use = true; + for (unsigned int j=0; jInsertElement(chIdx, m_Directions->GetElement(i)); + ++chIdx; + MITK_INFO << "Using channel " << i; + } + } +} + +template< class TInPixelType > +void RemoveDwiChannelFilter< TInPixelType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType id ) +{ + typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); + + ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); + oit.GoToBegin(); + + typedef ImageRegionConstIterator< InputImageType > InputIteratorType; + typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); + + InputIteratorType git( inputImagePointer, outputRegionForThread ); + git.GoToBegin(); + while( !git.IsAtEnd() ) + { + int chIdx = 0; + typename OutputImageType::PixelType pix = oit.Get(); + for (unsigned int i=0; iGetVectorLength(); i++) + { + bool use = true; + for (unsigned int j=0; j +void +RemoveDwiChannelFilter< TInPixelType> +::PrintSelf(std::ostream& os, Indent indent) const +{ + Superclass::PrintSelf(os,indent); +} + +} + +#endif // __itkRemoveDwiChannelFilter_txx diff --git a/Modules/DiffusionImaging/DiffusionCore/files.cmake b/Modules/DiffusionImaging/DiffusionCore/files.cmake index c7b3f04aed..1e2a79653d 100644 --- a/Modules/DiffusionImaging/DiffusionCore/files.cmake +++ b/Modules/DiffusionImaging/DiffusionCore/files.cmake @@ -1,129 +1,131 @@ set(CPP_FILES # DicomImport DicomImport/mitkDicomDiffusionImageReader.cpp # DicomImport/mitkGroupDiffusionHeadersFilter.cpp DicomImport/mitkDicomDiffusionImageHeaderReader.cpp DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp # DataStructures -> DWI IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSource.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp IODataStructures/DiffusionWeightedImages/mitkImageToDiffusionImageSource.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp # DataStructures -> QBall IODataStructures/QBallImages/mitkQBallImageSource.cpp IODataStructures/QBallImages/mitkQBallImage.cpp # DataStructures -> Tensor IODataStructures/TensorImages/mitkTensorImage.cpp #IODataStructures/mitkRegistrationObject.cpp # Rendering Rendering/vtkMaskedProgrammableGlyphFilter.cpp Rendering/mitkVectorImageVtkGlyphMapper3D.cpp Rendering/vtkOdfSource.cxx Rendering/vtkThickPlane.cxx Rendering/mitkOdfNormalizationMethodProperty.cpp Rendering/mitkOdfScaleByProperty.cpp # Algorithms Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp Algorithms/itkDwiGradientLengthCorrectionFilter.cpp # Registration Algorithms & Co. Algorithms/Registration/mitkRegistrationWrapper.cpp Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp # MultishellProcessing Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp # Function Collection mitkDiffusionFunctionCollection.cpp ) set(H_FILES # function Collection mitkDiffusionFunctionCollection.h # Rendering Rendering/mitkDiffusionImageMapper.h Rendering/mitkOdfVtkMapper2D.h # Reconstruction Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h Algorithms/Reconstruction/itkPointShell.h Algorithms/Reconstruction/itkOrientationDistributionFunction.h Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h # MultishellProcessing Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h # IO Datastructures IODataStructures/DiffusionWeightedImages/mitkDiffusionImage.h # Algorithms Algorithms/itkDiffusionQballGeneralizedFaImageFilter.h Algorithms/itkDiffusionQballPrepareVisualizationImageFilter.h Algorithms/itkTensorDerivedMeasurementsFilter.h Algorithms/itkBrainMaskExtractionImageFilter.h Algorithms/itkB0ImageExtractionImageFilter.h Algorithms/itkB0ImageExtractionToSeparateImageFilter.h Algorithms/itkTensorImageToDiffusionImageFilter.h Algorithms/itkTensorToL2NormImageFilter.h Algorithms/itkGaussianInterpolateImageFunction.h Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h Algorithms/itkCartesianToPolarVectorImageFilter.h Algorithms/itkPolarToCartesianVectorImageFilter.h Algorithms/itkDistanceMapFilter.h Algorithms/itkProjectionFilter.h Algorithms/itkResidualImageFilter.h Algorithms/itkExtractChannelFromRgbaImageFilter.h Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h Algorithms/itkMergeDiffusionImagesFilter.h Algorithms/itkDwiPhantomGenerationFilter.h Algorithms/itkFiniteDiffOdfMaximaExtractionFilter.h Algorithms/itkMrtrixPeakImageConverter.h Algorithms/itkFslPeakImageConverter.h Algorithms/itkShCoefficientImageImporter.h Algorithms/itkShCoefficientImageExporter.h Algorithms/itkOdfMaximaExtractionFilter.h Algorithms/itkResampleDwiImageFilter.h Algorithms/itkDwiGradientLengthCorrectionFilter.h Algorithms/itkAdcImageFilter.h Algorithms/itkDwiNormilzationFilter.h Algorithms/itkSplitDWImageFilter.h + Algorithms/itkRemoveDwiChannelFilter.h + Algorithms/itkExtractDwiChannelFilter.h Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h Algorithms/mitkDiffusionImageToDiffusionImageFilter.h Algorithms/itkNonLocalMeansDenoisingFilter.h Algorithms/itkVectorImageToImageFilter.h ) set( TOOL_FILES ) diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index 39ab109160..b8ec972e16 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,1210 +1,1204 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkTractsToDWIImageFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk { template< class PixelType > TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter() : m_FiberBundle(NULL) , m_StatusText("") , m_UseConstantRandSeed(false) , m_RandGen(itk::Statistics::MersenneTwisterRandomVariateGenerator::New()) { m_RandGen->SetSeed(); } template< class PixelType > TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter() { } template< class PixelType > TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images ) { + int numFiberCompartments = m_Parameters.m_FiberModelList.size(); // create slice object ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); Vector< double, 2 > sliceSpacing; sliceSpacing[0] = m_UpsampledSpacing[0]; sliceSpacing[1] = m_UpsampledSpacing[1]; // frequency map slice SliceType::Pointer fMapSlice = NULL; if (m_Parameters.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); fMapSlice->SetLargestPossibleRegion( region ); fMapSlice->SetBufferedRegion( region ); fMapSlice->SetRequestedRegion( region ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } DoubleDwiType::Pointer newImage = DoubleDwiType::New(); newImage->SetSpacing( m_Parameters.m_ImageSpacing ); newImage->SetOrigin( m_Parameters.m_ImageOrigin ); newImage->SetDirection( m_Parameters.m_ImageDirection ); newImage->SetLargestPossibleRegion( m_Parameters.m_ImageRegion ); newImage->SetBufferedRegion( m_Parameters.m_ImageRegion ); newImage->SetRequestedRegion( m_Parameters.m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); std::vector< unsigned int > spikeVolume; for (unsigned int i=0; iGetIntegerVariate()%images.at(0)->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (unsigned int i=0; i* signalModel; - if (iSetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->SetSpacing(sliceSpacing); slice->Allocate(); slice->FillBuffer(0.0); // extract slice from channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]); if (fMapSlice.IsNotNull() && i==0) fMapSlice->SetPixel(index2D, m_Parameters.m_FrequencyMap->GetPixel(index3D)); } compartmentSlices.push_back(slice); t2Vector.push_back(signalModel->GetT2()); } if (this->GetAbortGenerateData()) return NULL; // create k-sapce (inverse fourier transform slices) itk::Size<2> outSize; outSize.SetElement(0, m_Parameters.m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_Parameters.m_ImageRegion.GetSize(1)); itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetT2(t2Vector); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(m_Parameters); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); idft->SetDiffusionGradientDirection(m_Parameters.GetGradientDirection(g)); idft->SetFrequencyMapSlice(fMapSlice); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; // fourier transform slice SliceType::Pointer newSlice; itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D); pix3D[g] = newSlice->GetPixel(index2D); newImage->SetPixel(index3D, pix3D); } ++disp; newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; return newImage; } template< class PixelType > void TractsToDWIImageFilter< PixelType >::GenerateData() { m_TimeProbe.Start(); m_StatusText = "Starting simulation\n"; // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); if (m_Parameters.m_FiberModelList.empty()) itkExceptionMacro("No diffusion model for fiber compartments defined!"); if (m_Parameters.m_NonFiberModelList.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); int baselineIndex = m_Parameters.GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); - if (m_Parameters.m_UsePrototypeSignals) + if (!m_Parameters.m_SimulateKspaceAcquisition) m_Parameters.m_DoAddGibbsRinging = false; if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); // initialize output dwi image ImageRegion<3> croppedRegion = m_Parameters.m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_CroppingFactor); itk::Point shiftedOrigin = m_Parameters.m_ImageOrigin; shiftedOrigin[1] += (m_Parameters.m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Parameters.m_ImageSpacing[1]/2; typename OutputImageType::Pointer outImage = OutputImageType::New(); outImage->SetSpacing( m_Parameters.m_ImageSpacing ); outImage->SetOrigin( shiftedOrigin ); outImage->SetDirection( m_Parameters.m_ImageDirection ); outImage->SetLargestPossibleRegion( croppedRegion ); outImage->SetBufferedRegion( croppedRegion ); outImage->SetRequestedRegion( croppedRegion ); outImage->SetVectorLength( m_Parameters.GetNumVolumes() ); outImage->Allocate(); typename OutputImageType::PixelType temp; temp.SetSize(m_Parameters.GetNumVolumes()); temp.Fill(0.0); outImage->FillBuffer(temp); // ADJUST GEOMETRY FOR FURTHER PROCESSING // is input slize size a power of two? unsigned int x=m_Parameters.m_ImageRegion.GetSize(0); unsigned int y=m_Parameters.m_ImageRegion.GetSize(1); ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0; m_Parameters.m_ImageRegion.SetSize(0, x+pad[0]); m_Parameters.m_ImageRegion.SetSize(1, y+pad[1]); if (m_Parameters.m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_FrequencyMap); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_FrequencyMap = zeroPadder->GetOutput(); } if (m_Parameters.m_MaskImage.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_MaskImage); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_MaskImage = zeroPadder->GetOutput(); } // Apply in-plane upsampling for Gibbs ringing artifact double upsampling = 1; if (m_Parameters.m_DoAddGibbsRinging) upsampling = 2; m_UpsampledSpacing = m_Parameters.m_ImageSpacing; m_UpsampledSpacing[0] /= upsampling; m_UpsampledSpacing[1] /= upsampling; m_UpsampledImageRegion = m_Parameters.m_ImageRegion; m_UpsampledImageRegion.SetSize(0, m_Parameters.m_ImageRegion.GetSize()[0]*upsampling); m_UpsampledImageRegion.SetSize(1, m_Parameters.m_ImageRegion.GetSize()[1]*upsampling); m_UpsampledOrigin = m_Parameters.m_ImageOrigin; m_UpsampledOrigin[0] -= m_Parameters.m_ImageSpacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; m_UpsampledOrigin[1] -= m_Parameters.m_ImageSpacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; m_UpsampledOrigin[2] -= m_Parameters.m_ImageSpacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; // generate double images to store the individual compartment signals - std::vector< DoubleDwiType::Pointer > compartments; - for (unsigned int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_UpsampledOrigin ); doubleDwi->SetDirection( m_Parameters.m_ImageDirection ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); doubleDwi->SetVectorLength( m_Parameters.GetNumVolumes() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; pix.SetSize(m_Parameters.GetNumVolumes()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); - compartments.push_back(doubleDwi); + m_CompartmentImages.push_back(doubleDwi); } // initialize output volume fraction images m_VolumeFractions.clear(); - for (unsigned int i=0; iSetSpacing( m_UpsampledSpacing ); doubleImg->SetOrigin( m_UpsampledOrigin ); doubleImg->SetDirection( m_Parameters.m_ImageDirection ); doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleImg->SetBufferedRegion( m_UpsampledImageRegion ); doubleImg->SetRequestedRegion( m_UpsampledImageRegion ); doubleImg->Allocate(); doubleImg->FillBuffer(0); m_VolumeFractions.push_back(doubleImg); } // get volume fraction images ItkDoubleImgType::Pointer sumImage = ItkDoubleImgType::New(); bool foundVolumeFractionImage = false; - for (unsigned int i=0; iGetVolumeFractionImage().IsNotNull()) { foundVolumeFractionImage = true; itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(zeroPadder->GetOutput()); sumImage->SetSpacing( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetSpacing() ); sumImage->SetOrigin( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetOrigin() ); sumImage->SetDirection( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetDirection() ); sumImage->SetLargestPossibleRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetBufferedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetRequestedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->Allocate(); sumImage->FillBuffer(0); break; } } if (!foundVolumeFractionImage) { sumImage->SetSpacing( m_UpsampledSpacing ); sumImage->SetOrigin( m_UpsampledOrigin ); sumImage->SetDirection( m_Parameters.m_ImageDirection ); sumImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); sumImage->SetBufferedRegion( m_UpsampledImageRegion ); sumImage->SetRequestedRegion( m_UpsampledImageRegion ); sumImage->Allocate(); sumImage->FillBuffer(0.0); } - for (unsigned int i=0; iGetVolumeFractionImage().IsNull()) { ItkDoubleImgType::Pointer doubleImg = ItkDoubleImgType::New(); doubleImg->SetSpacing( sumImage->GetSpacing() ); doubleImg->SetOrigin( sumImage->GetOrigin() ); doubleImg->SetDirection( sumImage->GetDirection() ); doubleImg->SetLargestPossibleRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetBufferedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetRequestedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->Allocate(); - doubleImg->FillBuffer(1.0/m_Parameters.m_NonFiberModelList.size()); + doubleImg->FillBuffer(1.0/numNonFiberCompartments); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(doubleImg); } ImageRegionIterator it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { sumImage->SetPixel(it.GetIndex(), sumImage->GetPixel(it.GetIndex())+it.Get()); ++it; } } - for (unsigned int i=0; i it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (sumImage->GetPixel(it.GetIndex())>0) it.Set(it.Get()/sumImage->GetPixel(it.GetIndex())); ++it; } } // resample mask image and frequency map to fit upsampled geometry if (m_Parameters.m_DoAddGibbsRinging) { if (m_Parameters.m_MaskImage.IsNotNull()) { // rescale mask image (otherwise there are problems with the resampling) itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); rescaler->SetInput(0,m_Parameters.m_MaskImage); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); // resample mask image itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); resampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_MaskImage = resampler->GetOutput(); itk::ImageFileWriter::Pointer w = itk::ImageFileWriter::New(); w->SetFileName("/local/mask_ups.nrrd"); w->SetInput(m_Parameters.m_MaskImage); w->Update(); } // resample frequency map if (m_Parameters.m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(m_Parameters.m_FrequencyMap); resampler->SetOutputParametersFromImage(m_Parameters.m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); m_Parameters.m_FrequencyMap = resampler->GetOutput(); } } // no input tissue mask is set -> create default bool maskImageSet = true; if (m_Parameters.m_MaskImage.IsNull()) { m_StatusText += "No tissue mask set\n"; MITK_INFO << "No tissue mask set"; m_Parameters.m_MaskImage = ItkUcharImgType::New(); m_Parameters.m_MaskImage->SetSpacing( m_UpsampledSpacing ); m_Parameters.m_MaskImage->SetOrigin( m_UpsampledOrigin ); m_Parameters.m_MaskImage->SetDirection( m_Parameters.m_ImageDirection ); m_Parameters.m_MaskImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->SetBufferedRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->SetRequestedRegion( m_UpsampledImageRegion ); m_Parameters.m_MaskImage->Allocate(); m_Parameters.m_MaskImage->FillBuffer(1); maskImageSet = false; } else { m_StatusText += "Using tissue mask\n"; MITK_INFO << "Using tissue mask"; } m_Parameters.m_ImageRegion = croppedRegion; x=m_Parameters.m_ImageRegion.GetSize(0); y=m_Parameters.m_ImageRegion.GetSize(1); if ( x%2 == 1 ) m_Parameters.m_ImageRegion.SetSize(0, x+1); if ( y%2 == 1 ) m_Parameters.m_ImageRegion.SetSize(1, y+1); // resample fiber bundle for sufficient voxel coverage m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n"; double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); double volumeAccuracy = 10; fiberBundle->ResampleFibers(minSpacing/volumeAccuracy); double mmRadius = m_Parameters.m_AxonRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/volumeAccuracy; double maxVolume = 0; double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; ofstream logFile; if (m_Parameters.m_DoAddMotion) { std::string fileName = "fiberfox_motion_0.log"; std::string filePath = mitk::IOUtil::GetTempPath(); if (m_Parameters.m_OutputPath.size()>0) filePath = m_Parameters.m_OutputPath; int c = 1; while (itksys::SystemTools::FileExists((filePath+fileName).c_str())) { fileName = "fiberfox_motion_"; fileName += boost::lexical_cast(c); fileName += ".log"; c++; } logFile.open((filePath+fileName).c_str()); logFile << "0 rotation: 0,0,0; translation: 0,0,0\n"; if (m_Parameters.m_DoRandomizeMotion) { m_StatusText += "Adding random motion artifacts:\n"; m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; } else { m_StatusText += "Adding linear motion artifacts:\n"; m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; m_StatusText += "Maximum translation: " + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; } m_StatusText += "Motion logfile: " + (filePath+fileName) + "\n"; MITK_INFO << "Adding motion artifacts"; MITK_INFO << "Maximum rotation: " << m_Parameters.m_Rotation; MITK_INFO << "Maxmimum translation: " << m_Parameters.m_Translation; } maxVolume = 0; - m_StatusText += "\n"+this->GetTime()+" > Generating " + boost::lexical_cast(m_Parameters.m_FiberModelList.size()+m_Parameters.m_NonFiberModelList.size()) + "-compartment diffusion-weighted signal.\n"; + m_StatusText += "\n"+this->GetTime()+" > Generating " + boost::lexical_cast(numFiberCompartments+numNonFiberCompartments) + "-compartment diffusion-weighted signal.\n"; int numFibers = m_FiberBundle->GetNumFibers(); boost::progress_display disp(numFibers*m_Parameters.GetNumVolumes()); // get transform for motion artifacts FiberBundleType fiberBundleTransformed = fiberBundle; - VectorType rotation = m_Parameters.m_Rotation/m_Parameters.GetNumVolumes(); - VectorType translation = m_Parameters.m_Translation/m_Parameters.GetNumVolumes(); + DoubleVectorType rotation = m_Parameters.m_Rotation/m_Parameters.GetNumVolumes(); + DoubleVectorType translation = m_Parameters.m_Translation/m_Parameters.GetNumVolumes(); // creat image to hold transformed mask (motion artifact) ItkUcharImgType::Pointer tempTissueMask = ItkUcharImgType::New(); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_MaskImage); duplicator->Update(); tempTissueMask = duplicator->GetOutput(); // second upsampling needed for motion artifacts ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; - itk::Vector upsampledSpacing = m_UpsampledSpacing; + DoubleVectorType upsampledSpacing = m_UpsampledSpacing; upsampledSpacing[0] /= 4; upsampledSpacing[1] /= 4; upsampledSpacing[2] /= 4; upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4); upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4); upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4); itk::Point upsampledOrigin = m_UpsampledOrigin; upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2; upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2; upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2; ItkUcharImgType::Pointer upsampledTissueMask = ItkUcharImgType::New(); itk::ResampleImageFilter::Pointer upsampler = itk::ResampleImageFilter::New(); upsampler->SetInput(m_Parameters.m_MaskImage); upsampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); upsampler->SetSize(upsampledImageRegion.GetSize()); upsampler->SetOutputSpacing(upsampledSpacing); upsampler->SetOutputOrigin(upsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); upsampler->SetInterpolator(nn_interpolator); upsampler->Update(); upsampledTissueMask = upsampler->GetOutput(); unsigned long lastTick = 0; - if (!m_Parameters.m_UsePrototypeSignals) + switch (m_Parameters.m_DiffusionDirectionMode) + { + case(FiberfoxParameters<>::FIBER_TANGENT_DIRECTIONS): { - m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; for (unsigned int g=0; gSetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); vtkPolyData* fiberPolyData = fiberBundleTransformed->GetFiberPolyData(); // generate fiber signal (if there are any fiber models present) if (!m_Parameters.m_FiberModelList.empty()) for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; for( int j=0; jGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } double* temp = points->GetPoint(j); itk::Point vertex = GetItkPoint(temp); itk::Vector v = GetItkVector(temp); itk::Vector dir(3); if (jGetPoint(j+1))-v; else dir = v-GetItkVector(points->GetPoint(j-1)); if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2]) continue; itk::Index<3> idx; itk::ContinuousIndex contIndex; tempTissueMask->TransformPhysicalPointToIndex(vertex, idx); tempTissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); if (!tempTissueMask->GetLargestPossibleRegion().IsInside(idx) || tempTissueMask->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment - for (unsigned int k=0; kSetFiberDirection(dir); - DoubleDwiType::PixelType pix = compartments.at(k)->GetPixel(idx); + DoubleDwiType::PixelType pix = m_CompartmentImages.at(k)->GetPixel(idx); pix[g] += segmentVolume*m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g); - compartments.at(k)->SetPixel(idx, pix); + + m_CompartmentImages.at(k)->SetPixel(idx, pix); } // update fiber volume image double vol = intraAxonalVolumeImage->GetPixel(idx) + segmentVolume; intraAxonalVolumeImage->SetPixel(idx, vol); if (g==0 && vol>maxVolume) maxVolume = vol; } // progress report ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } // generate non-fiber signal ImageRegionIterator it3(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); double fact = 1; if (m_Parameters.m_AxonRadius<0.0001 || maxVolume>voxelVolume) fact = voxelVolume/maxVolume; while(!it3.IsAtEnd()) { if (it3.Get()>0) { DoubleDwiType::IndexType index = it3.GetIndex(); // get fiber volume fraction double intraAxonalVolume = intraAxonalVolumeImage->GetPixel(index)*fact; - for (unsigned int i=0; iGetPixel(index); + DoubleDwiType::PixelType pix = m_CompartmentImages.at(i)->GetPixel(index); pix[g] *= fact; - compartments.at(i)->SetPixel(index, pix); + m_CompartmentImages.at(i)->SetPixel(index, pix); } if (intraAxonalVolume>0.0001 && m_Parameters.m_DoDisablePartialVolume) // only fiber in voxel { - DoubleDwiType::PixelType pix = compartments.at(0)->GetPixel(index); + DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index); pix[g] *= voxelVolume/intraAxonalVolume; - compartments.at(0)->SetPixel(index, pix); + m_CompartmentImages.at(0)->SetPixel(index, pix); m_VolumeFractions.at(0)->SetPixel(index, 1); - for (unsigned int i=1; iGetPixel(index); + DoubleDwiType::PixelType pix = m_CompartmentImages.at(i)->GetPixel(index); pix[g] = 0; - compartments.at(i)->SetPixel(index, pix); + m_CompartmentImages.at(i)->SetPixel(index, pix); } } else { m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/voxelVolume); double extraAxonalVolume = voxelVolume-intraAxonalVolume; // non-fiber volume double interAxonalVolume = 0; - if (m_Parameters.m_FiberModelList.size()>1) + if (numFiberCompartments>1) interAxonalVolume = extraAxonalVolume * intraAxonalVolume/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f double other = extraAxonalVolume - interAxonalVolume; // rest of compartment - double singleinter = interAxonalVolume/(m_Parameters.m_FiberModelList.size()-1); + double singleinter = interAxonalVolume/(numFiberCompartments-1); // adjust non-fiber and intra-axonal signal - for (unsigned int i=1; iGetPixel(index); + DoubleDwiType::PixelType pix = m_CompartmentImages.at(i)->GetPixel(index); if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment pix[g] /= intraAxonalVolume; pix[g] *= singleinter; - compartments.at(i)->SetPixel(index, pix); + m_CompartmentImages.at(i)->SetPixel(index, pix); m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume); } - for (unsigned int i=0; i point; - tempTissueMask->TransformIndexToPhysicalPoint(index, point); - - if (m_Parameters.m_DoAddMotion) - { - if (m_Parameters.m_DoRandomizeMotion && g>0) - point = fiberBundle->TransformPoint(point.GetVnlVector(), -rotation[0],-rotation[1],-rotation[2],-translation[0],-translation[1],-translation[2]); - else - point = fiberBundle->TransformPoint(point.GetVnlVector(), -rotation[0]*g,-rotation[1]*g,-rotation[2]*g,-translation[0]*g,-translation[1]*g,-translation[2]*g); - } + itk::Point point; + tempTissueMask->TransformIndexToPhysicalPoint(index, point); + if (m_Parameters.m_DoAddMotion) + { + if (m_Parameters.m_DoRandomizeMotion && g>0) + point = fiberBundle->TransformPoint(point.GetVnlVector(), -rotation[0],-rotation[1],-rotation[2],-translation[0],-translation[1],-translation[2]); + else + point = fiberBundle->TransformPoint(point.GetVnlVector(), -rotation[0]*g,-rotation[1]*g,-rotation[2]*g,-translation[0]*g,-translation[1]*g,-translation[2]*g); + } + for (int i=0; i1) + if (numNonFiberCompartments>1) { DoubleDwiType::IndexType newIndex; m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) - { - MITK_WARN << "Volume fraction image is too small for the chosen motion artifacts! Due to motion a volume fraction outside of the specified image volume is requested."; continue; - } weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); } - DoubleDwiType::Pointer doubleDwi = compartments.at(i+m_Parameters.m_FiberModelList.size()); + DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(i+numFiberCompartments); DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*weight; doubleDwi->SetPixel(index, pix); - m_VolumeFractions.at(i+m_Parameters.m_FiberModelList.size())->SetPixel(index, other/voxelVolume*weight); + m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, other/voxelVolume*weight); } } } ++it3; } // move fibers if (m_Parameters.m_DoAddMotion && gGetDeepCopy(); rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[0]*2)-m_Parameters.m_Rotation[0]; rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[1]*2)-m_Parameters.m_Rotation[1]; rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[2]*2)-m_Parameters.m_Rotation[2]; translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[0]*2)-m_Parameters.m_Translation[0]; translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[1]*2)-m_Parameters.m_Translation[1]; translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[2]*2)-m_Parameters.m_Translation[2]; } // rotate mask image if (maskImageSet) { ImageRegionIterator maskIt(upsampledTissueMask, upsampledTissueMask->GetLargestPossibleRegion()); tempTissueMask->FillBuffer(0); while(!maskIt.IsAtEnd()) { if (maskIt.Get()<=0) { ++maskIt; continue; } DoubleDwiType::IndexType index = maskIt.GetIndex(); itk::Point point; upsampledTissueMask->TransformIndexToPhysicalPoint(index, point); if (m_Parameters.m_DoRandomizeMotion) point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); else point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0]*(g+1),rotation[1]*(g+1),rotation[2]*(g+1),translation[0]*(g+1),translation[1]*(g+1),translation[2]*(g+1)); tempTissueMask->TransformPhysicalPointToIndex(point, index); if (tempTissueMask->GetLargestPossibleRegion().IsInside(index)) tempTissueMask->SetPixel(index,100); ++maskIt; } } // rotate fibers if (logFile.is_open()) { logFile << g+1 << " rotation: " << rotation[0] << "," << rotation[1] << "," << rotation[2] << ";"; logFile << " translation: " << translation[0] << "," << translation[1] << "," << translation[2] << "\n"; } fiberBundleTransformed->TransformFibers(rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); } } + break; } - else + case (FiberfoxParameters<>::MAIN_FIBER_DIRECTIONS): { - if (m_Parameters.m_UseMainFiberDirections) + typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; + typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; + + itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); + fOdfFilter->SetFiberBundle(fiberBundle); + fOdfFilter->SetMaskImage(tempTissueMask); + fOdfFilter->SetAngularThreshold(cos(45*M_PI/180)); + fOdfFilter->SetNormalizeVectors(false); + fOdfFilter->SetUseWorkingCopy(false); + fOdfFilter->SetSizeThreshold(0); + fOdfFilter->SetMaxNumDirections(3); + fOdfFilter->Update(); + ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); + { - typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; - typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; - - itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); - fOdfFilter->SetFiberBundle(fiberBundle); - fOdfFilter->SetMaskImage(tempTissueMask); - fOdfFilter->SetAngularThreshold(cos(45*M_PI/180)); - fOdfFilter->SetNormalizeVectors(false); - fOdfFilter->SetUseWorkingCopy(false); - fOdfFilter->SetSizeThreshold(0); - fOdfFilter->SetMaxNumDirections(3); - fOdfFilter->Update(); - ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); + ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); + typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; + WriterType::Pointer writer = WriterType::New(); + writer->SetFileName("/local/NumDirections.nrrd"); + writer->SetInput(numDirImage); + writer->Update(); + } - { - ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); - typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; - WriterType::Pointer writer = WriterType::New(); - writer->SetFileName("/local/NumDirections.nrrd"); - writer->SetInput(numDirImage); - writer->Update(); - } + ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); + intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); + intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); + intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); + intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); + intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); + intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); + intraAxonalVolumeImage->Allocate(); + intraAxonalVolumeImage->FillBuffer(0); + + itk::TractDensityImageFilter< ItkDoubleImgType >::Pointer generator = itk::TractDensityImageFilter< ItkDoubleImgType >::New(); + generator->SetFiberBundle(fiberBundle); + generator->SetBinaryOutput(false); + generator->SetOutputAbsoluteValues(false); + generator->SetInputImage(intraAxonalVolumeImage); + generator->SetUseImageGeometry(true); + generator->Update(); + intraAxonalVolumeImage = generator->GetOutput(); - ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); - intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); - intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); - intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); - intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); - intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); - intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); - intraAxonalVolumeImage->Allocate(); - intraAxonalVolumeImage->FillBuffer(0); + m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; + m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; + boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); + ImageRegionIterator< ItkUcharImgType > it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) + { + ++disp; + unsigned long newTick = 50*disp.count()/disp.expected_count(); + for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) + m_StatusText += "*"; + lastTick = newTick; - itk::TractDensityImageFilter< ItkDoubleImgType >::Pointer generator = itk::TractDensityImageFilter< ItkDoubleImgType >::New(); - generator->SetFiberBundle(fiberBundle); - generator->SetBinaryOutput(false); - generator->SetOutputAbsoluteValues(false); - generator->SetInputImage(intraAxonalVolumeImage); - generator->SetUseImageGeometry(true); - generator->Update(); - intraAxonalVolumeImage = generator->GetOutput(); - - m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; - m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; - boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); - ImageRegionIterator< ItkUcharImgType > it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); - while(!it.IsAtEnd()) + if (this->GetAbortGenerateData()) { - ++disp; - unsigned long newTick = 50*disp.count()/disp.expected_count(); - for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) - m_StatusText += "*"; - lastTick = newTick; - - if (this->GetAbortGenerateData()) - { - m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; - return; - } + m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; + return; + } - if (it.Get()>0) + if (it.Get()>0) + { + int count = 0; + DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); + for (unsigned int i=0; iSize(); i++) { - int count = 0; - DoubleDwiType::PixelType pix = compartments.at(0)->GetPixel(it.GetIndex()); - for (unsigned int i=0; iSize(); i++) - { - itk::Vector< float, 3> dir = directionImageContainer->GetElement(i)->GetPixel(it.GetIndex()); - double norm = dir.GetNorm(); - if (norm>0.0001) - { - int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_FiberModelList.size()-1); - m_Parameters.m_FiberModelList.at(modelIndex)->SetFiberDirection(dir); - pix += m_Parameters.m_FiberModelList.at(modelIndex)->SimulateMeasurement()*norm; - count++; - } - } - if (count>0) - pix /= count; - pix *= intraAxonalVolumeImage->GetPixel(it.GetIndex()); - + itk::Vector< float, 3> dir = directionImageContainer->GetElement(i)->GetPixel(it.GetIndex()); + double norm = dir.GetNorm(); + if (norm>0.0001) { - int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); - pix += (1-intraAxonalVolumeImage->GetPixel(it.GetIndex()))*m_Parameters.m_NonFiberModelList.at(modelIndex)->SimulateMeasurement(); + int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_FiberModelList.size()-1); + m_Parameters.m_FiberModelList.at(modelIndex)->SetFiberDirection(dir); + pix += m_Parameters.m_FiberModelList.at(modelIndex)->SimulateMeasurement()*norm; + count++; } + } + if (count>0) + pix /= count; - compartments.at(0)->SetPixel(it.GetIndex(), pix); + pix *= intraAxonalVolumeImage->GetPixel(it.GetIndex()); + // GM/CSF + { + int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); + pix += (1-intraAxonalVolumeImage->GetPixel(it.GetIndex()))*m_Parameters.m_NonFiberModelList.at(modelIndex)->SimulateMeasurement(); } - ++it; + + m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); } + ++it; } - else if (m_Parameters.m_UseRandomDirections) + break; + } + case (FiberfoxParameters<>::RANDOM_DIRECTIONS): + { + ItkUcharImgType::Pointer numDirectionsImage = ItkUcharImgType::New(); + numDirectionsImage->SetSpacing( m_UpsampledSpacing ); + numDirectionsImage->SetOrigin( m_UpsampledOrigin ); + numDirectionsImage->SetDirection( m_Parameters.m_ImageDirection ); + numDirectionsImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); + numDirectionsImage->SetBufferedRegion( m_UpsampledImageRegion ); + numDirectionsImage->SetRequestedRegion( m_UpsampledImageRegion ); + numDirectionsImage->Allocate(); + numDirectionsImage->FillBuffer(0); + + m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; + m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; + boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); + ImageRegionIterator it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) { - ItkUcharImgType::Pointer numDirectionsImage = ItkUcharImgType::New(); - numDirectionsImage->SetSpacing( m_UpsampledSpacing ); - numDirectionsImage->SetOrigin( m_UpsampledOrigin ); - numDirectionsImage->SetDirection( m_Parameters.m_ImageDirection ); - numDirectionsImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); - numDirectionsImage->SetBufferedRegion( m_UpsampledImageRegion ); - numDirectionsImage->SetRequestedRegion( m_UpsampledImageRegion ); - numDirectionsImage->Allocate(); - numDirectionsImage->FillBuffer(0); - - m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; - m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; - boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); - ImageRegionIterator it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); - while(!it.IsAtEnd()) + ++disp; + unsigned long newTick = 50*disp.count()/disp.expected_count(); + for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) + m_StatusText += "*"; + lastTick = newTick; + + if (this->GetAbortGenerateData()) + { + m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; + return; + } + + if (it.Get()>0) { - ++disp; - unsigned long newTick = 50*disp.count()/disp.expected_count(); - for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) - m_StatusText += "*"; - lastTick = newTick; + int numFibs = m_RandGen->GetIntegerVariate(2)+1; + DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); + double volume = m_RandGen->GetVariateWithClosedRange(0.3); - if (this->GetAbortGenerateData()) + double sum = 0; + std::vector< double > fractions; + for (int i=0; iGetTime()+" > Simulation aborted\n"; - return; +// fractions.push_back(1); + fractions.push_back(0.5+m_RandGen->GetVariateWithClosedRange(0.5)); + sum += fractions.at(i); } + for (int i=0; i0) + std::vector< itk::Vector > directions; + for (int i=0; iGetIntegerVariate(2)+1; - DoubleDwiType::PixelType pix = compartments.at(0)->GetPixel(it.GetIndex()); - double volume = m_RandGen->GetVariateWithClosedRange(0.3); - - double sum = 0; - std::vector< double > fractions; - for (int i=0; iGetVariateWithClosedRange(2)-1.0; + fib[1] = m_RandGen->GetVariateWithClosedRange(2)-1.0; + fib[2] = m_RandGen->GetVariateWithClosedRange(2)-1.0; + fib.Normalize(); + + double min = 0; + for (unsigned int d=0; dGetVariateWithClosedRange(0.5)); - sum += fractions.at(i); + double angle = fabs(fib*directions[d]); + if (angle>min) + min = angle; } - for (int i=0; i > directions; - for (int i=0; iGetIntegerVariate(m_Parameters.m_FiberModelList.size()-1); - itk::Vector fib; - fib[0] = m_RandGen->GetVariateWithClosedRange(2)-1.0; - fib[1] = m_RandGen->GetVariateWithClosedRange(2)-1.0; - fib[2] = m_RandGen->GetVariateWithClosedRange(2)-1.0; - fib.Normalize(); - - double min = 0; - for (unsigned int d=0; dmin) - min = angle; - } - if (min<0.5) - { - m_Parameters.m_FiberModelList.at(modelIndex)->SetFiberDirection(fib); - pix += m_Parameters.m_FiberModelList.at(modelIndex)->SimulateMeasurement()*fractions[i]; - directions.push_back(fib); - } - else - i--; - } - pix *= (1-volume); - - // CSF/GM + if (min<0.5) { - int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); - pix += volume*m_Parameters.m_NonFiberModelList.at(modelIndex)->SimulateMeasurement(); + m_Parameters.m_FiberModelList.at(0)->SetFiberDirection(fib); + pix += m_Parameters.m_FiberModelList.at(0)->SimulateMeasurement()*fractions[i]; + directions.push_back(fib); } + else + i--; + } + pix *= (1-volume); - compartments.at(0)->SetPixel(it.GetIndex(), pix); - numDirectionsImage->SetPixel(it.GetIndex(), numFibs); + // CSF/GM + { +// int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); + pix += volume*m_Parameters.m_NonFiberModelList.at(0)->SimulateMeasurement(); } - ++it; - } - itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); - wr->SetInput(numDirectionsImage); - wr->SetFileName("/local/NumDirections.nrrd"); - wr->Update(); + m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); + numDirectionsImage->SetPixel(it.GetIndex(), numFibs); + } + ++it; } + + itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); + wr->SetInput(numDirectionsImage); + wr->SetFileName("/local/NumDirections.nrrd"); + wr->Update(); + } } if (logFile.is_open()) { logFile << "DONE"; logFile.close(); } m_StatusText += "\n\n"; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } // do k-space stuff DoubleDwiType::Pointer doubleOutImage; - if ( !m_Parameters.m_UsePrototypeSignals && (m_Parameters.m_Spikes>0 || m_Parameters.m_FrequencyMap.IsNotNull() || m_Parameters.m_KspaceLineOffset>0 || m_Parameters.m_DoSimulateRelaxation || m_Parameters.m_EddyStrength>0 || m_Parameters.m_DoAddGibbsRinging || m_Parameters.m_CroppingFactor<1.0) ) + if ( m_Parameters.m_SimulateKspaceAcquisition ) { m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; MITK_INFO << "Adjusting complex signal:"; if (m_Parameters.m_DoSimulateRelaxation) m_StatusText += "Simulating signal relaxation\n"; if (m_Parameters.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; if (m_Parameters.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; if (m_Parameters.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; if (m_Parameters.m_Spikes>0) m_StatusText += "Simulating spikes\n"; if (m_Parameters.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; if (m_Parameters.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; - doubleOutImage = DoKspaceStuff(compartments); - m_Parameters.m_SignalScale = 1; + doubleOutImage = DoKspaceStuff(m_CompartmentImages); + m_Parameters.m_SignalScale = 1; // already scaled in DoKspaceStuff } else { m_StatusText += this->GetTime()+" > Summing compartments\n"; MITK_INFO << "Summing compartments"; - doubleOutImage = compartments.at(0); + doubleOutImage = m_CompartmentImages.at(0); - for (unsigned int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); - adder->SetInput2(compartments.at(i)); + adder->SetInput2(m_CompartmentImages.at(i)); adder->Update(); doubleOutImage = adder->GetOutput(); } } if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } m_StatusText += this->GetTime()+" > Finalizing image\n"; MITK_INFO << "Finalizing image"; if (m_Parameters.m_SignalScale>1) m_StatusText += " Scaling signal\n"; if (m_Parameters.m_NoiseModel!=NULL) m_StatusText += " Adding noise\n"; unsigned int window = 0; unsigned int min = itk::NumericTraits::max(); ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.GetNumVolumes()); boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; lastTick = 0; while(!it4.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp2; unsigned long newTick = 50*disp2.count()/disp2.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename OutputImageType::IndexType index = it4.GetIndex(); signal = doubleOutImage->GetPixel(index)*m_Parameters.m_SignalScale; if (m_Parameters.m_NoiseModel!=NULL) - { -// DoubleDwiType::PixelType accu = signal; accu.Fill(0.0); -// for (unsigned int i=0; iAddNoise(signal); -// accu += temp; -// } -// signal = accu/m_Parameters.m_Repetitions; - } + m_Parameters.m_NoiseModel->AddNoise(signal); for (unsigned int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); - if (!m_Parameters.IsBaselineIndex(i) && signal[i]>window) + if ( (!m_Parameters.IsBaselineIndex(i) || signal.Size()==1) && signal[i]>window) window = signal[i]; - if (!m_Parameters.IsBaselineIndex(i) && signal[i]SetNthOutput(0, outImage); m_StatusText += "\n\n"; m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); m_TimeProbe.Stop(); } template< class PixelType > itk::Point TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > itk::Vector TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } template< class PixelType > double TractsToDWIImageFilter< PixelType >::RoundToNearest(double num) { return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5); } template< class PixelType > std::string TractsToDWIImageFilter< PixelType >::GetTime() { m_TimeProbe.Stop(); unsigned long total = RoundToNearest(m_TimeProbe.GetTotal()); unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); m_TimeProbe.Start(); return out; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h index eb4f23f239..dfb640ad23 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h @@ -1,111 +1,111 @@ /*=================================================================== 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__ #include #include #include #include #include #include #include #include #include namespace itk { /** * \brief Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. * See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details. */ template< class PixelType > class TractsToDWIImageFilter : public ImageSource< itk::VectorImage< PixelType, 3 > > { public: typedef TractsToDWIImageFilter Self; typedef ImageSource< itk::VectorImage< PixelType, 3 > > Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef typename Superclass::OutputImageType OutputImageType; typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef mitk::FiberBundleX::Pointer FiberBundleType; typedef itk::VectorImage< double, 3 > DoubleDwiType; typedef itk::Matrix MatrixType; typedef itk::Image< double, 2 > SliceType; typedef itk::VnlForwardFFTImageFilter::OutputImageType ComplexSliceType; - typedef itk::Vector< double,3> VectorType; + typedef itk::Vector< double,3> DoubleVectorType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( TractsToDWIImageFilter, ImageSource ) /** Input */ itkSetMacro( FiberBundle, FiberBundleType ) ///< Input fiber bundle itkSetMacro( UseConstantRandSeed, bool ) ///< Seed for random generator. - itkSetMacro( InputDwi, mitk::DiffusionImage::Pointer ) void SetParameters( FiberfoxParameters param ) ///< Simulation parameters. { m_Parameters = param; } /** Output */ FiberfoxParameters GetParameters(){ return m_Parameters; } std::vector< ItkDoubleImgType::Pointer > GetVolumeFractions() ///< one double image for each compartment containing the corresponding volume fraction per voxel { return m_VolumeFractions; } mitk::LevelWindow GetLevelWindow(){ return m_LevelWindow; } itkGetMacro( StatusText, std::string ) 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); double RoundToNearest(double num); std::string GetTime(); /** Transform generated image compartment by compartment, channel by channel and slice by slice using DFT and add k-space artifacts. */ DoubleDwiType::Pointer DoKspaceStuff(std::vector< DoubleDwiType::Pointer >& images); mitk::FiberfoxParameters m_Parameters; itk::Vector m_UpsampledSpacing; itk::Point m_UpsampledOrigin; ImageRegion<3> m_UpsampledImageRegion; FiberBundleType m_FiberBundle; mitk::LevelWindow m_LevelWindow; std::vector< ItkDoubleImgType::Pointer > m_VolumeFractions; std::string m_StatusText; itk::TimeProbe m_TimeProbe; bool m_UseConstantRandSeed; - mitk::DiffusionImage::Pointer m_InputDwi; itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen; + + std::vector< DoubleDwiType::Pointer > m_CompartmentImages; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkTractsToDWIImageFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp index f799ab8a12..6c437a400b 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp @@ -1,557 +1,556 @@ #include "itkTractsToVectorImageFilter.h" // VTK #include #include #include // ITK #include #include // misc #define _USE_MATH_DEFINES #include #include namespace itk{ static bool CompareVectorLengths(const vnl_vector_fixed< double, 3 >& v1, const vnl_vector_fixed< double, 3 >& v2) { return (v1.magnitude()>v2.magnitude()); } template< class PixelType > TractsToVectorImageFilter< PixelType >::TractsToVectorImageFilter(): m_AngularThreshold(0.7), m_Epsilon(0.999), m_MaskImage(NULL), m_NormalizeVectors(false), m_UseWorkingCopy(true), m_MaxNumDirections(3), m_SizeThreshold(0.2), m_NumDirectionsImage(NULL) { this->SetNumberOfRequiredOutputs(1); } template< class PixelType > TractsToVectorImageFilter< PixelType >::~TractsToVectorImageFilter() { } template< class PixelType > vnl_vector_fixed TractsToVectorImageFilter< PixelType >::GetVnlVector(double point[]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > itk::Point TractsToVectorImageFilter< PixelType >::GetItkPoint(double point[]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > void TractsToVectorImageFilter< PixelType >::GenerateData() { mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry(); // calculate new image parameters itk::Vector spacing; itk::Point origin; itk::Matrix direction; ImageRegion<3> imageRegion; if (!m_MaskImage.IsNull()) { spacing = m_MaskImage->GetSpacing(); imageRegion = m_MaskImage->GetLargestPossibleRegion(); origin = m_MaskImage->GetOrigin(); direction = m_MaskImage->GetDirection(); } else { spacing = geometry->GetSpacing(); origin = geometry->GetOrigin(); mitk::BaseGeometry::BoundsArrayType bounds = geometry->GetBounds(); origin[0] += bounds.GetElement(0); origin[1] += bounds.GetElement(2); origin[2] += bounds.GetElement(4); for (int i=0; i<3; i++) for (int j=0; j<3; j++) direction[j][i] = geometry->GetMatrixColumn(i)[j]; imageRegion.SetSize(0, geometry->GetExtent(0)); imageRegion.SetSize(1, geometry->GetExtent(1)); imageRegion.SetSize(2, geometry->GetExtent(2)); m_MaskImage = ItkUcharImgType::New(); m_MaskImage->SetSpacing( spacing ); m_MaskImage->SetOrigin( origin ); m_MaskImage->SetDirection( direction ); m_MaskImage->SetRegions( imageRegion ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } OutputImageType::RegionType::SizeType outImageSize = imageRegion.GetSize(); m_OutImageSpacing = m_MaskImage->GetSpacing(); m_ClusteredDirectionsContainer = ContainerType::New(); // initialize num directions image m_NumDirectionsImage = ItkUcharImgType::New(); m_NumDirectionsImage->SetSpacing( spacing ); m_NumDirectionsImage->SetOrigin( origin ); m_NumDirectionsImage->SetDirection( direction ); m_NumDirectionsImage->SetRegions( imageRegion ); m_NumDirectionsImage->Allocate(); m_NumDirectionsImage->FillBuffer(0); // initialize direction images m_DirectionImageContainer = DirectionImageContainerType::New(); - for (unsigned int i=0; iSetSpacing( spacing ); - directionImage->SetOrigin( origin ); - directionImage->SetDirection( direction ); - directionImage->SetRegions( imageRegion ); - directionImage->Allocate(); - Vector< float, 3 > nullVec; nullVec.Fill(0.0); - directionImage->FillBuffer(nullVec); - m_DirectionImageContainer->InsertElement(i, directionImage); - } // resample fiber bundle double minSpacing = 1; if(m_OutImageSpacing[0]GetDeepCopy(); // resample fiber bundle for sufficient voxel coverage m_FiberBundle->ResampleFibers(minSpacing/10); // iterate over all fibers vtkSmartPointer fiberPolyData = m_FiberBundle->GetFiberPolyData(); int numFibers = m_FiberBundle->GetNumFibers(); m_DirectionsContainer = ContainerType::New(); MITK_INFO << "Generating directions from tractogram"; boost::progress_display disp(numFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; vnl_vector_fixed dir; itk::Point worldPos; vnl_vector v; for( int j=0; jGetPoint(j); worldPos = GetItkPoint(temp); itk::Index<3> index; m_MaskImage->TransformPhysicalPointToIndex(worldPos, index); if (!m_MaskImage->GetLargestPossibleRegion().IsInside(index) || m_MaskImage->GetPixel(index)==0) continue; // get fiber tangent direction at this position v = GetVnlVector(temp); dir = GetVnlVector(points->GetPoint(j+1))-v; if (dir.is_zero()) continue; dir.normalize(); // add direction to container unsigned int idx = index[0] + outImageSize[0]*(index[1] + outImageSize[1]*index[2]); DirectionContainerType::Pointer dirCont; if (m_DirectionsContainer->IndexExists(idx)) { dirCont = m_DirectionsContainer->GetElement(idx); if (dirCont.IsNull()) { dirCont = DirectionContainerType::New(); dirCont->push_back(dir); m_DirectionsContainer->InsertElement(idx, dirCont); } else dirCont->push_back(dir); } else { dirCont = DirectionContainerType::New(); dirCont->push_back(dir); m_DirectionsContainer->InsertElement(idx, dirCont); } } } vtkSmartPointer m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); itk::ImageRegionIterator dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion()); MITK_INFO << "Clustering directions"; boost::progress_display disp2(outImageSize[0]*outImageSize[1]*outImageSize[2]); while(!dirIt.IsAtEnd()) { ++disp2; OutputImageType::IndexType index = dirIt.GetIndex(); int idx = index[0]+(index[1]+index[2]*outImageSize[1])*outImageSize[0]; if (!m_DirectionsContainer->IndexExists(idx)) { ++dirIt; continue; } DirectionContainerType::Pointer dirCont = m_DirectionsContainer->GetElement(idx); if (dirCont.IsNull() || dirCont->empty()) { ++dirIt; continue; } std::vector< double > lengths; lengths.resize(dirCont->size(), 1); // all peaks have size 1 DirectionContainerType::Pointer directions = FastClustering(dirCont, lengths); std::sort( directions->begin(), directions->end(), CompareVectorLengths ); unsigned int numDir = directions->size(); - if (numDir>m_MaxNumDirections) + if (m_MaxNumDirections>0 && numDir>m_MaxNumDirections) numDir = m_MaxNumDirections; int count = 0; for (unsigned int i=0; i container = vtkSmartPointer::New(); itk::ContinuousIndex center; center[0] = index[0]; center[1] = index[1]; center[2] = index[2]; itk::Point worldCenter; m_MaskImage->TransformContinuousIndexToPhysicalPoint( center, worldCenter ); DirectionType dir = directions->at(i); if (dir.magnitude()size()) + { + ItkDirectionImageType::Pointer directionImage = ItkDirectionImageType::New(); + directionImage->SetSpacing( spacing ); + directionImage->SetOrigin( origin ); + directionImage->SetDirection( direction ); + directionImage->SetRegions( imageRegion ); + directionImage->Allocate(); + Vector< float, 3 > nullVec; nullVec.Fill(0.0); + directionImage->FillBuffer(nullVec); + m_DirectionImageContainer->InsertElement(i, directionImage); + } + // set direction image pixel ItkDirectionImageType::Pointer directionImage = m_DirectionImageContainer->GetElement(i); Vector< float, 3 > pixel; pixel.SetElement(0, dir[0]); pixel.SetElement(1, dir[1]); pixel.SetElement(2, dir[2]); directionImage->SetPixel(index, pixel); // add direction to vector field (with spacing compensation) itk::Point worldStart; worldStart[0] = worldCenter[0]-dir[0]/2*minSpacing; worldStart[1] = worldCenter[1]-dir[1]/2*minSpacing; worldStart[2] = worldCenter[2]-dir[2]/2*minSpacing; vtkIdType id = m_VtkPoints->InsertNextPoint(worldStart.GetDataPointer()); container->GetPointIds()->InsertNextId(id); itk::Point worldEnd; worldEnd[0] = worldCenter[0]+dir[0]/2*minSpacing; worldEnd[1] = worldCenter[1]+dir[1]/2*minSpacing; worldEnd[2] = worldCenter[2]+dir[2]/2*minSpacing; id = m_VtkPoints->InsertNextPoint(worldEnd.GetDataPointer()); container->GetPointIds()->InsertNextId(id); m_VtkCellArray->InsertNextCell(container); } dirIt.Set(count); ++dirIt; } vtkSmartPointer directionsPolyData = vtkSmartPointer::New(); directionsPolyData->SetPoints(m_VtkPoints); directionsPolyData->SetLines(m_VtkCellArray); m_OutputFiberBundle = mitk::FiberBundleX::New(directionsPolyData); } template< class PixelType > typename TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths) { DirectionContainerType::Pointer outDirs = DirectionContainerType::New(); if (inDirs->size()<2) return inDirs; DirectionType oldMean, currentMean; std::vector< int > touched; // initialize touched.resize(inDirs->size(), 0); bool free = true; currentMean = inDirs->at(0); // initialize first seed + currentMean.normalize(); double length = lengths.at(0); + touched[0] = 1; std::vector< double > newLengths; bool meanChanged = false; double max = 0; while (free) { oldMean.fill(0.0); // start mean-shift clustering double angle = 0; - int counter = 0; - while (dot_product(currentMean, oldMean)<0.99) + while (fabs(dot_product(currentMean, oldMean))<0.99) { - counter = 0; oldMean = currentMean; currentMean.fill(0.0); for (unsigned int i=0; isize(); i++) { angle = dot_product(oldMean, inDirs->at(i)); if (angle>=m_AngularThreshold) { currentMean += inDirs->at(i); if (meanChanged) length += lengths.at(i); touched[i] = 1; - counter++; meanChanged = true; } else if (-angle>=m_AngularThreshold) { currentMean -= inDirs->at(i); if (meanChanged) length += lengths.at(i); touched[i] = 1; - counter++; meanChanged = true; } } - if (currentMean.magnitude()>0.001) + if(!meanChanged) + currentMean = oldMean; + else currentMean.normalize(); } // found stable mean - if (counter>0) - { - outDirs->push_back(currentMean); - newLengths.push_back(length); - if (length>max) - max = length; - } + outDirs->push_back(currentMean); + newLengths.push_back(length); + if (length>max) + max = length; // find next unused seed free = false; for (unsigned int i=0; iat(i); free = true; meanChanged = false; length = lengths.at(i); + touched[i] = 1; break; } } if (inDirs->size()==outDirs->size()) { if (!m_NormalizeVectors && max>0) for (unsigned int i=0; isize(); i++) outDirs->SetElement(i, outDirs->at(i)*newLengths.at(i)/max); return outDirs; } else return FastClustering(outDirs, newLengths); } //template< class PixelType > //std::vector< DirectionType > TractsToVectorImageFilter< PixelType >::Clustering(std::vector< DirectionType >& inDirs) //{ // std::vector< DirectionType > outDirs; // if (inDirs.empty()) // return outDirs; // DirectionType oldMean, currentMean, workingMean; // std::vector< DirectionType > normalizedDirs; // std::vector< int > touched; // for (std::size_t i=0; i0.0001) // { // counter = 0; // oldMean = currentMean; // workingMean = oldMean; // workingMean.normalize(); // currentMean.fill(0.0); // for (std::size_t i=0; i=m_AngularThreshold) // { // currentMean += inDirs[i]; // counter++; // } // else if (-angle>=m_AngularThreshold) // { // currentMean -= inDirs[i]; // counter++; // } // } // } // // found stable mean // if (counter>0) // { // bool add = true; // DirectionType normMean = currentMean; // normMean.normalize(); // for (std::size_t i=0; i0) // { // if (mag>max) // max = mag; // outDirs.push_back(currentMean); // } // } // } // } // if (m_NormalizeVectors) // for (std::size_t i=0; i0) // for (std::size_t i=0; i //TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::MeanShiftClustering(DirectionContainerType::Pointer dirCont) //{ // DirectionContainerType::Pointer container = DirectionContainerType::New(); // double max = 0; // for (DirectionContainerType::ConstIterator it = dirCont->Begin(); it!=dirCont->End(); ++it) // { // vnl_vector_fixed mean = ClusterStep(dirCont, it.Value()); // if (mean.is_zero()) // continue; // bool addMean = true; // for (DirectionContainerType::ConstIterator it2 = container->Begin(); it2!=container->End(); ++it2) // { // vnl_vector_fixed dir = it2.Value(); // double angle = fabs(dot_product(mean, dir)/(mean.magnitude()*dir.magnitude())); // if (angle>=m_Epsilon) // { // addMean = false; // break; // } // } // if (addMean) // { // if (m_NormalizeVectors) // mean.normalize(); // else if (mean.magnitude()>max) // max = mean.magnitude(); // container->InsertElement(container->Size(), mean); // } // } // // max normalize voxel directions // if (max>0 && !m_NormalizeVectors) // for (std::size_t i=0; iSize(); i++) // container->ElementAt(i) /= max; // if (container->Size()Size()) // return MeanShiftClustering(container); // else // return container; //} //template< class PixelType > //vnl_vector_fixed TractsToVectorImageFilter< PixelType >::ClusterStep(DirectionContainerType::Pointer dirCont, vnl_vector_fixed currentMean) //{ // vnl_vector_fixed newMean; newMean.fill(0); // for (DirectionContainerType::ConstIterator it = dirCont->Begin(); it!=dirCont->End(); ++it) // { // vnl_vector_fixed dir = it.Value(); // double angle = dot_product(currentMean, dir)/(currentMean.magnitude()*dir.magnitude()); // if (angle>=m_AngularThreshold) // newMean += dir; // else if (-angle>=m_AngularThreshold) // newMean -= dir; // } // if (fabs(dot_product(currentMean, newMean)/(currentMean.magnitude()*newMean.magnitude()))>=m_Epsilon || newMean.is_zero()) // return newMean; // else // return ClusterStep(dirCont, newMean); //} } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index 485fd29b19..41425b0fd2 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,472 +1,471 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::FiberfoxParameters() : m_SignalScale(100) , m_tEcho(100) , m_tLine(1) , m_tInhom(50) , m_Bvalue(1000) + , m_SimulateKspaceAcquisition(false) , m_AxonRadius(0) + , m_DiffusionDirectionMode(FIBER_TANGENT_DIRECTIONS) , m_Spikes(0) , m_SpikeAmplitude(1) , m_KspaceLineOffset(0) , m_EddyStrength(0) , m_Tau(70) , m_CroppingFactor(1) , m_DoAddGibbsRinging(false) , m_DoSimulateRelaxation(true) , m_DoDisablePartialVolume(false) , m_DoAddMotion(false) , m_DoRandomizeMotion(true) , m_NoiseModel(NULL) , m_FrequencyMap(NULL) , m_MaskImage(NULL) , m_ResultNode(mitk::DataNode::New()) , m_ParentNode(NULL) , m_SignalModelString("") , m_ArtifactModelString("") , m_OutputPath("") , m_NumBaseline(1) , m_NumGradients(6) - , m_UsePrototypeSignals(false) - , m_UseRandomDirections(false) - , m_UseMainFiberDirections(false) { m_ImageDirection.SetIdentity(); m_ImageOrigin.Fill(0.0); m_ImageRegion.SetSize(0, 11); m_ImageRegion.SetSize(1, 11); m_ImageRegion.SetSize(2, 3); m_ImageSpacing.Fill(2.0); m_Translation.Fill(0.0); m_Rotation.Fill(0.0); GenerateGradientHalfShell(); } template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::~FiberfoxParameters() { // if (m_NoiseModel!=NULL) // delete m_NoiseModel; } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::GenerateGradientHalfShell() { int NPoints = 2*m_NumGradients; m_GradientDirections.clear(); m_NumBaseline = NPoints/20; if (m_NumBaseline==0) m_NumBaseline=1; GradientType g; g.Fill(0.0); for (unsigned int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector< int > mitk::FiberfoxParameters< ScalarType >::GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) result.push_back(i); return result; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) return i; return -1; } template< class ScalarType > bool mitk::FiberfoxParameters< ScalarType >::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumWeightedVolumes() { return m_NumGradients; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumBaselineVolumes() { return m_NumBaseline; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumVolumes() { return m_GradientDirections.size(); } template< class ScalarType > typename mitk::FiberfoxParameters< ScalarType >::GradientListType mitk::FiberfoxParameters< ScalarType >::GetGradientDirections() { return m_GradientDirections; } template< class ScalarType > typename mitk::FiberfoxParameters< ScalarType >::GradientType mitk::FiberfoxParameters< ScalarType >::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SetNumWeightedGradients(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(GradientListType gradientList) { m_GradientDirections = gradientList; m_NumGradients = 0; m_NumBaseline = 0; for( unsigned int i=0; im_GradientDirections.size(); i++) { if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList) { m_NumGradients = 0; m_NumBaseline = 0; m_GradientDirections.clear(); for( unsigned int i=0; iSize(); i++) { GradientType g; g[0] = gradientList->at(i)[0]; g[1] = gradientList->at(i)[1]; g[2] = gradientList->at(i)[2]; m_GradientDirections.push_back(g); if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::LoadParameters(string filename) { boost::property_tree::ptree parameters; boost::property_tree::xml_parser::read_xml(filename, parameters); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel!=NULL) delete m_NoiseModel; BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") ) { if( v1.first == "image" ) { m_ImageRegion.SetSize(0, v1.second.get("basic.size.x")); m_ImageRegion.SetSize(1, v1.second.get("basic.size.y")); m_ImageRegion.SetSize(2, v1.second.get("basic.size.z")); m_ImageSpacing[0] = v1.second.get("basic.spacing.x"); m_ImageSpacing[1] = v1.second.get("basic.spacing.y"); m_ImageSpacing[2] = v1.second.get("basic.spacing.z"); m_NumGradients = v1.second.get("basic.numgradients"); GenerateGradientHalfShell(); m_Bvalue = v1.second.get("basic.bvalue"); m_SignalScale = v1.second.get("signalScale"); m_tEcho = v1.second.get("tEcho"); m_tLine = v1.second.get("tLine"); m_tInhom = v1.second.get("tInhom"); m_AxonRadius = v1.second.get("axonRadius"); m_DoSimulateRelaxation = v1.second.get("doSimulateRelaxation"); m_DoDisablePartialVolume = v1.second.get("doDisablePartialVolume"); if (v1.second.get("artifacts.addnoise")) { switch (v1.second.get("artifacts.noisedistribution")) { case 0: { m_NoiseModel = new mitk::RicianNoiseModel< ScalarType >(); break; } case 1: { m_NoiseModel = new mitk::ChiSquareNoiseModel< ScalarType >(); break; } default: { m_NoiseModel = new mitk::RicianNoiseModel< ScalarType >(); } } m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); } m_KspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset"); m_CroppingFactor = (100-v1.second.get("artifacts.aliasingfactor"))/100; m_Spikes = v1.second.get("artifacts.spikesnum"); m_SpikeAmplitude = v1.second.get("artifacts.spikesscale"); m_EddyStrength = v1.second.get("artifacts.eddyStrength"); m_DoAddGibbsRinging = v1.second.get("artifacts.addringing"); m_DoAddMotion = v1.second.get("artifacts.doAddMotion"); m_DoRandomizeMotion = v1.second.get("artifacts.randomMotion"); m_Translation[0] = v1.second.get("artifacts.translation0"); m_Translation[1] = v1.second.get("artifacts.translation1"); m_Translation[2] = v1.second.get("artifacts.translation2"); m_Rotation[0] = v1.second.get("artifacts.rotation0"); m_Rotation[1] = v1.second.get("artifacts.rotation1"); m_Rotation[2] = v1.second.get("artifacts.rotation2"); // compartment 1 switch (v1.second.get("compartment1.index")) { case 0: { mitk::StickModel* stickModel = new mitk::StickModel(); stickModel->SetGradientList(m_GradientDirections); stickModel->SetBvalue(m_Bvalue); stickModel->SetDiffusivity(v1.second.get("compartment1.stick.d")); stickModel->SetT2(v1.second.get("compartment1.stick.t2")); m_FiberModelList.push_back(stickModel); break; } case 1: { mitk::TensorModel* zeppelinModel = new mitk::TensorModel(); zeppelinModel->SetGradientList(m_GradientDirections); zeppelinModel->SetBvalue(m_Bvalue); zeppelinModel->SetDiffusivity1(v1.second.get("compartment1.zeppelin.d1")); zeppelinModel->SetDiffusivity2(v1.second.get("compartment1.zeppelin.d2")); zeppelinModel->SetDiffusivity3(v1.second.get("compartment1.zeppelin.d2")); zeppelinModel->SetT2(v1.second.get("compartment1.zeppelin.t2")); m_FiberModelList.push_back(zeppelinModel); break; } case 2: { mitk::TensorModel* tensorModel = new mitk::TensorModel(); tensorModel->SetGradientList(m_GradientDirections); tensorModel->SetBvalue(m_Bvalue); tensorModel->SetDiffusivity1(v1.second.get("compartment1.tensor.d1")); tensorModel->SetDiffusivity2(v1.second.get("compartment1.tensor.d2")); tensorModel->SetDiffusivity3(v1.second.get("compartment1.tensor.d3")); tensorModel->SetT2(v1.second.get("compartment1.tensor.t2")); m_FiberModelList.push_back(tensorModel); break; } } // compartment 2 switch (v1.second.get("compartment2.index")) { case 0: { mitk::StickModel* stickModel = new mitk::StickModel(); stickModel->SetGradientList(m_GradientDirections); stickModel->SetBvalue(m_Bvalue); stickModel->SetDiffusivity(v1.second.get("compartment2.stick.d")); stickModel->SetT2(v1.second.get("compartment2.stick.t2")); m_FiberModelList.push_back(stickModel); break; } case 1: { mitk::TensorModel* zeppelinModel = new mitk::TensorModel(); zeppelinModel->SetGradientList(m_GradientDirections); zeppelinModel->SetBvalue(m_Bvalue); zeppelinModel->SetDiffusivity1(v1.second.get("compartment2.zeppelin.d1")); zeppelinModel->SetDiffusivity2(v1.second.get("compartment2.zeppelin.d2")); zeppelinModel->SetDiffusivity3(v1.second.get("compartment2.zeppelin.d2")); zeppelinModel->SetT2(v1.second.get("compartment2.zeppelin.t2")); m_FiberModelList.push_back(zeppelinModel); break; } case 2: { mitk::TensorModel* tensorModel = new mitk::TensorModel(); tensorModel->SetGradientList(m_GradientDirections); tensorModel->SetBvalue(m_Bvalue); tensorModel->SetDiffusivity1(v1.second.get("compartment2.tensor.d1")); tensorModel->SetDiffusivity2(v1.second.get("compartment2.tensor.d2")); tensorModel->SetDiffusivity3(v1.second.get("compartment2.tensor.d3")); tensorModel->SetT2(v1.second.get("compartment2.tensor.t2")); m_FiberModelList.push_back(tensorModel); break; } } // compartment 3 switch (v1.second.get("compartment3.index")) { case 0: { mitk::BallModel* ballModel = new mitk::BallModel(); ballModel->SetGradientList(m_GradientDirections); ballModel->SetBvalue(m_Bvalue); ballModel->SetDiffusivity(v1.second.get("compartment3.ball.d")); ballModel->SetT2(v1.second.get("compartment3.ball.t2")); m_NonFiberModelList.push_back(ballModel); break; } case 1: { mitk::AstroStickModel* astrosticksModel = new mitk::AstroStickModel(); astrosticksModel->SetGradientList(m_GradientDirections); astrosticksModel->SetBvalue(m_Bvalue); astrosticksModel->SetDiffusivity(v1.second.get("compartment3.astrosticks.d")); astrosticksModel->SetT2(v1.second.get("compartment3.astrosticks.t2")); astrosticksModel->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); m_NonFiberModelList.push_back(astrosticksModel); break; } case 2: { mitk::DotModel* dotModel = new mitk::DotModel(); dotModel->SetGradientList(m_GradientDirections); dotModel->SetT2(v1.second.get("compartment3.dot.t2")); m_NonFiberModelList.push_back(dotModel); break; } } // compartment 4 switch (v1.second.get("compartment4.index")) { case 0: { mitk::BallModel* ballModel = new mitk::BallModel(); ballModel->SetGradientList(m_GradientDirections); ballModel->SetBvalue(m_Bvalue); ballModel->SetDiffusivity(v1.second.get("compartment4.ball.d")); ballModel->SetT2(v1.second.get("compartment4.ball.t2")); m_NonFiberModelList.push_back(ballModel); break; } case 1: { mitk::AstroStickModel* astrosticksModel = new mitk::AstroStickModel(); astrosticksModel->SetGradientList(m_GradientDirections); astrosticksModel->SetBvalue(m_Bvalue); astrosticksModel->SetDiffusivity(v1.second.get("compartment4.astrosticks.d")); astrosticksModel->SetT2(v1.second.get("compartment4.astrosticks.t2")); astrosticksModel->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); m_NonFiberModelList.push_back(astrosticksModel); break; } case 2: { mitk::DotModel* dotModel = new mitk::DotModel(); dotModel->SetGradientList(m_GradientDirections); dotModel->SetT2(v1.second.get("compartment4.dot.t2")); m_NonFiberModelList.push_back(dotModel); break; } } } } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::PrintSelf() { MITK_INFO << "m_ImageRegion: " << m_ImageRegion; MITK_INFO << "m_ImageSpacing: " << m_ImageSpacing; MITK_INFO << "m_ImageOrigin: " << m_ImageOrigin; MITK_INFO << "m_ImageDirection: " << m_ImageDirection; MITK_INFO << "m_NumGradients: " << m_NumGradients; MITK_INFO << "m_Bvalue: " << m_Bvalue; MITK_INFO << "m_SignalScale: " << m_SignalScale; MITK_INFO << "m_tEcho: " << m_tEcho; MITK_INFO << "m_tLine: " << m_tLine; MITK_INFO << "m_tInhom: " << m_tInhom; MITK_INFO << "m_AxonRadius: " << m_AxonRadius; MITK_INFO << "m_KspaceLineOffset: " << m_KspaceLineOffset; MITK_INFO << "m_AddGibbsRinging: " << m_DoAddGibbsRinging; MITK_INFO << "m_EddyStrength: " << m_EddyStrength; MITK_INFO << "m_Spikes: " << m_Spikes; MITK_INFO << "m_SpikeAmplitude: " << m_SpikeAmplitude; MITK_INFO << "m_CroppingFactor: " << m_CroppingFactor; MITK_INFO << "m_DoSimulateRelaxation: " << m_DoSimulateRelaxation; MITK_INFO << "m_DoDisablePartialVolume: " << m_DoDisablePartialVolume; MITK_INFO << "m_DoAddMotion: " << m_DoAddMotion; MITK_INFO << "m_RandomMotion: " << m_DoRandomizeMotion; MITK_INFO << "m_Translation: " << m_Translation; MITK_INFO << "m_Rotation: " << m_Rotation; MITK_INFO << "m_SignalModelString: " << m_SignalModelString; MITK_INFO << "m_ArtifactModelString: " << m_ArtifactModelString; MITK_INFO << "m_OutputPath: " << m_OutputPath; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h index ff652b56b2..c2a71cd84c 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h @@ -1,177 +1,187 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_FiberfoxParameters_H #define _MITK_FiberfoxParameters_H #include #include #include #include #include #include #include #include using namespace std; namespace mitk { /** * \brief Datastructure to manage the Fiberfox signal generation parameters. * */ -template< class ScalarType > +template< class ScalarType = double > class FiberfoxParameters { public: + enum DiffusionDirectionMode { + FIBER_TANGENT_DIRECTIONS, + MAIN_FIBER_DIRECTIONS, + RANDOM_DIRECTIONS + }; + typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef std::vector< DiffusionSignalModel* > DiffusionModelListType; typedef DiffusionSignalModel::GradientListType GradientListType; typedef DiffusionSignalModel::GradientType GradientType; typedef DiffusionNoiseModel NoiseModelType; typedef DiffusionSignalModel* DiffusionModelType; FiberfoxParameters(); ~FiberfoxParameters(); /** Get same parameter object with different template parameter */ template< class OutType > FiberfoxParameters< OutType > CopyParameters() { FiberfoxParameters< OutType > out; out.m_ImageRegion = m_ImageRegion; out.m_ImageSpacing = m_ImageSpacing; out.m_ImageOrigin = m_ImageOrigin; out.m_ImageDirection = m_ImageDirection; out.SetNumWeightedGradients(m_NumGradients); out.m_Bvalue = m_Bvalue; out.m_SignalScale = m_SignalScale; out.m_tEcho = m_tEcho; out.m_tLine = m_tLine; out.m_tInhom = m_tInhom; out.m_AxonRadius = m_AxonRadius; out.m_KspaceLineOffset = m_KspaceLineOffset; out.m_DoAddGibbsRinging = m_DoAddGibbsRinging; out.m_EddyStrength = m_EddyStrength; out.m_Spikes = m_Spikes; out.m_SpikeAmplitude = m_SpikeAmplitude; out.m_CroppingFactor = m_CroppingFactor; out.m_DoSimulateRelaxation = m_DoSimulateRelaxation; out.m_DoDisablePartialVolume = m_DoDisablePartialVolume; out.m_DoAddMotion = m_DoAddMotion; out.m_DoRandomizeMotion = m_DoRandomizeMotion; out.m_Translation = m_Translation; out.m_Rotation = m_Rotation; if (m_NoiseModel!=NULL) { if (dynamic_cast*>(m_NoiseModel)) out.m_NoiseModel = new mitk::RicianNoiseModel(); else if (dynamic_cast*>(m_NoiseModel)) out.m_NoiseModel = new mitk::ChiSquareNoiseModel(); out.m_NoiseModel->SetNoiseVariance(m_NoiseModel->GetNoiseVariance()); } out.m_FrequencyMap = m_FrequencyMap; out.m_MaskImage = m_MaskImage; out.m_ResultNode = m_ResultNode; out.m_ParentNode = m_ParentNode; out.m_SignalModelString = m_SignalModelString; out.m_ArtifactModelString = m_ArtifactModelString; out.m_OutputPath = m_OutputPath; +// out.m_DiffusionDirectionMode = m_DiffusionDirectionMode; +// out.m_SignalGenerationMode = m_SignalGenerationMode; + out.m_SimulateKspaceAcquisition = m_SimulateKspaceAcquisition; + + // TODO: copy constructor für singalmodelle und rauschen return out; } /** Output image specifications */ itk::ImageRegion<3> m_ImageRegion; ///< Image size. itk::Vector m_ImageSpacing; ///< Image voxel size. itk::Point m_ImageOrigin; ///< Image origin. itk::Matrix m_ImageDirection; ///< Image rotation matrix. /** Other acquisitions parameters */ double m_SignalScale; ///< Scaling factor for output signal (before noise is added). double m_tEcho; ///< Echo time TE. double m_tLine; ///< k-space line readout time. double m_tInhom; ///< T2' - double m_Bvalue; + double m_Bvalue; ///< Acquisition b-value + bool m_SimulateKspaceAcquisition;///< /** Signal generation */ DiffusionModelListType m_FiberModelList; ///< Intra- and inter-axonal compartments. DiffusionModelListType m_NonFiberModelList; ///< Extra-axonal compartments. double m_AxonRadius; ///< Determines compartment volume fractions (0 == automatic axon radius estimation) - bool m_UsePrototypeSignals; - bool m_UseRandomDirections; - bool m_UseMainFiberDirections; + DiffusionDirectionMode m_DiffusionDirectionMode; ///< Determines how the main diffusion direction of the signal models is selected /** Artifacts */ unsigned int m_Spikes; ///< Number of spikes randomly appearing in the image double m_SpikeAmplitude; ///< amplitude of spikes relative to the largest signal intensity (magnitude of complex) double m_KspaceLineOffset; ///< Causes N/2 ghosts. Larger offset means stronger ghost. double m_EddyStrength; ///< Strength of eddy current induced gradients in mT/m. double m_Tau; ///< Eddy current decay constant (in ms) double m_CroppingFactor; ///< FOV size in y-direction is multiplied by this factor. Causes aliasing artifacts. bool m_DoAddGibbsRinging; ///< Add Gibbs ringing artifact bool m_DoSimulateRelaxation; ///< Add T2 relaxation effects bool m_DoDisablePartialVolume; ///< Disable partial volume effects. Each voxel is either all fiber or all non-fiber. bool m_DoAddMotion; ///< Enable motion artifacts. bool m_DoRandomizeMotion; ///< Toggles between random and linear motion. itk::Vector m_Translation; ///< Maximum translational motion. itk::Vector m_Rotation; ///< Maximum rotational motion. NoiseModelType* m_NoiseModel; ///< If != NULL, noise is added to the image. ItkDoubleImgType::Pointer m_FrequencyMap; ///< If != NULL, distortions are added to the image using this frequency map. ItkUcharImgType::Pointer m_MaskImage; ///< Signal is only genrated inside of the mask image. /** Output parameters (only relevant in GUI application) */ mitk::DataNode::Pointer m_ResultNode; ///< Stores resulting image. mitk::DataNode::Pointer m_ParentNode; ///< Parent node or result node. string m_SignalModelString; ///< Appendet to the name of the result node string m_ArtifactModelString; ///< Appendet to the name of the result node string m_OutputPath; ///< Image is automatically saved to the specified folder after simulation is finished. void PrintSelf(); ///< Print parameters to stdout. void LoadParameters(string filename); ///< Load image generation parameters from .ffp file. void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions) std::vector< int > GetBaselineIndices(); unsigned int GetFirstBaselineIndex(); bool IsBaselineIndex(unsigned int idx); unsigned int GetNumWeightedVolumes(); unsigned int GetNumBaselineVolumes(); unsigned int GetNumVolumes(); GradientListType GetGradientDirections(); GradientType GetGradientDirection(unsigned int i); void SetNumWeightedGradients(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. void SetGradienDirections(GradientListType gradientList); void SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList); protected: unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes. unsigned int m_NumGradients; ///< Number of diffusion-weighted image volumes. GradientListType m_GradientDirections; ///< Total number of image volumes. }; } #include "mitkFiberfoxParameters.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h index ec45c9e94c..b9d35f00b0 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h @@ -1,107 +1,110 @@ /*=================================================================== 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_AstroStickModel_H #define _MITK_AstroStickModel_H #include #include namespace mitk { /** * \brief Generates the diffusion signal using a collection of idealised cylinder with zero radius: e^(-bd(ng)²) * */ template< class ScalarType > class AstroStickModel : public DiffusionSignalModel< ScalarType > { public: AstroStickModel(); ~AstroStickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); + void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } + void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } + void SetSeed(int s); ///< set seed for random generator that creates the stick orientations void SetRandomizeSticks(bool randomize=true){ m_RandomizeSticks=randomize; } ///< Random stick configuration in each voxel void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant void SetNumSticks(unsigned int order) { vnl_matrix sticks; switch (order) { case 1: m_NumSticks = 12; sticks = itk::PointShell<12, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 2: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 3: m_NumSticks = 92; sticks = itk::PointShell<92, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 4: m_NumSticks = 162; sticks = itk::PointShell<162, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 5: m_NumSticks = 252; sticks = itk::PointShell<252, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; default: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; } for (int i=0; i namespace mitk { /** * \brief Generates direction independent diffusion measurement employing a scalar diffusion constant d: e^(-bd) * */ template< class ScalarType > class BallModel : public DiffusionSignalModel< ScalarType > { public: BallModel(); ~BallModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; + typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); void SetDiffusivity(ScalarType D) { m_Diffusivity = D; } void SetBvalue(ScalarType bValue) { m_BValue = bValue; } + void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } + void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } + protected: ScalarType m_Diffusivity; ///< Scalar diffusion constant ScalarType m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkBallModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h index a2b86d5fae..a9a29831aa 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h @@ -1,72 +1,72 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_DiffusionSignalModel_H #define _MITK_DiffusionSignalModel_H #include #include #include #include #include namespace mitk { /** * \brief Abstract class for diffusion signal models * */ template< class ScalarType > class DiffusionSignalModel { public: DiffusionSignalModel() : m_T2(100) {} ~DiffusionSignalModel(){} typedef itk::Image ItkDoubleImgType; typedef itk::VariableLengthVector< ScalarType > PixelType; typedef itk::Vector GradientType; typedef std::vector GradientListType; /** Realizes actual signal generation. Has to be implemented in subclass. **/ virtual PixelType SimulateMeasurement() = 0; virtual ScalarType SimulateMeasurement(unsigned int dir) = 0; - void SetFiberDirection(GradientType fiberDirection){ m_FiberDirection = fiberDirection; } - void SetGradientList(GradientListType gradientList) { m_GradientList = gradientList; } + virtual void SetFiberDirection(GradientType fiberDirection) = 0; + virtual void SetGradientList(GradientListType gradientList) = 0; void SetT2(double T2) { m_T2 = T2; } void SetVolumeFractionImage(ItkDoubleImgType::Pointer img){ m_VolumeFractionImage = img; } ItkDoubleImgType::Pointer GetVolumeFractionImage(){ return m_VolumeFractionImage; } GradientType GetGradientDirection(int i) { return m_GradientList.at(i); } double GetT2() { return m_T2; } protected: GradientType m_FiberDirection; ///< Needed to generate anisotropc signal to determin direction of anisotropy GradientListType m_GradientList; ///< Diffusion gradient direction container double m_T2; ///< Tissue specific relaxation time ItkDoubleImgType::Pointer m_VolumeFractionImage; ///< Tissue specific volume fraction for each voxel (only relevant for non fiber compartments) }; } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h index 02a3181a7d..3e4a4c9da9 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h @@ -1,53 +1,57 @@ /*=================================================================== 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_DotModel_H #define _MITK_DotModel_H #include namespace mitk { /** * \brief Generates constant direction independent signal. * */ template< class ScalarType > class DotModel : public DiffusionSignalModel< ScalarType > { public: DotModel(); ~DotModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; + typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); + void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } + void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } + protected: }; } #include "mitkDotModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp index f9ae2e518a..2fdb8eae50 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp @@ -1,215 +1,257 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include using namespace mitk; using namespace boost::math; template< class ScalarType > RawShModel< ScalarType >::RawShModel() : m_ShOrder(0) + , m_ModelIndex(-1) + , m_MaxNumKernels(1000) { - + m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); + m_RandGen->SetSeed(); + m_AdcRange.first = 0; + m_AdcRange.second = 0.004; + m_FaRange.first = 0; + m_FaRange.second = 1; } template< class ScalarType > RawShModel< ScalarType >::~RawShModel() { } +template< class ScalarType > +void RawShModel< ScalarType >::Clear() +{ + m_ShCoefficients.clear(); + m_PrototypeMaxDirection.clear(); + m_B0Signal.clear(); +} + +template< class ScalarType > +void RawShModel< ScalarType >::RandomModel() +{ + m_ModelIndex = m_RandGen->GetIntegerVariate(m_B0Signal.size()-1); +} + +template< class ScalarType > +unsigned int RawShModel< ScalarType >::GetNumberOfKernels() +{ + return m_B0Signal.size(); +} + // convert cartesian to spherical coordinates template< class ScalarType > -void RawShModel< ScalarType >::Cart2Sph() +void RawShModel< ScalarType >::Cart2Sph( GradientListType gradients ) { - GradientListType tempDirs = m_RotatedGradientList; - m_SphCoords.set_size(tempDirs.size(), 2); + m_SphCoords.set_size(gradients.size(), 2); m_SphCoords.fill(0.0); - for (unsigned int i=0; i 0.0001 ) { - tempDirs[i].Normalize(); - m_SphCoords(i,0) = acos(tempDirs[i][2]); // theta - m_SphCoords(i,1) = atan2(tempDirs[i][1], tempDirs[i][0]); // phi + gradients[i].Normalize(); + m_SphCoords(i,0) = acos(gradients[i][2]); // theta + m_SphCoords(i,1) = atan2(gradients[i][1], gradients[i][0]); // phi } } } template< class ScalarType > void RawShModel< ScalarType >::SetFiberDirection(GradientType fiberDirection) { this->m_FiberDirection = fiberDirection; this->m_FiberDirection.Normalize(); - GradientType unit; unit.Fill(0.0); unit[0] = 1; - GradientType axis = itk::CrossProduct(this->m_FiberDirection, m_PrototypeMaxDirection); + RandomModel(); + GradientType axis = itk::CrossProduct(this->m_FiberDirection, m_PrototypeMaxDirection.at(m_ModelIndex)); axis.Normalize(); - vnl_quaternion rotation(axis.GetVnlVector(), acos(dot_product(this->m_FiberDirection.GetVnlVector(), m_PrototypeMaxDirection.GetVnlVector()))); + vnl_quaternion rotation(axis.GetVnlVector(), acos(dot_product(this->m_FiberDirection.GetVnlVector(), m_PrototypeMaxDirection.at(m_ModelIndex).GetVnlVector()))); rotation.normalize(); - m_RotatedGradientList.clear(); + GradientListType gradients; for (unsigned int i=0; im_GradientList.size(); i++) { GradientType dir = this->m_GradientList.at(i); - dir.Normalize(); - vnl_vector_fixed< double, 3 > vnlDir = rotation.rotate(dir.GetVnlVector()); - dir[0] = vnlDir[0]; dir[1] = vnlDir[1]; dir[2] = vnlDir[2]; - dir.Normalize(); - m_RotatedGradientList.push_back(dir); + if( dir.GetNorm() > 0.0001 ) + { + dir.Normalize(); + vnl_vector_fixed< double, 3 > vnlDir = rotation.rotate(dir.GetVnlVector()); + dir[0] = vnlDir[0]; dir[1] = vnlDir[1]; dir[2] = vnlDir[2]; + dir.Normalize(); + } + gradients.push_back(dir); } - Cart2Sph(); + Cart2Sph( gradients ); } template< class ScalarType > -bool RawShModel< ScalarType >::SetShCoefficients(vnl_vector< double > shCoefficients) +bool RawShModel< ScalarType >::SetShCoefficients(vnl_vector< double > shCoefficients, ScalarType b0 ) { - m_ShCoefficients = shCoefficients; m_ShOrder = 2; - while ( (m_ShOrder*m_ShOrder + m_ShOrder + 2)/2 + m_ShOrder <= m_ShCoefficients.size() ) + while ( (m_ShOrder*m_ShOrder + m_ShOrder + 2)/2 + m_ShOrder <= shCoefficients.size() ) m_ShOrder += 2; m_ShOrder -= 2; - itk::OrientationDistributionFunction odf; - m_RotatedGradientList.clear(); - for (unsigned int i=0; i odf; +// GradientListType gradients; +// for (unsigned int i=0; im_GradientList ); +// PixelType signal = SimulateMeasurement(); + +// int minDirIdx = 0; +// double min = itk::NumericTraits::max(); +// for (unsigned int i=0; ib0 || signal[i]<0) +// { +// MITK_INFO << "Corrupted signal value detected. Kernel rejected."; +// m_B0Signal.pop_back(); +// m_ShCoefficients.pop_back(); +// return false; +// } +// if (signal[i]m_GradientList.at(minDirIdx); +// maxDir.Normalize(); +// m_PrototypeMaxDirection.push_back(maxDir); + + Cart2Sph( this->m_GradientList ); + m_ModelIndex = -1; - int minDirIdx = 0; - double min = itk::NumericTraits::max(); - for (unsigned int i=0; im_B0Signal || signal[i]<0) - { - MITK_INFO << "Corrupted signal value detected. Kernel rejected."; - return false; - } - if (signal[i] ScalarType RawShModel< ScalarType >::SimulateMeasurement(unsigned int dir) { ScalarType signal = 0; - if (dir>=m_RotatedGradientList.size()) + if (m_ModelIndex==-1) + RandomModel(); + + if (dir>=this->m_GradientList.size()) return signal; int j, m; double mag, plm; - vnl_vector< double > shBasis; - shBasis.set_size(m_ShCoefficients.size()); - shBasis.fill(0.0); - if (m_RotatedGradientList[dir].GetNorm()>0.001) + if (this->m_GradientList[dir].GetNorm()>0.001) { j=0; for (int l=0; l<=m_ShOrder; l=l+2) for (m=-l; m<=l; m++) { plm = legendre_p(l,abs(m),cos(m_SphCoords(dir,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; + double basis; if (m<0) - shBasis[j] = sqrt(2.0)*mag*cos(fabs((double)m)*m_SphCoords(dir,1)); + basis = sqrt(2.0)*mag*cos(fabs((double)m)*m_SphCoords(dir,1)); else if (m==0) - shBasis[j] = mag; + basis = mag; else - shBasis[j] = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*m_SphCoords(dir,1)); + basis = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*m_SphCoords(dir,1)); + signal += m_ShCoefficients.at(m_ModelIndex)[j]*basis; j++; } } + else + signal = m_B0Signal.at(m_ModelIndex); - for (unsigned int i=0; i typename RawShModel< ScalarType >::PixelType RawShModel< ScalarType >::SimulateMeasurement() { + if (m_ModelIndex==-1) + RandomModel(); + PixelType signal; - signal.SetSize(m_RotatedGradientList.size()); + signal.SetSize(this->m_GradientList.size()); - int M = m_RotatedGradientList.size(); + int M = this->m_GradientList.size(); int j, m; double mag, plm; vnl_matrix< double > shBasis; - shBasis.set_size(M, m_ShCoefficients.size()); + shBasis.set_size(M, m_ShCoefficients.at(m_ModelIndex).size()); shBasis.fill(0.0); for (int p=0; p0.001) + if (this->m_GradientList[p].GetNorm()>0.001) { j=0; for (int l=0; l<=m_ShOrder; l=l+2) for (m=-l; m<=l; m++) { plm = legendre_p(l,abs(m),cos(m_SphCoords(p,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; if (m<0) shBasis(p,j) = sqrt(2.0)*mag*cos(fabs((double)m)*m_SphCoords(p,1)); else if (m==0) shBasis(p,j) = mag; else shBasis(p,j) = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*m_SphCoords(p,1)); j++; } double val = 0; - for (unsigned int cidx=0; cidxm_B0Signal || val<0) -// { -// MITK_INFO << "SIGNALGEN ERROR: " << val; -// val = 0; -// } } else - signal[p] = m_B0Signal; + signal[p] = m_B0Signal.at(m_ModelIndex); } + m_ModelIndex = -1; + return signal; } diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.h index a1d4e0c202..ae1e6041ce 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.h @@ -1,68 +1,80 @@ /*=================================================================== 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_RawShModel_H #define _MITK_RawShModel_H #include namespace mitk { /** * \brief The spherical harmonic representation of a prototype diffusion weighted MR signal is used to obtain the direction dependent signal. * */ template< class ScalarType > class RawShModel : public DiffusionSignalModel< ScalarType > { public: RawShModel(); ~RawShModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; typedef itk::Matrix< double, 3, 3 > MatrixType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; Cart2Sph(); } - bool SetShCoefficients(vnl_vector< double > shCoefficients); + bool SetShCoefficients(vnl_vector< double > shCoefficients, ScalarType b0); void SetFiberDirection(GradientType fiberDirection); - void SetB0Signal(ScalarType signal){ m_B0Signal = signal; } + void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } + void SetFaRange(double min, double max){ m_FaRange.first = min; m_FaRange.second = max; } + void SetAdcRange(double min, double max){ m_AdcRange.first = min; m_AdcRange.second = max; } + void SetMaxNumKernels(unsigned int max){ m_MaxNumKernels = max; } + unsigned int GetNumberOfKernels(); + std::pair< double, double > GetFaRange(){ return m_FaRange; } + std::pair< double, double > GetAdcRange(){ return m_AdcRange; } + unsigned int GetMaxNumKernels(){ return m_MaxNumKernels; } + void Clear(); + vector< GradientType > m_PrototypeMaxDirection; protected: - void Cart2Sph(); + void Cart2Sph( GradientListType gradients ); + void RandomModel(); - vnl_vector< double > m_ShCoefficients; - GradientType m_PrototypeMaxDirection; + std::pair< double, double > m_AdcRange; + std::pair< double, double > m_FaRange; + vector< vnl_vector< double > > m_ShCoefficients; + vector< ScalarType > m_B0Signal; vnl_matrix m_SphCoords; - int m_ShOrder; - GradientListType m_RotatedGradientList; - ScalarType m_B0Signal; + unsigned int m_ShOrder; + int m_ModelIndex; + unsigned int m_MaxNumKernels; + itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen; }; } #include "mitkRawShModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h index d2c4de06f1..6af5a320f1 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h @@ -1,58 +1,62 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_StickModel_H #define _MITK_StickModel_H #include namespace mitk { /** * \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²) * */ template< class ScalarType > class StickModel : public DiffusionSignalModel< ScalarType > { public: StickModel(); ~StickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; + typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } + void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } + protected: ScalarType m_Diffusivity; ///< Scalar diffusion constant ScalarType m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkStickModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h index 57fd1c2d92..4ebe00bc6e 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h @@ -1,65 +1,69 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_TensorModel_H #define _MITK_TensorModel_H #include #include namespace mitk { /** * \brief Generates diffusion measurement employing a second rank tensor model: e^(-bg^TDg) * */ template< class ScalarType > class TensorModel : public DiffusionSignalModel< ScalarType > { public: TensorModel(); ~TensorModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef itk::DiffusionTensor3D< ScalarType > ItkTensorType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; + typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); void SetBvalue(ScalarType bValue) { m_BValue = bValue; } void SetDiffusivity1(ScalarType d1){ m_KernelTensorMatrix[0][0] = d1; } void SetDiffusivity2(ScalarType d2){ m_KernelTensorMatrix[1][1] = d2; } void SetDiffusivity3(ScalarType d3){ m_KernelTensorMatrix[2][2] = d3; } + void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } + void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } + protected: /** Calculates tensor matrix from FA and ADC **/ void UpdateKernelTensor(); GradientType m_KernelDirection; ///< Direction of the kernel tensors principal eigenvector vnl_matrix_fixed m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values ScalarType m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkTensorModel.cpp" #endif diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidget.h index f6d523dc14..218d32396c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidget.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidget.h @@ -1,62 +1,66 @@ /*=================================================================== 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 _QmitkPrototypeSignalParametersWidget_H_INCLUDED #define _QmitkPrototypeSignalParametersWidget_H_INCLUDED //QT headers #include #include #include "ui_QmitkPrototypeSignalParametersWidgetControls.h" #include class QmitkStdMultiWidget; /** @brief */ class DIFFUSIONIMAGING_EXPORT QmitkPrototypeSignalParametersWidget : public QWidget { //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkPrototypeSignalParametersWidget (QWidget* parent = 0, Qt::WindowFlags f = 0); virtual ~QmitkPrototypeSignalParametersWidget(); virtual void CreateQtPartControl(QWidget *parent); - void SetMinFa(double minFA){ m_Controls->m_MinFaBox->setValue(minFA); } - void SetMaxFa(double maxFA){ m_Controls->m_MaxFaBox->setValue(maxFA); } + void SetMinAdc(double min){ m_Controls->m_MinAdcBox->setValue(min); } + void SetMaxAdc(double max){ m_Controls->m_MaxAdcBox->setValue(max); } + void SetMinFa(double min){ m_Controls->m_MinFaBox->setValue(min); } + void SetMaxFa(double max){ m_Controls->m_MaxFaBox->setValue(max); } void SetNumberOfSamples(int n){ m_Controls->m_NumSamplesBox->setValue(n); } + double GetMinAdc(){ return m_Controls->m_MinAdcBox->value(); } + double GetMaxAdc(){ return m_Controls->m_MaxAdcBox->value(); } double GetMinFa(){ return m_Controls->m_MinFaBox->value(); } double GetMaxFa(){ return m_Controls->m_MaxFaBox->value(); } double GetNumberOfSamples(){ return m_Controls->m_NumSamplesBox->value(); } public slots: protected: // member variables Ui::QmitkPrototypeSignalParametersWidgetControls* m_Controls; private: }; #endif // _QmitkPrototypeSignalParametersWidget_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidgetControls.ui index f7300b584c..8bef318689 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkPrototypeSignalParametersWidgetControls.ui @@ -1,125 +1,163 @@ QmitkPrototypeSignalParametersWidgetControls 0 0 297 165 0 0 Form 0 0 0 0 - - - - <html><head/><body><p><span style=" font-style:italic;">Min. ADC [mm2/s]</span>:</p></body></html> - - - - - + + - <html><head/><body><p><span style=" font-style:italic;">Max. FA</span>:</p></body></html> - - - - - - - 999999999 - - - 1000 + <html><head/><body><p><span style=" font-style:italic;">Number of Samples</span>:</p></body></html> <html><head/><body><p><span style=" font-style:italic;">Min. FA</span>:</p></body></html> - - - - <html><head/><body><p><span style=" font-style:italic;">Number of Samples</span>:</p></body></html> + + + + Diffusivity along second eigenvector. + + + 5 + + + 1.000000000000000 + + + 0.010000000000000 + + + 0.700000000000000 Diffusivity along second eigenvector. 5 1.000000000000000 0.010000000000000 0.900000000000000 - - + + Diffusivity along second eigenvector. 5 1.000000000000000 - 0.010000000000000 + 0.000100000000000 - 0.700000000000000 + 0.000000000000000 + + + + + + + <html><head/><body><p><span style=" font-style:italic;">Max. FA</span>:</p></body></html> + + + + + + + <html><head/><body><p><span style=" font-style:italic;">Min. ADC [mm2/s]</span>:</p></body></html> + + + + + + + 999999999 + + + 1000 <html><head/><body><p><span style=" font-style:italic;">Max. ADC [mm2/s]</span>:</p></body></html> + + + + Diffusivity along second eigenvector. + + + 5 + + + 1.000000000000000 + + + 0.000100000000000 + + + 0.001000000000000 + + + m_MaxFaBox diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp index 05823a7544..ee96ee2772 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp @@ -1,486 +1,561 @@ /*=================================================================== 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. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberProcessingView.h" #include // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include #include #include #include +#include #include - +#include const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkFiberProcessingView::QmitkFiberProcessingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_UpsamplingFactor(5) { } // Destructor QmitkFiberProcessingView::~QmitkFiberProcessingView() { } void QmitkFiberProcessingView::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::QmitkFiberProcessingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_ProcessFiberBundleButton, SIGNAL(clicked()), this, SLOT(ProcessSelectedBundles()) ); connect( m_Controls->m_ResampleFibersButton, SIGNAL(clicked()), this, SLOT(ResampleSelectedBundles()) ); connect(m_Controls->m_FaColorFibersButton, SIGNAL(clicked()), this, SLOT(DoImageColorCoding())); connect( m_Controls->m_PruneFibersButton, SIGNAL(clicked()), this, SLOT(PruneBundle()) ); connect( m_Controls->m_CurvatureThresholdButton, SIGNAL(clicked()), this, SLOT(ApplyCurvatureThreshold()) ); connect( m_Controls->m_MirrorFibersButton, SIGNAL(clicked()), this, SLOT(MirrorFibers()) ); connect( m_Controls->m_CompressFibersButton, SIGNAL(clicked()), this, SLOT(CompressSelectedBundles()) ); + connect( m_Controls->m_ExtractFiberPeaks, SIGNAL(clicked()), this, SLOT(CalculateFiberDirections()) ); } } void QmitkFiberProcessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberProcessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } +void QmitkFiberProcessingView::CalculateFiberDirections() +{ + typedef itk::Image ItkUcharImgType; + typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; + typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; + + // load fiber bundle + mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(m_SelectedFB.back()->GetData()); + + itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); + // load/create mask image + if (m_SelectedImage.IsNotNull()) + { + ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); + mitk::CastToItkImage(m_SelectedImage, itkMaskImage); + fOdfFilter->SetMaskImage(itkMaskImage); + } + + // extract directions from fiber bundle + fOdfFilter->SetFiberBundle(inputTractogram); + fOdfFilter->SetAngularThreshold(cos(m_Controls->m_AngularThreshold->value()*M_PI/180)); + fOdfFilter->SetNormalizeVectors(true); + fOdfFilter->SetUseWorkingCopy(true); + fOdfFilter->SetSizeThreshold(m_Controls->m_PeakThreshold->value()); + fOdfFilter->SetMaxNumDirections(m_Controls->m_MaxNumDirections->value()); + fOdfFilter->Update(); + + QString name = m_SelectedFB.back()->GetName().c_str(); + + if (m_Controls->m_VectorFieldBox->isChecked()) + { + mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle(); + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(directions); + node->SetName((name+"_vectorfield").toStdString().c_str()); + + node->SetName(name.toStdString().c_str()); +// node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing)); + node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false)); + node->SetProperty("color", mitk::ColorProperty::New(1.0f, 1.0f, 1.0f)); + + GetDefaultDataStorage()->Add(node, m_SelectedFB.back()); + } + + if (m_Controls->m_NumDirectionsBox->isChecked()) + { + mitk::Image::Pointer mitkImage = mitk::Image::New(); + mitkImage->InitializeByItk( fOdfFilter->GetNumDirectionsImage().GetPointer() ); + mitkImage->SetVolume( fOdfFilter->GetNumDirectionsImage()->GetBufferPointer() ); + + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(mitkImage); + node->SetName((name+"_numdirections").toStdString().c_str()); + GetDefaultDataStorage()->Add(node, m_SelectedFB.back()); + } + + if (m_Controls->m_DirectionImagesBox->isChecked()) + { + ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); + for (unsigned int i=0; i<1; i++) + { + itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); + + if (itkImg.IsNull()) + return; + + mitk::Image::Pointer mitkImage = mitk::Image::New(); + mitkImage->InitializeByItk( itkImg.GetPointer() ); + mitkImage->SetVolume( itkImg->GetBufferPointer() ); + + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(mitkImage); + node->SetName( (name+"_direction_"+boost::lexical_cast(i).c_str()).toStdString().c_str()); + node->SetVisibility(false); + GetDefaultDataStorage()->Add(node, m_SelectedFB.back()); + } + } +} + void QmitkFiberProcessingView::UpdateGui() { + m_Controls->m_CompressFibersButton->setEnabled(!m_SelectedFB.empty()); + m_Controls->m_ProcessFiberBundleButton->setEnabled(!m_SelectedFB.empty()); + m_Controls->m_ResampleFibersButton->setEnabled(!m_SelectedFB.empty()); + m_Controls->m_FaColorFibersButton->setEnabled(!m_SelectedFB.empty()); + m_Controls->m_PruneFibersButton->setEnabled(!m_SelectedFB.empty()); + m_Controls->m_CurvatureThresholdButton->setEnabled(!m_SelectedFB.empty()); + m_Controls->m_ExtractFiberPeaks->setEnabled(!m_SelectedFB.empty()); + // are fiber bundles selected? if ( m_SelectedFB.empty() ) { - m_Controls->m_CompressFibersButton->setEnabled(false); - m_Controls->m_ProcessFiberBundleButton->setEnabled(false); - m_Controls->m_ResampleFibersButton->setEnabled(false); - m_Controls->m_FaColorFibersButton->setEnabled(false); - m_Controls->m_PruneFibersButton->setEnabled(false); - m_Controls->m_CurvatureThresholdButton->setEnabled(false); - if (m_SelectedSurfaces.size()>0) m_Controls->m_MirrorFibersButton->setEnabled(true); else m_Controls->m_MirrorFibersButton->setEnabled(false); } else { - m_Controls->m_CompressFibersButton->setEnabled(true); - m_Controls->m_ProcessFiberBundleButton->setEnabled(true); - m_Controls->m_ResampleFibersButton->setEnabled(true); - m_Controls->m_PruneFibersButton->setEnabled(true); - m_Controls->m_CurvatureThresholdButton->setEnabled(true); - m_Controls->m_MirrorFibersButton->setEnabled(true); - if (m_SelectedImage.IsNotNull()) m_Controls->m_FaColorFibersButton->setEnabled(true); } } void QmitkFiberProcessingView::OnSelectionChanged( std::vector nodes ) { //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection m_SelectedFB.clear(); m_SelectedSurfaces.clear(); m_SelectedImage = NULL; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) { m_SelectedFB.push_back(node); } else if (dynamic_cast(node->GetData())) m_SelectedImage = dynamic_cast(node->GetData()); else if (dynamic_cast(node->GetData())) { m_SelectedSurfaces.push_back(dynamic_cast(node->GetData())); } } UpdateGui(); GenerateStats(); } void QmitkFiberProcessingView::Activated() { } void QmitkFiberProcessingView::PruneBundle() { int minLength = this->m_Controls->m_PruneFibersSpinBox->value(); int maxLength = this->m_Controls->m_MaxPruneFibersSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); if (!fib->RemoveShortFibers(minLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); else if (!fib->RemoveLongFibers(maxLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::ApplyCurvatureThreshold() { int mm = this->m_Controls->m_MinCurvatureRadiusBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); if (!fib->ApplyCurvatureThreshold(mm, this->m_Controls->m_RemoveFiberDueToCurvatureCheckbox->isChecked())) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::GenerateStats() { if ( m_SelectedFB.empty() ) return; QString stats(""); for( int i=0; i(node->GetData())) { if (i>0) stats += "\n-----------------------------\n"; stats += QString(node->GetName().c_str()) + "\n"; mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); stats += "Number of fibers: "+ QString::number(fib->GetNumFibers()) + "\n"; stats += "Number of points: "+ QString::number(fib->GetNumberOfPoints()) + "\n"; stats += "Min. length: "+ QString::number(fib->GetMinFiberLength(),'f',1) + " mm\n"; stats += "Max. length: "+ QString::number(fib->GetMaxFiberLength(),'f',1) + " mm\n"; stats += "Mean length: "+ QString::number(fib->GetMeanFiberLength(),'f',1) + " mm\n"; stats += "Median length: "+ QString::number(fib->GetMedianFiberLength(),'f',1) + " mm\n"; stats += "Standard deviation: "+ QString::number(fib->GetLengthStDev(),'f',1) + " mm\n"; } } this->m_Controls->m_StatsTextEdit->setText(stats); } void QmitkFiberProcessingView::ProcessSelectedBundles() { if ( m_SelectedFB.empty() ){ QMessageBox::information( NULL, "Warning", "No fibe bundle selected!"); MITK_WARN("QmitkFiberProcessingView") << "no fibe bundle selected"; return; } int generationMethod = m_Controls->m_GenerationBox->currentIndex(); for( int i=0; i(node->GetData())) { mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); QString name(node->GetName().c_str()); DataNode::Pointer newNode = NULL; switch(generationMethod){ case 0: newNode = GenerateTractDensityImage(fib, false, true); name += "_TDI"; break; case 1: newNode = GenerateTractDensityImage(fib, false, false); name += "_TDI"; break; case 2: newNode = GenerateTractDensityImage(fib, true, false); name += "_envelope"; break; case 3: newNode = GenerateColorHeatmap(fib); break; case 4: newNode = GenerateFiberEndingsImage(fib); name += "_fiber_endings"; break; case 5: newNode = GenerateFiberEndingsPointSet(fib); name += "_fiber_endings"; break; } if (newNode.IsNotNull()) { newNode->SetName(name.toStdString()); GetDataStorage()->Add(newNode); } } } } // generate pointset displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); vtkSmartPointer fiberPolyData = fib->GetFiberPolyData(); vtkSmartPointer vLines = fiberPolyData->GetLines(); vLines->InitTraversal(); int count = 0; int numFibers = fib->GetNumFibers(); for( int i=0; iGetNextCell ( numPoints, points ); if (numPoints>0) { double* point = fiberPolyData->GetPoint(points[0]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } if (numPoints>2) { double* point = fiberPolyData->GetPoint(points[numPoints-1]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( pointSet ); return node; } // generate image displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib) { typedef unsigned char OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToFiberEndingsImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image OutImageType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate rgba heatmap from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib) { typedef itk::RGBAPixel OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToRgbaImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { itk::Image::Pointer itkImage = itk::Image::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate tract density image from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary, bool absolute) { typedef float OutPixType; typedef itk::Image OutImageType; itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); generator->SetFiberBundle(fib); generator->SetBinaryOutput(binary); generator->SetOutputAbsoluteValues(absolute); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } void QmitkFiberProcessingView::ResampleSelectedBundles() { double factor = this->m_Controls->m_ResampleFibersSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->DoFiberSmoothing(factor); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::CompressSelectedBundles() { double factor = this->m_Controls->m_FiberErrorSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->CompressFibers(factor); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::MirrorFibers() { unsigned int axis = this->m_Controls->m_AxisSelectionBox->currentIndex(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->MirrorFibers(axis); } if (m_SelectedFB.size()>0) GenerateStats(); if (m_SelectedSurfaces.size()>0) { for (int i=0; i poly = surf->GetVtkPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); for (int i=0; iGetNumberOfPoints(); i++) { double* point = poly->GetPoint(i); point[axis] *= -1; vtkNewPoints->InsertNextPoint(point); } poly->SetPoints(vtkNewPoints); surf->CalculateBoundingBox(); } } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::DoImageColorCoding() { if (m_SelectedImage.IsNull()) return; for( int i=0; i(m_SelectedFB.at(i)->GetData()); fib->SetFAMap(m_SelectedImage); fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_FA_BASED); fib->DoColorCodingFaBased(); } if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h index 11809cf546..e6677bf8f2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h @@ -1,155 +1,156 @@ /*=================================================================== 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 QmitkFiberProcessingView_h #define QmitkFiberProcessingView_h #include #include "ui_QmitkFiberProcessingViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief View to process fiber bundles. Supplies methods to generate images from the selected bundle and much more. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkFiberProcessingView : public QmitkFunctionality { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: typedef itk::Image< unsigned char, 3 > itkUCharImageType; static const std::string VIEW_ID; QmitkFiberProcessingView(); virtual ~QmitkFiberProcessingView(); virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); virtual void Activated(); protected slots: void PruneBundle(); ///< remove too short/too long fibers void MirrorFibers(); ///< mirror bundle on the specified plane void ProcessSelectedBundles(); ///< start selected operation on fiber bundle (e.g. tract density image generation) void ResampleSelectedBundles(); ///< smooth fiber bundle using the specified number of sampling points per cm. void DoImageColorCoding(); ///< color fibers by selected scalar image void ApplyCurvatureThreshold(); ///< remove/split fibers with a too high curvature threshold void CompressSelectedBundles(); ///< remove points below certain error threshold + void CalculateFiberDirections(); ///< Calculate main fiber directions from tractogram protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkFiberProcessingViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; /** Connection from VTK to ITK */ template void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template < typename TPixel, unsigned int VImageDimension > void InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName ); template < typename TPixel, unsigned int VImageDimension > void InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::Geometry3D* planegeo3D, int additionalIndex ); void GenerateStats(); ///< generate statistics of selected fiber bundles void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection std::vector m_SelectedFB; ///< selected fiber bundle nodes mitk::Image::Pointer m_SelectedImage; float m_UpsamplingFactor; ///< upsampling factor for all image generations std::vector m_SelectedSurfaces; mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary, bool absolute); mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib); }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui index 167ce23d86..6ac64c09ff 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui @@ -1,559 +1,694 @@ QmitkFiberProcessingViewControls 0 0 498 866 Form - - - - Fiber Statistics - - - - - - - Courier 10 Pitch - - - - false - - - true - - - - - - - + Qt::Vertical 20 40 Fiber Processing QFormLayout::AllNonFixedFieldsGrow false 0 0 200 16777215 11 Perform selected operation on all selected fiber bundles. Generate Image QFrame::NoFrame QFrame::Raised 0 0 0 0 0 0 0 0 Tract Density Image (TDI) Normalized TDI Binary Envelope Fiber Bundle Image Fiber Endings Image Fiber Endings Pointset Upsampling factor 1 0.100000000000000 10.000000000000000 0.100000000000000 1.000000000000000 false 0 0 200 16777215 11 Resample fibers using a Kochanek spline interpolation. Smooth Fibers false 0 0 200 16777215 11 Remove fibers shorter/longer than the specified length (in mm). Length Threshold QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Minimum fiber length in mm 0 1000 20 Maximum fiber length in mm 0 10000 500 false 0 0 200 16777215 11 Remove fibers with a too high curvature Curvature Threshold QFrame::NoFrame QFrame::Raised 0 0 0 0 6 0 Minimum radius of circle created by three consecutive points of a fiber 100.000000000000000 0.100000000000000 2.000000000000000 Remove whole fiber if it is exceeding the curvature threshold, otherwise remove only high curvature part. Remove Fiber true false 0 0 200 16777215 11 Mirror fibers around specified axis. Mirror Fibers 0 3 3 Sagittal Coronal Axial false 0 0 200 16777215 11 Apply float image values (0-1) as color coding to the selected fiber bundle. Color By Scalar Map Fiber point distance in mm 1 0.100000000000000 0.100000000000000 1.000000000000000 false 0 0 200 16777215 11 Remove points from fibers with the specified error constraint. Compress Fibers Allowed error in mm. 3 0.000000000000000 10.000000000000000 0.010000000000000 0.100000000000000 + + + + Fiber Statistics + + + + + + + Courier 10 Pitch + + + + false + + + true + + + + + + + + + + Calculate Main Fiber Directions + + + + + + Peak threshold: + + + + + + + Angular threshold: + + + + + + + Minimum radius of circle created by three consecutive points of a fiber + + + 2 + + + 0.000000000000000 + + + 90.000000000000000 + + + 1.000000000000000 + + + 30.000000000000000 + + + + + + + Maximum Number of Fibers: + + + + + + + Output Direction images + + + + + + + Output Vector Field + + + true + + + + + + + false + + + + 0 + 0 + + + + + 200 + 16777215 + + + + + 11 + + + + + + + Start + + + + + + + 100 + + + 3 + + + + + + + Minimum radius of circle created by three consecutive points of a fiber + + + 3 + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.300000000000000 + + + + + + + Output #Directions per Voxel + + + + + + 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 2b0eb3ee89..5f9327f551 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2510 +1,2543 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include +#include #define _USE_MATH_DEFINES #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ switch (m_FilterType) { case 0: m_View->m_TractsToDwiFilter->Update(); break; case 1: m_View->m_ArtifactsToDwiFilter->Update(); break; } } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; switch (m_Worker.m_FilterType) { case 0: m_TractsToDwiFilter->SetAbortGenerateData(true); break; case 1: m_ArtifactsToDwiFilter->SetAbortGenerateData(true); break; } m_Controls->m_AbortSimulationButton->setEnabled(false); m_Controls->m_AbortSimulationButton->setText("Aborting simulation ..."); } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_AbortSimulationButton->setEnabled(true); m_Controls->m_AbortSimulationButton->setText("Abort simulation"); m_Controls->m_GenerateImageButton->setVisible(true); m_ThreadIsRunning = false; QString statusText; FiberfoxParameters parameters; mitk::DiffusionImage::Pointer mitkImage = mitk::DiffusionImage::New(); switch (m_Worker.m_FilterType) { case 0: { statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage->SetVectorImage( m_TractsToDwiFilter->GetOutput() ); mitkImage->SetReferenceBValue(parameters.m_Bvalue); mitkImage->SetDirections(parameters.GetGradientDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_ResultNode->SetData( mitkImage ); parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName() +"_D"+QString::number(parameters.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(parameters.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(parameters.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(parameters.m_ImageSpacing[0]).toStdString() +"-"+QString::number(parameters.m_ImageSpacing[1]).toStdString() +"-"+QString::number(parameters.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(parameters.m_Bvalue).toStdString() +"_"+parameters.m_SignalModelString +parameters.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); parameters.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(parameters.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_ParentNode); } } m_TractsToDwiFilter = NULL; break; } case 1: { statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); if (m_ArtifactsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_ArtifactsToDwiFilter->GetParameters().CopyParameters(); mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(parameters.m_ParentNode->GetData()); mitkImage = mitk::DiffusionImage::New(); mitkImage->SetVectorImage( m_ArtifactsToDwiFilter->GetOutput() ); mitkImage->SetReferenceBValue(diffImg->GetReferenceBValue()); mitkImage->SetDirections(diffImg->GetDirections()); mitkImage->InitializeFromVectorImage(); parameters.m_ResultNode->SetData( mitkImage ); parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName()+parameters.m_ArtifactModelString); GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); m_ArtifactsToDwiFilter = NULL; break; } } mitk::BaseData::Pointer basedata = parameters.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_OutputPath.empty()) { try{ QString outputFileName(parameters.m_OutputPath.c_str()); outputFileName += parameters.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::SaveBaseData(mitkImage, outputFileName.toStdString()); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_FrequencyMap = NULL; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText; switch (m_Worker.m_FilterType) { case 0: statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); break; case 1: statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); break; } if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); statusText = "
"+statusText+"
"; m_Controls->m_SimulationStatusText->setText(statusText); QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); m_Controls->m_PrototypeWidget2->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); + m_Controls->m_PrototypeWidget3->SetMinFa(0.0); m_Controls->m_PrototypeWidget3->SetMaxFa(0.15); + m_Controls->m_PrototypeWidget4->SetMinFa(0.0); + m_Controls->m_PrototypeWidget4->SetMaxFa(0.15); + m_Controls->m_PrototypeWidget3->SetMinAdc(0.0); + m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001); + m_Controls->m_PrototypeWidget4->SetMinAdc(0.003); + m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetPredicate(finalPredicate); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); } } template< class ScalarType > FiberfoxParameters< ScalarType > QmitkFiberfoxView::UpdateImageParameters() { FiberfoxParameters< ScalarType > parameters; parameters.m_OutputPath = ""; string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { parameters.m_OutputPath = outputPath; parameters.m_OutputPath += "/"; } if (m_MaskImageNode.IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_MaskImageNode->GetData()); mitk::CastToItkImage(mitkMaskImage, parameters.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(parameters.m_MaskImage); duplicator->Update(); parameters.m_MaskImage = duplicator->GetOutput(); } if (m_SelectedDWI.IsNotNull()) // use parameters of selected DWI { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); parameters.m_ImageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_ImageSpacing = dwi->GetVectorImage()->GetSpacing(); parameters.m_ImageOrigin = dwi->GetVectorImage()->GetOrigin(); parameters.m_ImageDirection = dwi->GetVectorImage()->GetDirection(); parameters.m_Bvalue = dwi->GetReferenceBValue(); parameters.SetGradienDirections(dwi->GetDirections()); } else if (m_SelectedImage.IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); parameters.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_ImageDirection = itkImg->GetDirection(); parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); } else // use GUI parameters { parameters.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); parameters.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); parameters.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); parameters.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); parameters.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); parameters.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); parameters.m_ImageOrigin[0] = parameters.m_ImageSpacing[0]/2; parameters.m_ImageOrigin[1] = parameters.m_ImageSpacing[1]/2; parameters.m_ImageOrigin[2] = parameters.m_ImageSpacing[2]/2; parameters.m_ImageDirection.SetIdentity(); parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); parameters.GenerateGradientHalfShell(); } // signal relaxation parameters.m_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); + parameters.m_SimulateKspaceAcquisition = parameters.m_DoSimulateRelaxation; if (parameters.m_DoSimulateRelaxation && m_SelectedBundles.size()>0 ) parameters.m_ArtifactModelString += "_RELAX"; // N/2 ghosts if (m_Controls->m_AddGhosts->isChecked()) { + parameters.m_SimulateKspaceAcquisition = true; parameters.m_ArtifactModelString += "_GHOST"; parameters.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); parameters.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(parameters.m_KspaceLineOffset)); } else parameters.m_KspaceLineOffset = 0; // Aliasing if (m_Controls->m_AddAliasing->isChecked()) { + parameters.m_SimulateKspaceAcquisition = true; parameters.m_ArtifactModelString += "_ALIASING"; parameters.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; parameters.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } + // Spikes + if (m_Controls->m_AddSpikes->isChecked()) + { + parameters.m_SimulateKspaceAcquisition = true; + parameters.m_Spikes = m_Controls->m_SpikeNumBox->value(); + parameters.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); + parameters.m_ArtifactModelString += "_SPIKES"; + parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_Spikes)); + parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SpikeAmplitude)); + } + + // gibbs ringing + parameters.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); + if (m_Controls->m_AddGibbsRinging->isChecked()) + { + parameters.m_SimulateKspaceAcquisition = true; + parameters.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); + parameters.m_ArtifactModelString += "_RINGING"; + } + + // add distortions + if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) + { + mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); + mitk::Image* img = dynamic_cast(fMapNode->GetData()); + ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); + CastToItkImage< ItkDoubleImgType >(img, itkImg); + + if (parameters.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && + parameters.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && + parameters.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) + { + parameters.m_SimulateKspaceAcquisition = true; + itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); + duplicator->SetInputImage(itkImg); + duplicator->Update(); + parameters.m_FrequencyMap = duplicator->GetOutput(); + parameters.m_ArtifactModelString += "_DISTORTED"; + parameters.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); + } + } + + parameters.m_EddyStrength = 0; + if (m_Controls->m_AddEddy->isChecked()) + { + parameters.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); + parameters.m_ArtifactModelString += "_EDDY"; + parameters.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_EddyStrength)); + } + // Motion parameters.m_DoAddMotion = m_Controls->m_AddMotion->isChecked(); parameters.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); parameters.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); parameters.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); parameters.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); parameters.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); parameters.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); parameters.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); if ( m_Controls->m_AddMotion->isChecked() && m_SelectedBundles.size()>0 ) { parameters.m_ArtifactModelString += "_MOTION"; parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(parameters.m_DoRandomizeMotion)); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(parameters.m_Translation[0])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(parameters.m_Translation[1])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(parameters.m_Translation[2])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(parameters.m_Rotation[0])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(parameters.m_Rotation[1])); parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(parameters.m_Rotation[2])); } // other imaging parameters parameters.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); parameters.m_tInhom = m_Controls->m_T2starBox->value(); parameters.m_tEcho = m_Controls->m_TEbox->value(); parameters.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); parameters.m_AxonRadius = m_Controls->m_FiberRadius->value(); parameters.m_SignalScale = m_Controls->m_SignalScaleBox->value(); - if (m_Controls->m_AddSpikes->isChecked()) - { - parameters.m_Spikes = m_Controls->m_SpikeNumBox->value(); - parameters.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); - parameters.m_ArtifactModelString += "_SPIKES"; - parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_Spikes)); - parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SpikeAmplitude)); - - } - // adjust echo time if needed if ( parameters.m_tEcho < parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ) { this->m_Controls->m_TEbox->setValue( parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ); parameters.m_tEcho = m_Controls->m_TEbox->value(); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(parameters.m_tEcho)+" ms"); } - // rician noise + // Noise if (m_Controls->m_AddNoise->isChecked()) { double noiseVariance = m_Controls->m_NoiseLevel->value(); { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_ArtifactModelString += "_RICIAN-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); break; } case 1: { parameters.m_NoiseModel = new mitk::ChiSquareNoiseModel(); parameters.m_ArtifactModelString += "_CHISQUARED-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); break; } default: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); parameters.m_ArtifactModelString += "_RICIAN-"; parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); } } } parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); parameters.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } - // gibbs ringing - parameters.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); - if (m_Controls->m_AddGibbsRinging->isChecked()) - { - parameters.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); - parameters.m_ArtifactModelString += "_RINGING"; - } - // adjusting line readout time to the adapted image size needed for the DFT unsigned int y = parameters.m_ImageRegion.GetSize(1); y += y%2; if ( y>parameters.m_ImageRegion.GetSize(1) ) parameters.m_tLine *= (double)parameters.m_ImageRegion.GetSize(1)/y; - // add distortions - if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) - { - mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); - mitk::Image* img = dynamic_cast(fMapNode->GetData()); - ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); - CastToItkImage< ItkDoubleImgType >(img, itkImg); - - if (parameters.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && - parameters.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && - parameters.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) - { - itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); - duplicator->SetInputImage(itkImg); - duplicator->Update(); - parameters.m_FrequencyMap = duplicator->GetOutput(); - parameters.m_ArtifactModelString += "_DISTORTED"; - parameters.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); - } - } - - parameters.m_EddyStrength = 0; - if (m_Controls->m_AddEddy->isChecked()) - { - parameters.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); - parameters.m_ArtifactModelString += "_EDDY"; - parameters.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_EddyStrength)); - } - // signal models + m_PrototypeModel1.Clear(); + m_PrototypeModel3.Clear(); + m_PrototypeModel4.Clear(); // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: m_StickModel1.SetGradientList(parameters.GetGradientDirections()); m_StickModel1.SetBvalue(parameters.m_Bvalue); m_StickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); m_StickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_StickModel1); parameters.m_SignalModelString += "Stick"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_StickModel1.GetT2()) ); break; case 1: m_ZeppelinModel1.SetGradientList(parameters.GetGradientDirections()); m_ZeppelinModel1.SetBvalue(parameters.m_Bvalue); m_ZeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); m_ZeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); m_ZeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); m_ZeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_ZeppelinModel1); parameters.m_SignalModelString += "Zeppelin"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; case 2: m_TensorModel1.SetGradientList(parameters.GetGradientDirections()); m_TensorModel1.SetBvalue(parameters.m_Bvalue); m_TensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); m_TensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); m_TensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); m_TensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); parameters.m_FiberModelList.push_back(&m_TensorModel1); parameters.m_SignalModelString += "Tensor"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); break; + case 3: + parameters.m_SimulateKspaceAcquisition = false; + m_PrototypeModel1.SetGradientList(parameters.GetGradientDirections()); + m_PrototypeModel1.SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); + m_PrototypeModel1.SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); + m_PrototypeModel1.SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); + parameters.m_FiberModelList.push_back(&m_PrototypeModel1); + parameters.m_SignalModelString += "Prototype"; + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); + break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: m_StickModel2.SetGradientList(parameters.GetGradientDirections()); m_StickModel2.SetBvalue(parameters.m_Bvalue); m_StickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); m_StickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_StickModel2); parameters.m_SignalModelString += "Stick"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_StickModel2.GetT2()) ); break; case 2: m_ZeppelinModel2.SetGradientList(parameters.GetGradientDirections()); m_ZeppelinModel2.SetBvalue(parameters.m_Bvalue); m_ZeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); m_ZeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); m_ZeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); m_ZeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_ZeppelinModel2); parameters.m_SignalModelString += "Zeppelin"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); break; case 3: m_TensorModel2.SetGradientList(parameters.GetGradientDirections()); m_TensorModel2.SetBvalue(parameters.m_Bvalue); m_TensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); m_TensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); m_TensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); m_TensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); parameters.m_FiberModelList.push_back(&m_TensorModel2); parameters.m_SignalModelString += "Tensor"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); break; } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: m_BallModel1.SetGradientList(parameters.GetGradientDirections()); m_BallModel1.SetBvalue(parameters.m_Bvalue); m_BallModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); m_BallModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); parameters.m_NonFiberModelList.push_back(&m_BallModel1); parameters.m_SignalModelString += "Ball"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_BallModel1.GetT2()) ); break; case 1: m_AstrosticksModel1.SetGradientList(parameters.GetGradientDirections()); m_AstrosticksModel1.SetBvalue(parameters.m_Bvalue); m_AstrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); m_AstrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); m_AstrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel1); parameters.m_SignalModelString += "Astrosticks"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_AstrosticksModel1.GetT2()) ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: m_DotModel1.SetGradientList(parameters.GetGradientDirections()); m_DotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); parameters.m_NonFiberModelList.push_back(&m_DotModel1); parameters.m_SignalModelString += "Dot"; parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_DotModel1.GetT2()) ); break; + case 3: + parameters.m_SimulateKspaceAcquisition = false; + m_PrototypeModel3.SetGradientList(parameters.GetGradientDirections()); + m_PrototypeModel3.SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); + m_PrototypeModel3.SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); + m_PrototypeModel3.SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); + parameters.m_NonFiberModelList.push_back(&m_PrototypeModel3); + parameters.m_SignalModelString += "Prototype"; + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); + break; } // compartment 4 - switch (m_Controls->m_Compartment4Box->currentIndex()) - { - case 0: - break; - case 1: + ItkDoubleImgType::Pointer comp4VolumeImage = NULL; + ItkDoubleImgType::Pointer comp3VolumeImage = NULL; + if (m_Controls->m_Compartment4Box->currentIndex()>0) { - m_BallModel2.SetGradientList(parameters.GetGradientDirections()); - m_BallModel2.SetBvalue(parameters.m_Bvalue); - m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); - m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); - mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); if (volumeNode.IsNull()) { MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; - break; } - mitk::Image* img = dynamic_cast(volumeNode->GetData()); - ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); - CastToItkImage< ItkDoubleImgType >(img, itkImg); - - double max = img->GetScalarValueMax(); - double min = img->GetScalarValueMin(); - - if (max>1 || min<0) // are volume fractions between 0 and 1? + else { - itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); - rescaler->SetInput(0, itkImg); - rescaler->SetOutputMaximum(1); - rescaler->SetOutputMinimum(0); - rescaler->Update(); - itkImg = rescaler->GetOutput(); - } + MITK_INFO << "Rescaling volume fraction image..."; + comp4VolumeImage = ItkDoubleImgType::New(); + mitk::Image* img = dynamic_cast(volumeNode->GetData()); + CastToItkImage< ItkDoubleImgType >(img, comp4VolumeImage); - m_BallModel2.SetVolumeFractionImage(itkImg); - parameters.m_NonFiberModelList.push_back(&m_BallModel2); - parameters.m_SignalModelString += "Ball"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) ); + double max = itk::NumericTraits::min(); + double min = itk::NumericTraits::max(); - itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); - inverter->SetMaximum(1.0); - inverter->SetInput(itkImg); - inverter->Update(); - parameters.m_NonFiberModelList.at(parameters.m_NonFiberModelList.size()-2)->SetVolumeFractionImage(inverter->GetOutput()); + itk::ImageRegionIterator< ItkDoubleImgType > it(comp4VolumeImage, comp4VolumeImage->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) + { + if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) + { + it.Set(0.0); + ++it; + continue; + } - break; + if (it.Get()>max) + max = it.Get(); + if (it.Get()::Pointer scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); + scaler->SetInput(comp4VolumeImage); + scaler->SetShift(-min); + scaler->SetScale(1/(max-min)); + scaler->Update(); + comp4VolumeImage = scaler->GetOutput(); + + itk::ImageFileWriter< ItkDoubleImgType >::Pointer wr = itk::ImageFileWriter< ItkDoubleImgType >::New(); + wr->SetInput(comp4VolumeImage); + wr->SetFileName("/local/comp4.nrrd"); + wr->Update(); + +// if (max>1 || min<0) // are volume fractions between 0 and 1? +// { +// itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); +// rescaler->SetInput(0, comp4VolumeImage); +// rescaler->SetOutputMaximum(1); +// rescaler->SetOutputMinimum(0); +// rescaler->Update(); +// comp4VolumeImage = rescaler->GetOutput(); +// } + + itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); + inverter->SetMaximum(1.0); + inverter->SetInput(comp4VolumeImage); + inverter->Update(); + comp3VolumeImage = inverter->GetOutput(); + } } - case 2: - { - m_AstrosticksModel2.SetGradientList(parameters.GetGradientDirections()); - m_AstrosticksModel2.SetBvalue(parameters.m_Bvalue); - m_AstrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); - m_AstrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); - m_AstrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); - mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); - if (volumeNode.IsNull()) + if (comp4VolumeImage.IsNotNull()) + switch (m_Controls->m_Compartment4Box->currentIndex()) { - MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; + case 0: + break; + case 1: + { + m_BallModel2.SetGradientList(parameters.GetGradientDirections()); + m_BallModel2.SetBvalue(parameters.m_Bvalue); + m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); + m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); + m_BallModel2.SetVolumeFractionImage(comp4VolumeImage); + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + parameters.m_NonFiberModelList.push_back(&m_BallModel2); + parameters.m_SignalModelString += "Ball"; + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) ); break; } - mitk::Image* img = dynamic_cast(volumeNode->GetData()); - ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); - CastToItkImage< ItkDoubleImgType >(img, itkImg); - - double max = img->GetScalarValueMax(); - double min = img->GetScalarValueMin(); - - if (max>1 || min<0) // are volume fractions between 0 and 1? + case 2: { - itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); - rescaler->SetInput(0, itkImg); - rescaler->SetOutputMaximum(1); - rescaler->SetOutputMinimum(0); - rescaler->Update(); - itkImg = rescaler->GetOutput(); + m_AstrosticksModel2.SetGradientList(parameters.GetGradientDirections()); + m_AstrosticksModel2.SetBvalue(parameters.m_Bvalue); + m_AstrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); + m_AstrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); + m_AstrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + m_AstrosticksModel2.SetVolumeFractionImage(comp4VolumeImage); + parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel2); + parameters.m_SignalModelString += "Astrosticks"; + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); + break; } - - m_AstrosticksModel2.SetVolumeFractionImage(itkImg); - parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel2); - parameters.m_SignalModelString += "Astrosticks"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); - - itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); - inverter->SetMaximum( 1.0 ); - inverter->SetInput(itkImg); - inverter->Update(); - parameters.m_NonFiberModelList.at(parameters.m_NonFiberModelList.size()-2)->SetVolumeFractionImage(inverter->GetOutput()); - - break; - } - case 3: - { - m_DotModel2.SetGradientList(parameters.GetGradientDirections()); - m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); - - mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); - if (volumeNode.IsNull()) + case 3: { - MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; + m_DotModel2.SetGradientList(parameters.GetGradientDirections()); + m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); + m_DotModel2.SetVolumeFractionImage(comp4VolumeImage); + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + parameters.m_NonFiberModelList.push_back(&m_DotModel2); + parameters.m_SignalModelString += "Dot"; + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) ); break; } - mitk::Image* img = dynamic_cast(volumeNode->GetData()); - ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); - CastToItkImage< ItkDoubleImgType >(img, itkImg); - - double max = img->GetScalarValueMax(); - double min = img->GetScalarValueMin(); - - if (max>1 || min<0) // are volume fractions between 0 and 1? + case 4: { - itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); - rescaler->SetInput(0, itkImg); - rescaler->SetOutputMaximum(1); - rescaler->SetOutputMinimum(0); - rescaler->Update(); - itkImg = rescaler->GetOutput(); + parameters.m_SimulateKspaceAcquisition = false; + m_PrototypeModel4.SetGradientList(parameters.GetGradientDirections()); + m_PrototypeModel4.SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); + m_PrototypeModel4.SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); + m_PrototypeModel4.SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); + m_PrototypeModel4.SetVolumeFractionImage(comp4VolumeImage); + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + parameters.m_NonFiberModelList.push_back(&m_PrototypeModel4); + parameters.m_SignalModelString += "Prototype"; + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); + parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); + break; + } } - m_DotModel2.SetVolumeFractionImage(itkImg); - parameters.m_NonFiberModelList.push_back(&m_DotModel2); - parameters.m_SignalModelString += "Dot"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) ); - - itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); - inverter->SetMaximum( 1.0 ); - inverter->SetInput(itkImg); - inverter->Update(); - parameters.m_NonFiberModelList.at(parameters.m_NonFiberModelList.size()-2)->SetVolumeFractionImage(inverter->GetOutput()); - - break; - } - } - - if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 ) - { - parameters.m_UsePrototypeSignals = true; - parameters.m_UseRandomDirections = true; - parameters.m_UseMainFiberDirections = false; - parameters.m_NonFiberModelList.clear(); - parameters.m_FiberModelList.clear(); - } + parameters.m_DiffusionDirectionMode = FiberfoxParameters::FIBER_TANGENT_DIRECTIONS; parameters.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(parameters.m_SignalScale)); parameters.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(parameters.m_AxonRadius)); parameters.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(parameters.m_tInhom)); parameters.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(parameters.m_tLine)); parameters.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(parameters.m_tEcho)); parameters.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(parameters.m_Bvalue)); parameters.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(parameters.m_DoDisablePartialVolume)); parameters.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(parameters.m_DoSimulateRelaxation)); parameters.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); return parameters; } void QmitkFiberfoxView::SaveParameters() { FiberfoxParameters ffParamaters = UpdateImageParameters(); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; if(!filename.endsWith(".ffp")) filename += ".ffp"; m_ParameterFile = filename; boost::property_tree::ptree parameters; // fiber generation parameters parameters.put("fiberfox.fibers.realtime", m_Controls->m_RealTimeFibers->isChecked()); parameters.put("fiberfox.fibers.showadvanced", m_Controls->m_AdvancedOptionsBox->isChecked()); parameters.put("fiberfox.fibers.distribution", m_Controls->m_DistributionBox->currentIndex()); parameters.put("fiberfox.fibers.variance", m_Controls->m_VarianceBox->value()); parameters.put("fiberfox.fibers.density", m_Controls->m_FiberDensityBox->value()); parameters.put("fiberfox.fibers.spline.sampling", m_Controls->m_FiberSamplingBox->value()); parameters.put("fiberfox.fibers.spline.tension", m_Controls->m_TensionBox->value()); parameters.put("fiberfox.fibers.spline.continuity", m_Controls->m_ContinuityBox->value()); parameters.put("fiberfox.fibers.spline.bias", m_Controls->m_BiasBox->value()); parameters.put("fiberfox.fibers.constantradius", m_Controls->m_ConstantRadiusBox->isChecked()); parameters.put("fiberfox.fibers.rotation.x", m_Controls->m_XrotBox->value()); parameters.put("fiberfox.fibers.rotation.y", m_Controls->m_YrotBox->value()); parameters.put("fiberfox.fibers.rotation.z", m_Controls->m_ZrotBox->value()); parameters.put("fiberfox.fibers.translation.x", m_Controls->m_XtransBox->value()); parameters.put("fiberfox.fibers.translation.y", m_Controls->m_YtransBox->value()); parameters.put("fiberfox.fibers.translation.z", m_Controls->m_ZtransBox->value()); parameters.put("fiberfox.fibers.scale.x", m_Controls->m_XscaleBox->value()); parameters.put("fiberfox.fibers.scale.y", m_Controls->m_YscaleBox->value()); parameters.put("fiberfox.fibers.scale.z", m_Controls->m_ZscaleBox->value()); parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); // image generation parameters parameters.put("fiberfox.image.basic.size.x", ffParamaters.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", ffParamaters.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", ffParamaters.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", ffParamaters.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", ffParamaters.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", ffParamaters.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.numgradients", ffParamaters.GetNumWeightedVolumes()); parameters.put("fiberfox.image.basic.bvalue", ffParamaters.m_Bvalue); parameters.put("fiberfox.image.showadvanced", m_Controls->m_AdvancedOptionsBox_2->isChecked()); parameters.put("fiberfox.image.signalScale", ffParamaters.m_SignalScale); parameters.put("fiberfox.image.tEcho", ffParamaters.m_tEcho); parameters.put("fiberfox.image.tLine", m_Controls->m_LineReadoutTimeBox->value()); parameters.put("fiberfox.image.tInhom", ffParamaters.m_tInhom); parameters.put("fiberfox.image.axonRadius", ffParamaters.m_AxonRadius); parameters.put("fiberfox.image.doSimulateRelaxation", ffParamaters.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", ffParamaters.m_DoDisablePartialVolume); parameters.put("fiberfox.image.outputvolumefractions", m_Controls->m_VolumeFractionsBox->isChecked()); parameters.put("fiberfox.image.artifacts.addnoise", m_Controls->m_AddNoise->isChecked()); parameters.put("fiberfox.image.artifacts.noisedistribution", m_Controls->m_NoiseDistributionBox->currentIndex()); parameters.put("fiberfox.image.artifacts.noisevariance", m_Controls->m_NoiseLevel->value()); parameters.put("fiberfox.image.artifacts.addghost", m_Controls->m_AddGhosts->isChecked()); parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_Controls->m_kOffsetBox->value()); parameters.put("fiberfox.image.artifacts.distortions", m_Controls->m_AddDistortions->isChecked()); parameters.put("fiberfox.image.artifacts.addeddy", m_Controls->m_AddEddy->isChecked()); parameters.put("fiberfox.image.artifacts.eddyStrength", m_Controls->m_EddyGradientStrength->value()); parameters.put("fiberfox.image.artifacts.addringing", m_Controls->m_AddGibbsRinging->isChecked()); parameters.put("fiberfox.image.artifacts.addspikes", m_Controls->m_AddSpikes->isChecked()); parameters.put("fiberfox.image.artifacts.spikesnum", m_Controls->m_SpikeNumBox->value()); parameters.put("fiberfox.image.artifacts.spikesscale", m_Controls->m_SpikeScaleBox->value()); parameters.put("fiberfox.image.artifacts.addaliasing", m_Controls->m_AddAliasing->isChecked()); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_Controls->m_WrapBox->value()); parameters.put("fiberfox.image.artifacts.doAddMotion", m_Controls->m_AddMotion->isChecked()); parameters.put("fiberfox.image.artifacts.randomMotion", m_Controls->m_RandomMotion->isChecked()); parameters.put("fiberfox.image.artifacts.translation0", m_Controls->m_MaxTranslationBoxX->value()); parameters.put("fiberfox.image.artifacts.translation1", m_Controls->m_MaxTranslationBoxY->value()); parameters.put("fiberfox.image.artifacts.translation2", m_Controls->m_MaxTranslationBoxZ->value()); parameters.put("fiberfox.image.artifacts.rotation0", m_Controls->m_MaxRotationBoxX->value()); parameters.put("fiberfox.image.artifacts.rotation1", m_Controls->m_MaxRotationBoxY->value()); parameters.put("fiberfox.image.artifacts.rotation2", m_Controls->m_MaxRotationBoxZ->value()); parameters.put("fiberfox.image.compartment1.index", m_Controls->m_Compartment1Box->currentIndex()); parameters.put("fiberfox.image.compartment2.index", m_Controls->m_Compartment2Box->currentIndex()); parameters.put("fiberfox.image.compartment3.index", m_Controls->m_Compartment3Box->currentIndex()); parameters.put("fiberfox.image.compartment4.index", m_Controls->m_Compartment4Box->currentIndex()); parameters.put("fiberfox.image.compartment1.stick.d", m_Controls->m_StickWidget1->GetD()); parameters.put("fiberfox.image.compartment1.stick.t2", m_Controls->m_StickWidget1->GetT2()); parameters.put("fiberfox.image.compartment1.zeppelin.d1", m_Controls->m_ZeppelinWidget1->GetD1()); parameters.put("fiberfox.image.compartment1.zeppelin.d2", m_Controls->m_ZeppelinWidget1->GetD2()); parameters.put("fiberfox.image.compartment1.zeppelin.t2", m_Controls->m_ZeppelinWidget1->GetT2()); parameters.put("fiberfox.image.compartment1.tensor.d1", m_Controls->m_TensorWidget1->GetD1()); parameters.put("fiberfox.image.compartment1.tensor.d2", m_Controls->m_TensorWidget1->GetD2()); parameters.put("fiberfox.image.compartment1.tensor.d3", m_Controls->m_TensorWidget1->GetD3()); parameters.put("fiberfox.image.compartment1.tensor.t2", m_Controls->m_TensorWidget1->GetT2()); parameters.put("fiberfox.image.compartment2.stick.d", m_Controls->m_StickWidget2->GetD()); parameters.put("fiberfox.image.compartment2.stick.t2", m_Controls->m_StickWidget2->GetT2()); parameters.put("fiberfox.image.compartment2.zeppelin.d1", m_Controls->m_ZeppelinWidget2->GetD1()); parameters.put("fiberfox.image.compartment2.zeppelin.d2", m_Controls->m_ZeppelinWidget2->GetD2()); parameters.put("fiberfox.image.compartment2.zeppelin.t2", m_Controls->m_ZeppelinWidget2->GetT2()); parameters.put("fiberfox.image.compartment2.tensor.d1", m_Controls->m_TensorWidget2->GetD1()); parameters.put("fiberfox.image.compartment2.tensor.d2", m_Controls->m_TensorWidget2->GetD2()); parameters.put("fiberfox.image.compartment2.tensor.d3", m_Controls->m_TensorWidget2->GetD3()); parameters.put("fiberfox.image.compartment2.tensor.t2", m_Controls->m_TensorWidget2->GetT2()); parameters.put("fiberfox.image.compartment3.ball.d", m_Controls->m_BallWidget1->GetD()); parameters.put("fiberfox.image.compartment3.ball.t2", m_Controls->m_BallWidget1->GetT2()); parameters.put("fiberfox.image.compartment3.astrosticks.d", m_Controls->m_AstrosticksWidget1->GetD()); parameters.put("fiberfox.image.compartment3.astrosticks.t2", m_Controls->m_AstrosticksWidget1->GetT2()); parameters.put("fiberfox.image.compartment3.astrosticks.randomize", m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); parameters.put("fiberfox.image.compartment3.dot.t2", m_Controls->m_DotWidget1->GetT2()); parameters.put("fiberfox.image.compartment4.ball.d", m_Controls->m_BallWidget2->GetD()); parameters.put("fiberfox.image.compartment4.ball.t2", m_Controls->m_BallWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.astrosticks.d", m_Controls->m_AstrosticksWidget2->GetD()); parameters.put("fiberfox.image.compartment4.astrosticks.t2", m_Controls->m_AstrosticksWidget2->GetT2()); parameters.put("fiberfox.image.compartment4.astrosticks.randomize", m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); parameters.put("fiberfox.image.compartment4.dot.t2", m_Controls->m_DotWidget2->GetT2()); boost::property_tree::xml_parser::write_xml(filename.toStdString(), parameters); } void QmitkFiberfoxView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; boost::property_tree::ptree parameters; boost::property_tree::xml_parser::read_xml(filename.toStdString(), parameters); BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_Controls->m_RealTimeFibers->setChecked(v1.second.get("realtime")); m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get("showadvanced")); m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get("distribution")); m_Controls->m_VarianceBox->setValue(v1.second.get("variance")); m_Controls->m_FiberDensityBox->setValue(v1.second.get("density")); m_Controls->m_IncludeFiducials->setChecked(v1.second.get("includeFiducials")); m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get("constantradius")); BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second ) { if( v2.first == "spline" ) { m_Controls->m_FiberSamplingBox->setValue(v2.second.get("sampling")); m_Controls->m_TensionBox->setValue(v2.second.get("tension")); m_Controls->m_ContinuityBox->setValue(v2.second.get("continuity")); m_Controls->m_BiasBox->setValue(v2.second.get("bias")); } if( v2.first == "rotation" ) { m_Controls->m_XrotBox->setValue(v2.second.get("x")); m_Controls->m_YrotBox->setValue(v2.second.get("y")); m_Controls->m_ZrotBox->setValue(v2.second.get("z")); } if( v2.first == "translation" ) { m_Controls->m_XtransBox->setValue(v2.second.get("x")); m_Controls->m_YtransBox->setValue(v2.second.get("y")); m_Controls->m_ZtransBox->setValue(v2.second.get("z")); } if( v2.first == "scale" ) { m_Controls->m_XscaleBox->setValue(v2.second.get("x")); m_Controls->m_YscaleBox->setValue(v2.second.get("y")); m_Controls->m_ZscaleBox->setValue(v2.second.get("z")); } } } if( v1.first == "image" ) { m_Controls->m_SizeX->setValue(v1.second.get("basic.size.x")); m_Controls->m_SizeY->setValue(v1.second.get("basic.size.y")); m_Controls->m_SizeZ->setValue(v1.second.get("basic.size.z")); m_Controls->m_SpacingX->setValue(v1.second.get("basic.spacing.x")); m_Controls->m_SpacingY->setValue(v1.second.get("basic.spacing.y")); m_Controls->m_SpacingZ->setValue(v1.second.get("basic.spacing.z")); m_Controls->m_NumGradientsBox->setValue(v1.second.get("basic.numgradients")); m_Controls->m_BvalueBox->setValue(v1.second.get("basic.bvalue")); m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get("showadvanced")); m_Controls->m_SignalScaleBox->setValue(v1.second.get("signalScale")); m_Controls->m_TEbox->setValue(v1.second.get("tEcho")); m_Controls->m_LineReadoutTimeBox->setValue(v1.second.get("tLine")); m_Controls->m_T2starBox->setValue(v1.second.get("tInhom")); m_Controls->m_FiberRadius->setValue(v1.second.get("axonRadius")); m_Controls->m_RelaxationBox->setChecked(v1.second.get("doSimulateRelaxation")); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(v1.second.get("doDisablePartialVolume")); m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get("outputvolumefractions")); m_Controls->m_AddNoise->setChecked(v1.second.get("artifacts.addnoise")); m_Controls->m_NoiseDistributionBox->setCurrentIndex(v1.second.get("artifacts.noisedistribution")); m_Controls->m_NoiseLevel->setValue(v1.second.get("artifacts.noisevariance")); m_Controls->m_AddGhosts->setChecked(v1.second.get("artifacts.addghost")); m_Controls->m_kOffsetBox->setValue(v1.second.get("artifacts.kspaceLineOffset")); m_Controls->m_AddAliasing->setChecked(v1.second.get("artifacts.addaliasing")); m_Controls->m_WrapBox->setValue(v1.second.get("artifacts.aliasingfactor")); m_Controls->m_AddDistortions->setChecked(v1.second.get("artifacts.distortions")); m_Controls->m_AddSpikes->setChecked(v1.second.get("artifacts.addspikes")); m_Controls->m_SpikeNumBox->setValue(v1.second.get("artifacts.spikesnum")); m_Controls->m_SpikeScaleBox->setValue(v1.second.get("artifacts.spikesscale")); m_Controls->m_AddEddy->setChecked(v1.second.get("artifacts.addeddy")); m_Controls->m_EddyGradientStrength->setValue(v1.second.get("artifacts.eddyStrength")); m_Controls->m_AddGibbsRinging->setChecked(v1.second.get("artifacts.addringing")); m_Controls->m_AddMotion->setChecked(v1.second.get("artifacts.doAddMotion")); m_Controls->m_RandomMotion->setChecked(v1.second.get("artifacts.randomMotion")); m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get("artifacts.translation0")); m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get("artifacts.translation1")); m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get("artifacts.translation2")); m_Controls->m_MaxRotationBoxX->setValue(v1.second.get("artifacts.rotation0")); m_Controls->m_MaxRotationBoxY->setValue(v1.second.get("artifacts.rotation1")); m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get("artifacts.rotation2")); m_Controls->m_Compartment1Box->setCurrentIndex(v1.second.get("compartment1.index")); m_Controls->m_Compartment2Box->setCurrentIndex(v1.second.get("compartment2.index")); m_Controls->m_Compartment3Box->setCurrentIndex(v1.second.get("compartment3.index")); m_Controls->m_Compartment4Box->setCurrentIndex(v1.second.get("compartment4.index")); m_Controls->m_StickWidget1->SetD(v1.second.get("compartment1.stick.d")); m_Controls->m_StickWidget1->SetT2(v1.second.get("compartment1.stick.t2")); m_Controls->m_ZeppelinWidget1->SetD1(v1.second.get("compartment1.zeppelin.d1")); m_Controls->m_ZeppelinWidget1->SetD2(v1.second.get("compartment1.zeppelin.d2")); m_Controls->m_ZeppelinWidget1->SetT2(v1.second.get("compartment1.zeppelin.t2")); m_Controls->m_TensorWidget1->SetD1(v1.second.get("compartment1.tensor.d1")); m_Controls->m_TensorWidget1->SetD2(v1.second.get("compartment1.tensor.d2")); m_Controls->m_TensorWidget1->SetD3(v1.second.get("compartment1.tensor.d3")); m_Controls->m_TensorWidget1->SetT2(v1.second.get("compartment1.tensor.t2")); m_Controls->m_StickWidget2->SetD(v1.second.get("compartment2.stick.d")); m_Controls->m_StickWidget2->SetT2(v1.second.get("compartment2.stick.t2")); m_Controls->m_ZeppelinWidget2->SetD1(v1.second.get("compartment2.zeppelin.d1")); m_Controls->m_ZeppelinWidget2->SetD2(v1.second.get("compartment2.zeppelin.d2")); m_Controls->m_ZeppelinWidget2->SetT2(v1.second.get("compartment2.zeppelin.t2")); m_Controls->m_TensorWidget2->SetD1(v1.second.get("compartment2.tensor.d1")); m_Controls->m_TensorWidget2->SetD2(v1.second.get("compartment2.tensor.d2")); m_Controls->m_TensorWidget2->SetD3(v1.second.get("compartment2.tensor.d3")); m_Controls->m_TensorWidget2->SetT2(v1.second.get("compartment2.tensor.t2")); m_Controls->m_BallWidget1->SetD(v1.second.get("compartment3.ball.d")); m_Controls->m_BallWidget1->SetT2(v1.second.get("compartment3.ball.t2")); m_Controls->m_AstrosticksWidget1->SetD(v1.second.get("compartment3.astrosticks.d")); m_Controls->m_AstrosticksWidget1->SetT2(v1.second.get("compartment3.astrosticks.t2")); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); m_Controls->m_DotWidget1->SetT2(v1.second.get("compartment3.dot.t2")); m_Controls->m_BallWidget2->SetD(v1.second.get("compartment4.ball.d")); m_Controls->m_BallWidget2->SetT2(v1.second.get("compartment4.ball.t2")); m_Controls->m_AstrosticksWidget2->SetD(v1.second.get("compartment4.astrosticks.d")); m_Controls->m_AstrosticksWidget2->SetT2(v1.second.get("compartment4.astrosticks.t2")); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); m_Controls->m_DotWidget2->SetT2(v1.second.get("compartment4.dot.t2")); } } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); - m_Controls->m_Compartment2Box->setEnabled(true); - m_Controls->m_Compartment4Box->setEnabled(true); - - if (m_Controls->m_Compartment3Box->currentIndex()==3 && index!=3) - m_Controls->m_Compartment3Box->setCurrentIndex(0); - - + m_Controls->m_PrototypeWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; case 3: - { m_Controls->m_PrototypeWidget1->setVisible(true); - if (m_Controls->m_Compartment3Box->currentIndex()!=3) - m_Controls->m_Compartment3Box->setCurrentIndex(3); - m_Controls->m_Compartment2Box->setCurrentIndex(0); - m_Controls->m_Compartment4Box->setCurrentIndex(0); - m_Controls->m_Compartment2Box->setEnabled(false); - m_Controls->m_Compartment4Box->setEnabled(false); break; } - } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); - m_Controls->m_Compartment2Box->setEnabled(true); - m_Controls->m_Compartment4Box->setEnabled(true); - - if (m_Controls->m_Compartment1Box->currentIndex()==3 && index!=3) - m_Controls->m_Compartment1Box->setCurrentIndex(0); + m_Controls->m_PrototypeWidget3->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; case 3: - { m_Controls->m_PrototypeWidget3->setVisible(true); - if (m_Controls->m_Compartment1Box->currentIndex()!=3) - m_Controls->m_Compartment1Box->setCurrentIndex(3); - m_Controls->m_Compartment2Box->setCurrentIndex(0); - m_Controls->m_Compartment4Box->setCurrentIndex(0); - m_Controls->m_Compartment2Box->setEnabled(false); - m_Controls->m_Compartment4Box->setEnabled(false); break; } - } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); + m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; + case 4: + m_Controls->m_PrototypeWidget4->setVisible(true); + m_Controls->m_Comp4FractionFrame->setVisible(true); + break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for(unsigned int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for(unsigned int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); node->SetBoolProperty("planarfigure.3drendering", true); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( node ); } UpdateGui(); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (unsigned int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (unsigned int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { if (m_SelectedBundles.empty() && m_SelectedDWI.IsNull()) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); } else if (!m_SelectedBundles.empty()) SimulateImageFromFibers(m_SelectedBundles.at(0)); else if (m_SelectedDWI.IsNotNull()) SimulateForExistingDwi(m_SelectedDWI); } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { if (!dynamic_cast*>(imageNode->GetData())) return; FiberfoxParameters parameters = UpdateImageParameters(); if (parameters.m_NoiseModel==NULL && parameters.m_Spikes==0 && parameters.m_FrequencyMap.IsNull() && parameters.m_KspaceLineOffset<=0.000001 && !parameters.m_DoAddGibbsRinging && !(parameters.m_EddyStrength>0) && parameters.m_CroppingFactor>0.999) { QMessageBox::information( NULL, "Simulation cancelled", "No valid artifact enabled! Motion artifacts and relaxation effects can NOT be added to an existing diffusion weighted image."); return; } mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(imageNode->GetData()); m_ArtifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); m_ArtifactsToDwiFilter->SetInput(diffImg->GetVectorImage()); parameters.m_ParentNode = imageNode; m_ArtifactsToDwiFilter->SetParameters(parameters); m_Worker.m_FilterType = 1; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) return; FiberfoxParameters parameters = UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); parameters.m_ParentNode = fiberNode; if (m_SelectedDWI.IsNotNull()) { mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedDWI->GetData()); - m_TractsToDwiFilter->SetInputDwi(diffImg); + + bool doSampling = false; + for (unsigned int i=0; i* >(parameters.m_FiberModelList[i]) ) + doSampling = true; + for (unsigned int i=0; i* >(parameters.m_NonFiberModelList[i]) ) + doSampling = true; // sample prototype signals - if (parameters.m_UsePrototypeSignals) + if ( doSampling ) { const int shOrder = 4; - parameters.m_SignalScale = 1; typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); filter->SetBValue(diffImg->GetReferenceBValue()); filter->Update(); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = filter->GetOutput(); const int NumCoeffs = (shOrder*shOrder + shOrder + 2)/2 + shOrder; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; typename QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); qballfilter->SetBValue(diffImg->GetReferenceBValue()); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); QballFilterType::CoefficientImageType::Pointer itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput(diffImg->GetVectorImage()); adcFilter->SetGradientDirections(diffImg->GetDirections()); adcFilter->SetB_value(diffImg->GetReferenceBValue()); adcFilter->Update(); ItkDoubleImgType::Pointer adcImage = adcFilter->GetOutput(); int b0Index; for (unsigned int i=0; iGetDirectionsWithoutMeasurementFrame()->Size(); i++) if ( diffImg->GetDirectionsWithoutMeasurementFrame()->GetElement(i).magnitude()<0.001 ) { b0Index = i; break; } + double max = 0; + { + itk::ImageRegionIterator< itk::VectorImage< short, 3 > > it(diffImg->GetVectorImage(), diffImg->GetVectorImage()->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) + { + if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) + { + ++it; + continue; + } + if (it.Get()[b0Index]>max) + max = it.Get()[b0Index]; + ++it; + } + } + MITK_INFO << "Sampling signal kernels."; + itk::ImageRegionIterator< itk::Image< itk::DiffusionTensor3D< double >, 3 > > it(tensorImage, tensorImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { - bool valid = true; - for (int i=0; iGetNumberOfChannels(); i++) + if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) { - if (diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]<=0 || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]>diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]) - valid = false; + ++it; + continue; } - - if (valid) + for (unsigned int i=0; iGetDirections()->Size(); i++) { - itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); - randGen->SetSeed(); - if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) + if (diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]<=0 || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]>diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]) { ++it; continue; } - itk::DiffusionTensor3D< double > tensor = it.Get(); - double FA = tensor.GetFractionalAnisotropy(); - if (FA>m_Controls->m_PrototypeWidget1->GetMinFa() && FAm_PrototypeWidget1->GetMaxFa() && parameters.m_FiberModelList.size()m_PrototypeWidget1->GetNumberOfSamples()) + } + + typedef itk::DiffusionTensor3D TensorType; + TensorType::EigenValuesArrayType eigenvalues; + TensorType::EigenVectorsMatrixType eigenvectors; + TensorType tensor = it.Get(); + double FA = tensor.GetFractionalAnisotropy(); + double ADC = adcImage->GetPixel(it.GetIndex()); + itk::Vector< float, NumCoeffs > itkv = itkFeatureImage->GetPixel(it.GetIndex()); + vnl_vector_fixed< double, NumCoeffs > coeffs; + for (unsigned int c=0; c* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); + if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { - RawShModel* model = new RawShModel(); - model->SetGradientList( parameters.GetGradientDirections() ); - itk::Vector< float, NumCoeffs > itkv = itkFeatureImage->GetPixel(it.GetIndex()); - vnl_vector_fixed< double, NumCoeffs > coeffs; - for (unsigned int c=0; cSetB0Signal( diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index] ); - if (!model->SetShCoefficients( coeffs )) + if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) { - ++it; - continue; + tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); + itk::Vector dir; + dir[0] = eigenvectors(2, 0); + dir[1] = eigenvectors(2, 1); + dir[2] = eigenvectors(2, 2); + model->m_PrototypeMaxDirection.push_back(dir); + MITK_INFO << "WM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } - parameters.m_FiberModelList.push_back(model); - MITK_INFO << "WM KERNEL: " << it.GetIndex(); } - else if (adcImage->GetPixel(it.GetIndex())<0.001 && FA>m_Controls->m_PrototypeWidget3->GetMinFa() && FAm_PrototypeWidget3->GetMaxFa() && parameters.m_NonFiberModelList.size()m_PrototypeWidget3->GetNumberOfSamples()) + } + for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); + if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { - RawShModel* model = new RawShModel(); - model->SetGradientList( parameters.GetGradientDirections() ); - itk::Vector< float, NumCoeffs > itkv = itkFeatureImage->GetPixel(it.GetIndex()); - vnl_vector_fixed< double, NumCoeffs > coeffs; - for (unsigned int c=0; cSetB0Signal( diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index] ); - if (!model->SetShCoefficients( coeffs )) - { - ++it; - continue; - } - itk::Vector fib; - fib[0] = randGen->GetVariateWithClosedRange(2)-1.0; - fib[1] = randGen->GetVariateWithClosedRange(2)-1.0; - fib[2] = randGen->GetVariateWithClosedRange(2)-1.0; - fib.Normalize(); - model->SetFiberDirection(fib); - parameters.m_NonFiberModelList.push_back(model); - MITK_INFO << "GM/CSF KERNEL: " << it.GetIndex(); + if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) + MITK_INFO << "CSF/GM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } - - if (parameters.m_FiberModelList.size()>=m_Controls->m_PrototypeWidget1->GetNumberOfSamples() && parameters.m_NonFiberModelList.size()>=m_Controls->m_PrototypeWidget3->GetNumberOfSamples()) - break; } ++it; } - MITK_INFO << "Using pool of " << parameters.m_FiberModelList.size() << " WM and " << parameters.m_NonFiberModelList.size() << " GM/CSF kernels"; + + for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); + if ( model && model->GetNumberOfKernels()<=0 ) + { + QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for fiber compartment "+QString::number(i)); + return; + } + } + for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); + if ( model && model->GetNumberOfKernels()<=0 ) + { + QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for non-fiber compartment "+QString::number(i)); + return; + } + } } } - else if (parameters.m_UsePrototypeSignals) + else if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 || m_Controls->m_Compartment4Box->currentIndex()==4 ) { QMessageBox::information( NULL, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } + m_TractsToDwiFilter->SetParameters(parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Worker.m_FilterType = 0; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for(unsigned int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { for (std::vector::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); pe->Modified(); } } } } } else { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); pe->Modified(); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } for (std::vector::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); newNode->SetBoolProperty("planarfigure.3drendering", true); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_MaskImageNode.IsNotNull() || m_SelectedImage.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (!m_SelectedBundles.empty()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = NULL; m_MaskImageNode = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isbinary = false; node->GetPropertyValue("binary", isbinary); if (isbinary) { m_MaskImageNode = node; m_Controls->m_TissueMaskLabel->setText(m_MaskImageNode->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(node->GetData())) m_SelectedImages.clear(); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( nonConstNode ); } MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG string outputPath = QFileDialog::getExistingDirectory(NULL, "Save images to...", QString(outputPath.c_str())).toStdString(); if (outputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { outputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str())); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h index 8e7101eafc..fc4f611076 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h @@ -1,224 +1,228 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include "ui_QmitkFiberfoxViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include /*! \brief View for fiber based diffusion software phantoms (Fiberfox). See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details. \sa QmitkFunctionality \ingroup Functionalities */ // Forward Qt class declarations using namespace std; class QmitkFiberfoxView; class QmitkFiberfoxWorker : public QObject { Q_OBJECT public: QmitkFiberfoxWorker(QmitkFiberfoxView* view); int m_FilterType; public slots: void run(); private: QmitkFiberfoxView* m_View; }; class QmitkFiberfoxView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const string VIEW_ID; QmitkFiberfoxView(); virtual ~QmitkFiberfoxView(); virtual void CreateQtPartControl(QWidget *parent); void SetFocus(); typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef vector GradientListType; template vector > MakeGradientList(); protected slots: void SetOutputPath(); ///< path where image is automatically saved to after the simulation is finished void LoadParameters(); ///< load fiberfox parameters void SaveParameters(); ///< save fiberfox parameters void BeforeThread(); void AfterThread(); void KillThread(); ///< abort simulation void UpdateSimulationStatus(); ///< print simulation progress and satus messages void OnDrawROI(); ///< adds new ROI, handles interactors etc. void OnAddBundle(); ///< adds new fiber bundle to datastorage void OnFlipButton(); ///< negate one coordinate of the fiber waypoints in the selcted planar figure. needed in case of unresolvable twists void GenerateFibers(); ///< generate fibers from the selected ROIs void GenerateImage(); ///< start image simulation void JoinBundles(); ///< merges selcted fiber bundles into one void CopyBundles(); ///< add copy of the selected bundle to the datamanager void ApplyTransform(); ///< rotate and shift selected bundles void AlignOnGrid(); ///< shift selected fiducials to nearest voxel center void Comp1ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 1 void Comp2ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 2 void Comp3ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 3 void Comp4ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 4 void ShowAdvancedOptions(int state); /** update fibers if any parameter changes */ void OnFiberDensityChanged(int value); void OnFiberSamplingChanged(double value); void OnTensionChanged(double value); void OnContinuityChanged(double value); void OnBiasChanged(double value); void OnVarianceChanged(double value); void OnDistributionChanged(int value); void OnConstantRadius(int value); /** update GUI elements */ void OnAddNoise(int value); void OnAddGhosts(int value); void OnAddDistortions(int value); void OnAddEddy(int value); void OnAddSpikes(int value); void OnAddAliasing(int value); void OnAddMotion(int value); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList&); GradientListType GenerateHalfShell(int NPoints); ///< generate vectors distributed over the halfsphere Ui::QmitkFiberfoxViewControls* m_Controls; void SimulateForExistingDwi(mitk::DataNode* imageNode); ///< add artifacts to existing diffusion weighted image void SimulateImageFromFibers(mitk::DataNode* fiberNode); ///< simulate new diffusion weighted image template< class ScalarType > FiberfoxParameters< ScalarType > UpdateImageParameters(); ///< update fiberfox paramater object (template parameter defines noise model type) void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection void PlanarFigureSelected( itk::Object* object, const itk::EventObject& ); void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts void NodeAdded( const mitk::DataNode* node ); ///< add observers void NodeRemoved(const mitk::DataNode* node); ///< remove observers /** structure to keep track of planar figures and observers */ struct QmitkPlanarFigureData { QmitkPlanarFigureData() : m_Figure(0) , m_EndPlacementObserverTag(0) , m_SelectObserverTag(0) , m_StartInteractionObserverTag(0) , m_EndInteractionObserverTag(0) , m_Flipped(0) { } mitk::PlanarFigure* m_Figure; unsigned int m_EndPlacementObserverTag; unsigned int m_SelectObserverTag; unsigned int m_StartInteractionObserverTag; unsigned int m_EndInteractionObserverTag; unsigned int m_Flipped; }; std::map m_DataNodeToPlanarFigureData; ///< map each planar figure uniquely to a QmitkPlanarFigureData mitk::DataNode::Pointer m_SelectedFiducial; ///< selected planar ellipse mitk::DataNode::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedDWI; vector< mitk::DataNode::Pointer > m_SelectedBundles; vector< mitk::DataNode::Pointer > m_SelectedBundles2; vector< mitk::DataNode::Pointer > m_SelectedFiducials; vector< mitk::DataNode::Pointer > m_SelectedImages; mitk::DataNode::Pointer m_MaskImageNode; /** intra and inter axonal compartments */ mitk::StickModel m_StickModel1; mitk::StickModel m_StickModel2; mitk::TensorModel m_ZeppelinModel1; mitk::TensorModel m_ZeppelinModel2; mitk::TensorModel m_TensorModel1; mitk::TensorModel m_TensorModel2; + mitk::RawShModel m_PrototypeModel1; /** extra axonal compartment models */ mitk::BallModel m_BallModel1; mitk::BallModel m_BallModel2; mitk::AstroStickModel m_AstrosticksModel1; mitk::AstroStickModel m_AstrosticksModel2; mitk::DotModel m_DotModel1; mitk::DotModel m_DotModel2; + mitk::RawShModel m_PrototypeModel3; + mitk::RawShModel m_PrototypeModel4; QString m_ParameterFile; ///< parameter file name // GUI thread QmitkFiberfoxWorker m_Worker; ///< runs filter QThread m_Thread; ///< worker thread bool m_ThreadIsRunning; QTimer* m_SimulationTimer; QTime m_SimulationTime; QString m_SimulationStatusText; /** Image filters that do all the simulations. */ itk::TractsToDWIImageFilter< short >::Pointer m_TractsToDwiFilter; itk::AddArtifactsToDwiImageFilter< short >::Pointer m_ArtifactsToDwiFilter; friend class QmitkFiberfoxWorker; }; 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 b357af2815..c4274ce619 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,3032 +1,3037 @@ QmitkFiberfoxViewControls 0 0 435 2305 Form Load Parameters :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Operations false Join Bundles :/QmitkDiffusionImaging/general_icons/plus.ico:/QmitkDiffusionImaging/general_icons/plus.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Copy Bundles :/QmitkDiffusionImaging/general_icons/copy2.ico:/QmitkDiffusionImaging/general_icons/copy2.ico false Transform Selection :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Distance of fiber sampling points (in mm) 1 0.100000000000000 0.100000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation Data Tissue Mask: false <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Save path: false QFrame::NoFrame QFrame::Raised 0 0 0 0 0 - ... Noise and other Artifacts Qt::Horizontal Add Noise false Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Shrink FOV (%): false Shrink FOV by this percentage. 1 0.000000000000000 90.000000000000000 0.100000000000000 25.000000000000000 Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Spikes: The number of randomly occurring signal spikes. 1 Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. 0.100000000000000 0.100000000000000 Scale: !!!EXPERIMENTAL!!! Add Eddy Current Effects false Add Spikes false QFrame::NoFrame QFrame::Raised 0 0 0 0 Variance: Variance of selected noise distribution. 4 0.000000000000000 999999999.000000000000000 0.001000000000000 50.000000000000000 Distribution: Noise distribution Rician Chi-squared Add N/2 Ghosts false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). Qt::Horizontal Qt::Horizontal Qt::Horizontal true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 6 0 0 Toggle between random movement and linear movement. Randomize motion true Rotation 0 9 0 0 Degree: false x false Axis: false Maximum rotation around x-axis. 1 360.000000000000000 1.000000000000000 0.000000000000000 Maximum rotation around z-axis. 1 360.000000000000000 1.000000000000000 15.000000000000000 y false z false Maximum rotation around y-axis. 1 360.000000000000000 1.000000000000000 0.000000000000000 Translation 0 0 0 Distance: false x false y false Axis: false z false Maximum translation along x-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along y-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along z-axis. 1 1000.000000000000000 1.000000000000000 0.000000000000000 Add Motion Artifacts false Add Distortions false Add Aliasing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.250000000000000 true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Magnitude: false Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). 5 1000.000000000000000 0.001000000000000 0.005000000000000 color: rgb(255, 0, 0); Experimental! Qt::Horizontal Qt::Horizontal Image Settings QFrame::NoFrame QFrame::Raised 0 0 0 0 6 TE in milliseconds 1 10000 1 100 <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 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 Line Readout Time: false Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 Fiber Radius: Signal Scale: <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 TE in milliseconds 1 10000 1 100 color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 <html><head/><body><p>b-Value<span style=" font-style:italic;"> [s/mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">]</span>:</p></body></html> false b-value in s/mm² 0 10000 100 1000 Advanced Options true <html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html> Start Simulation :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model PrototypeSignal true Stop current simulation. Abort Simulation :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico Extra-axonal Compartments QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model PrototypeSignal Qt::Horizontal Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model + + + Prototype Signal + + Qt::Vertical 20 40 Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model 8 true Save Parameters :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 QmitkPrototypeSignalParametersWidget QWidget
QmitkPrototypeSignalParametersWidget.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_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_AddNoise m_NoiseLevel m_AddSpikes m_SpikeNumBox m_SpikeScaleBox m_AddGhosts m_kOffsetBox m_AddAliasing m_WrapBox m_AddDistortions m_FrequencyMapBox m_AddMotion m_RandomMotion m_MaxRotationBoxX m_MaxRotationBoxY m_MaxRotationBoxZ m_MaxTranslationBoxX m_MaxTranslationBoxY m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_SaveParametersButton m_LoadParametersButton tabWidget diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp index 6d89e1c8ab..22e1d53838 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp @@ -1,1626 +1,1766 @@ /*=================================================================== 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. ===================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkPreprocessingView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" #include "itkB0ImageExtractionImageFilter.h" #include "itkB0ImageExtractionToSeparateImageFilter.h" #include "itkBrainMaskExtractionImageFilter.h" #include "itkCastImageFilter.h" #include "itkVectorContainer.h" #include #include #include #include // Multishell includes #include // Multishell Functors #include #include #include #include // mitk includes #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "mitkProperties.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkTransferFunction.h" #include "mitkTransferFunctionProperty.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include +#include +#include const std::string QmitkPreprocessingView::VIEW_ID = "org.mitk.views.preprocessing"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; QmitkPreprocessingView::QmitkPreprocessingView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL), m_DiffusionImage(NULL) { } QmitkPreprocessingView::~QmitkPreprocessingView() { } void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkPreprocessingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_MeasurementFrameTable->horizontalHeader()->setResizeMode(QHeaderView::Stretch); m_Controls->m_MeasurementFrameTable->verticalHeader()->setResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->horizontalHeader()->setResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->verticalHeader()->setResizeMode(QHeaderView::Stretch); } } void QmitkPreprocessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkPreprocessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { m_Controls->m_NormalizationMaskBox->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); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); finalPredicate = mitk::NodePredicateAnd::New(finalPredicate, isBinaryPredicate); m_Controls->m_NormalizationMaskBox->SetPredicate(finalPredicate); m_Controls->m_ExtractBrainMask->setVisible(false); m_Controls->m_BrainMaskIterationsBox->setVisible(false); m_Controls->m_ResampleIntFrame->setVisible(false); connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) ); connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) ); connect( (QObject*)(m_Controls->m_ModifyMeasurementFrame), SIGNAL(clicked()), this, SLOT(DoApplyMesurementFrame()) ); connect( (QObject*)(m_Controls->m_ReduceGradientsButton), SIGNAL(clicked()), this, SLOT(DoReduceGradientDirections()) ); connect( (QObject*)(m_Controls->m_ShowGradientsButton), SIGNAL(clicked()), this, SLOT(DoShowGradientDirections()) ); connect( (QObject*)(m_Controls->m_MirrorGradientToHalfSphereButton), SIGNAL(clicked()), this, SLOT(DoHalfSphereGradientDirections()) ); connect( (QObject*)(m_Controls->m_MergeDwisButton), SIGNAL(clicked()), this, SLOT(MergeDwis()) ); connect( (QObject*)(m_Controls->m_ProjectSignalButton), SIGNAL(clicked()), this, SLOT(DoProjectSignal()) ); connect( (QObject*)(m_Controls->m_B_ValueMap_Rounder_SpinBox), SIGNAL(valueChanged(int)), this, SLOT(UpdateDwiBValueMapRounder(int))); connect( (QObject*)(m_Controls->m_CreateLengthCorrectedDwi), SIGNAL(clicked()), this, SLOT(DoLengthCorrection()) ); connect( (QObject*)(m_Controls->m_CalcAdcButton), SIGNAL(clicked()), this, SLOT(DoAdcCalculation()) ); connect( (QObject*)(m_Controls->m_NormalizeImageValuesButton), SIGNAL(clicked()), this, SLOT(DoDwiNormalization()) ); connect( (QObject*)(m_Controls->m_ModifyDirection), SIGNAL(clicked()), this, SLOT(DoApplyDirectionMatrix()) ); connect( (QObject*)(m_Controls->m_ModifySpacingButton), SIGNAL(clicked()), this, SLOT(DoApplySpacing()) ); connect( (QObject*)(m_Controls->m_ModifyOriginButton), SIGNAL(clicked()), this, SLOT(DoApplyOrigin()) ); connect( (QObject*)(m_Controls->m_ResampleImageButton), SIGNAL(clicked()), this, SLOT(DoResampleImage()) ); connect( (QObject*)(m_Controls->m_ResampleTypeBox), SIGNAL(currentIndexChanged(int)), this, SLOT(DoUpdateInterpolationGui(int)) ); connect( (QObject*)(m_Controls->m_CropImageButton), SIGNAL(clicked()), this, SLOT(DoCropImage()) ); + connect( (QObject*)(m_Controls->m_RemoveGradientButton), SIGNAL(clicked()), this, SLOT(DoRemoveGradient()) ); + connect( (QObject*)(m_Controls->m_ExtractGradientButton), SIGNAL(clicked()), this, SLOT(DoExtractGradient()) ); + // connect( (QObject*)(m_Controls->m_ExtractBrainMask), SIGNAL(clicked()), this, SLOT(DoExtractBrainMask()) ); } } +void QmitkPreprocessingView::DoRemoveGradient() +{ + if (m_DiffusionImage.IsNull()) + return; + + std::vector< unsigned int > channelsToRemove; channelsToRemove.push_back(m_Controls->m_RemoveGradientBox->value()); + itk::RemoveDwiChannelFilter< short >::Pointer filter = itk::RemoveDwiChannelFilter< short >::New(); + filter->SetInput(m_DiffusionImage->GetVectorImage()); + filter->SetChannelIndices(channelsToRemove); + filter->SetDirections(m_DiffusionImage->GetDirections()); + filter->Update(); + + MitkDwiType::Pointer image = MitkDwiType::New(); + image->SetVectorImage( filter->GetOutput() ); + image->SetReferenceBValue( m_DiffusionImage->GetReferenceBValue() ); + image->SetDirections( filter->GetNewDirections() ); + image->InitializeFromVectorImage(); + + mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); + imageNode->SetData( image ); + QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); + imageNode->SetName((name+"_removedgradients").toStdString().c_str()); + GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); + mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +} + +void QmitkPreprocessingView::DoExtractGradient() +{ + if (m_DiffusionImage.IsNull()) + return; + + unsigned int channel = m_Controls->m_ExtractGradientBox->value(); + itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); + filter->SetInput(m_DiffusionImage->GetVectorImage()); + filter->SetChannelIndex(channel); + filter->Update(); + + mitk::Image::Pointer mitkImage = mitk::Image::New(); + mitkImage->InitializeByItk( filter->GetOutput() ); + mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); + + mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); + imageNode->SetData( mitkImage ); + QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); + imageNode->SetName((name+"_direction-"+QString::number(channel)).toStdString().c_str()); + GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); + + mitk::RenderingManager::GetInstance()->InitializeViews(imageNode->GetData()->GetTimeGeometry(),mitk::RenderingManager::REQUEST_UPDATE_ALL, true); +} + void QmitkPreprocessingView::DoCropImage() { if (m_DiffusionImage.IsNotNull()) { ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); itk::CropImageFilter< ItkDwiType, ItkDwiType >::Pointer cropper = itk::CropImageFilter< ItkDwiType, ItkDwiType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput(m_DiffusionImage->GetVectorImage()); cropper->Update(); MitkDwiType::Pointer image = MitkDwiType::New(); image->SetVectorImage( cropper->GetOutput() ); image->SetReferenceBValue( m_DiffusionImage->GetReferenceBValue() ); image->SetDirections( m_DiffusionImage->GetDirections() ); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if(m_SelectedImage.IsNotNull()) { AccessFixedDimensionByItk(m_SelectedImage, TemplatedCropImage,3); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedCropImage( itk::Image* itkImage) { ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); typedef itk::Image ImageType; typename itk::CropImageFilter< ImageType, ImageType >::Pointer cropper = itk::CropImageFilter< ImageType, ImageType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput(itkImage); cropper->Update(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( cropper->GetOutput() ); image->SetVolume( cropper->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedImageNode->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedImageNode); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoApplySpacing() { if (m_DiffusionImage.IsNotNull()) { mitk::Vector3D spacing; spacing[0] = m_Controls->m_HeaderSpacingX->value(); spacing[1] = m_Controls->m_HeaderSpacingY->value(); spacing[2] = m_Controls->m_HeaderSpacingZ->value(); MitkDwiType::Pointer image = m_DiffusionImage->Clone(); image->GetVectorImage()->SetSpacing(spacing); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_newspacing").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if(m_SelectedImage.IsNotNull()) { AccessFixedDimensionByItk(m_SelectedImage, TemplatedSetImageSpacing,3); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedSetImageSpacing( itk::Image* itkImage) { mitk::Vector3D spacing; spacing[0] = m_Controls->m_HeaderSpacingX->value(); spacing[1] = m_Controls->m_HeaderSpacingY->value(); spacing[2] = m_Controls->m_HeaderSpacingZ->value(); typedef itk::ImageDuplicator< itk::Image > DuplicateFilterType; typename DuplicateFilterType::Pointer duplicator = DuplicateFilterType::New(); duplicator->SetInputImage( itkImage ); duplicator->Update(); typename itk::Image::Pointer newImage = duplicator->GetOutput(); newImage->SetSpacing(spacing); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( newImage.GetPointer() ); image->SetVolume( newImage->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedImageNode->GetName().c_str(); imageNode->SetName((name+"_newspacing").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedImageNode); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoApplyOrigin() { if (m_DiffusionImage.IsNotNull()) { mitk::Vector3D origin; origin[0] = m_Controls->m_HeaderOriginX->value(); origin[1] = m_Controls->m_HeaderOriginY->value(); origin[2] = m_Controls->m_HeaderOriginZ->value(); MitkDwiType::Pointer image = m_DiffusionImage->Clone(); image->GetVectorImage()->SetOrigin(origin); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_neworigin").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if(m_SelectedImage.IsNotNull()) { AccessFixedDimensionByItk(m_SelectedImage, TemplatedSetImageOrigin,3); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedSetImageOrigin( itk::Image* itkImage) { mitk::Vector3D origin; origin[0] = m_Controls->m_HeaderOriginX->value(); origin[1] = m_Controls->m_HeaderOriginY->value(); origin[2] = m_Controls->m_HeaderOriginZ->value(); typedef itk::ImageDuplicator< itk::Image > DuplicateFilterType; typename DuplicateFilterType::Pointer duplicator = DuplicateFilterType::New(); duplicator->SetInputImage( itkImage ); duplicator->Update(); typename itk::Image::Pointer newImage = duplicator->GetOutput(); newImage->SetOrigin(origin); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( newImage.GetPointer() ); image->SetVolume( newImage->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedImageNode->GetName().c_str(); imageNode->SetName((name+"_neworigin").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedImageNode); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoUpdateInterpolationGui(int i) { switch (i) { case 0: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); break; } case 1: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); if (m_DiffusionImage.IsNotNull()) { ItkDwiType::Pointer itkDwi = m_DiffusionImage->GetVectorImage(); m_Controls->m_ResampleDoubleX->setValue(itkDwi->GetSpacing()[0]); m_Controls->m_ResampleDoubleY->setValue(itkDwi->GetSpacing()[1]); m_Controls->m_ResampleDoubleZ->setValue(itkDwi->GetSpacing()[2]); } else if (m_SelectedImage.IsNotNull()) { mitk::BaseGeometry* geom = m_SelectedImage->GetGeometry(); m_Controls->m_ResampleDoubleX->setValue(geom->GetSpacing()[0]); m_Controls->m_ResampleDoubleY->setValue(geom->GetSpacing()[1]); m_Controls->m_ResampleDoubleZ->setValue(geom->GetSpacing()[2]); } break; } case 2: { m_Controls->m_ResampleIntFrame->setVisible(true); m_Controls->m_ResampleDoubleFrame->setVisible(false); if (m_DiffusionImage.IsNotNull()) { ItkDwiType::Pointer itkDwi = m_DiffusionImage->GetVectorImage(); m_Controls->m_ResampleIntX->setValue(itkDwi->GetLargestPossibleRegion().GetSize(0)); m_Controls->m_ResampleIntY->setValue(itkDwi->GetLargestPossibleRegion().GetSize(1)); m_Controls->m_ResampleIntZ->setValue(itkDwi->GetLargestPossibleRegion().GetSize(2)); } else if (m_SelectedImage.IsNotNull()) { mitk::BaseGeometry* geom = m_SelectedImage->GetGeometry(); m_Controls->m_ResampleIntX->setValue(geom->GetExtent(0)); m_Controls->m_ResampleIntY->setValue(geom->GetExtent(1)); m_Controls->m_ResampleIntZ->setValue(geom->GetExtent(2)); } break; } default: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); } } } void QmitkPreprocessingView::DoExtractBrainMask() { // if (m_SelectedImage.IsNull()) // return; // typedef itk::Image ShortImageType; // ShortImageType::Pointer itkImage = ShortImageType::New(); // mitk::CastToItkImage(m_SelectedImage, itkImage); // typedef itk::BrainMaskExtractionImageFilter< unsigned char > FilterType; // FilterType::Pointer filter = FilterType::New(); // filter->SetInput(itkImage); // filter->SetMaxNumIterations(m_Controls->m_BrainMaskIterationsBox->value()); // filter->Update(); // mitk::Image::Pointer image = mitk::Image::New(); // image->InitializeByItk( filter->GetOutput() ); // image->SetVolume( filter->GetOutput()->GetBufferPointer() ); // mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); // imageNode->SetData( image ); // imageNode->SetName("BRAINMASK"); // GetDefaultDataStorage()->Add(imageNode); } void QmitkPreprocessingView::DoResampleImage() { if (m_DiffusionImage.IsNotNull()) { typedef itk::ResampleDwiImageFilter< short > ResampleFilter; ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput(m_DiffusionImage->GetVectorImage()); switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > samplingFactor; samplingFactor[0] = m_Controls->m_ResampleDoubleX->value(); samplingFactor[1] = m_Controls->m_ResampleDoubleY->value(); samplingFactor[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetSamplingFactor(samplingFactor); break; } case 1: { itk::Vector< double, 3 > newSpacing; newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetNewSpacing(newSpacing); break; } case 2: { itk::ImageRegion<3> newRegion; newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); resampler->SetNewImageSize(newRegion); break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; break; } case 1: { resampler->SetInterpolation(ResampleFilter::Interpolate_Linear); outAdd = "Linear"; break; } case 2: { resampler->SetInterpolation(ResampleFilter::Interpolate_BSpline); outAdd = "BSpline"; break; } case 3: { resampler->SetInterpolation(ResampleFilter::Interpolate_WindowedSinc); outAdd = "WindowedSinc"; break; } default: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; } } resampler->Update(); typedef mitk::DiffusionImage DiffusionImageType; DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( resampler->GetOutput() ); image->SetReferenceBValue( m_DiffusionImage->GetReferenceBValue() ); image->SetDirections( m_DiffusionImage->GetDirections() ); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); } else if (m_SelectedImage.IsNotNull()) { AccessFixedDimensionByItk(m_SelectedImage, TemplatedResampleImage,3); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedResampleImage( itk::Image* itkImage) { itk::Vector< double, 3 > newSpacing; itk::ImageRegion<3> newRegion; switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > sampling; sampling[0] = m_Controls->m_ResampleDoubleX->value(); sampling[1] = m_Controls->m_ResampleDoubleY->value(); sampling[2] = m_Controls->m_ResampleDoubleZ->value(); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 1: { newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); itk::Vector< double, 3 > oldSpacing = itkImage->GetSpacing(); itk::Vector< double, 3 > sampling; sampling[0] = oldSpacing[0]/newSpacing[0]; sampling[1] = oldSpacing[1]/newSpacing[1]; sampling[2] = oldSpacing[2]/newSpacing[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 2: { newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); itk::ImageRegion<3> oldRegion = itkImage->GetLargestPossibleRegion(); itk::Vector< double, 3 > sampling; sampling[0] = (double)newRegion.GetSize(0)/oldRegion.GetSize(0); sampling[1] = (double)newRegion.GetSize(1)/oldRegion.GetSize(1); sampling[2] = (double)newRegion.GetSize(2)/oldRegion.GetSize(2); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } itk::Point origin = itkImage->GetOrigin(); origin[0] -= itkImage->GetSpacing()[0]/2; origin[1] -= itkImage->GetSpacing()[1]/2; origin[2] -= itkImage->GetSpacing()[2]/2; origin[0] += newSpacing[0]/2; origin[1] += newSpacing[1]/2; origin[2] += newSpacing[2]/2; typedef itk::Image ImageType; typename ImageType::Pointer outImage = ImageType::New(); outImage->SetSpacing( newSpacing ); outImage->SetOrigin( origin ); outImage->SetDirection( itkImage->GetDirection() ); outImage->SetLargestPossibleRegion( newRegion ); outImage->SetBufferedRegion( newRegion ); outImage->SetRequestedRegion( newRegion ); outImage->Allocate(); typedef itk::ResampleImageFilter ResampleFilter; typename ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput(itkImage); resampler->SetOutputParametersFromImage(outImage); QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; break; } case 1: { typename itk::LinearInterpolateImageFunction::Pointer interp = itk::LinearInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "Linear"; break; } case 2: { typename itk::BSplineInterpolateImageFunction::Pointer interp = itk::BSplineInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "BSpline"; break; } case 3: { typename itk::WindowedSincInterpolateImageFunction::Pointer interp = itk::WindowedSincInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "WindowedSinc"; break; } default: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; } } resampler->Update(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( resampler->GetOutput() ); image->SetVolume( resampler->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedImageNode->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedImageNode); } void QmitkPreprocessingView::DoApplyDirectionMatrix() { if (m_DiffusionImage.IsNotNull()) { MitkDwiType::Pointer newDwi = m_DiffusionImage->Clone(); ItkDwiType::DirectionType newDirection; for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); if (!item) return; newDirection[r][c] = item->text().toDouble(); } ItkDwiType::Pointer itkDwi = newDwi->GetVectorImage(); typedef mitk::DiffusionImage MitkDwiType; vnl_matrix_fixed< double,3,3 > oldInverseDirection = itkDwi->GetDirection().GetInverse(); MitkDwiType::GradientDirectionContainerType::Pointer oldGradients = m_DiffusionImage->GetDirectionsWithoutMeasurementFrame(); MitkDwiType::GradientDirectionContainerType::Pointer newGradients = MitkDwiType::GradientDirectionContainerType::New(); for (unsigned int i=0; iSize(); i++) { MitkDwiType::GradientDirectionType g = oldGradients->GetElement(i); double mag = g.magnitude(); MitkDwiType::GradientDirectionType newG = oldInverseDirection*g; newG = newDirection.GetVnlMatrix()*newG; newG.normalize(); newGradients->InsertElement(i, newG*mag); } newDwi->SetDirections(newGradients); itkDwi->SetDirection(newDirection); newDwi->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_newdirection").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if (m_SelectedImage.IsNotNull()) { AccessFixedDimensionByItk(m_SelectedImage, TemplatedApplyRotation,3); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedApplyRotation( itk::Image* itkImage) { ItkDwiType::DirectionType newDirection; for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); if (!item) return; newDirection[r][c] = item->text().toDouble(); } typedef itk::Image ImageType; typename ImageType::Pointer newImage = ImageType::New(); newImage->SetSpacing( itkImage->GetSpacing() ); newImage->SetOrigin( itkImage->GetOrigin() ); newImage->SetDirection( newDirection ); newImage->SetLargestPossibleRegion( itkImage->GetLargestPossibleRegion() ); newImage->SetBufferedRegion( itkImage->GetLargestPossibleRegion() ); newImage->SetRequestedRegion( itkImage->GetLargestPossibleRegion() ); newImage->Allocate(); newImage->FillBuffer(0); itk::ImageRegionIterator< itk::Image > it(itkImage, itkImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { newImage->SetPixel(it.GetIndex(), it.Get()); ++it; } mitk::Image::Pointer newMitkImage = mitk::Image::New(); newMitkImage->InitializeByItk(newImage.GetPointer()); newMitkImage->SetVolume(newImage->GetBufferPointer()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newMitkImage ); QString name = m_SelectedImageNode->GetName().c_str(); imageNode->SetName((name+"_newdirection").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedImageNode); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoProjectSignal() { switch(m_Controls->m_ProjectionMethodBox->currentIndex()) { case 0: DoADCAverage(); break; case 1: DoAKCFit(); break; case 2: DoBiExpFit(); break; default: DoADCAverage(); } } void QmitkPreprocessingView::DoDwiNormalization() { if (m_DiffusionImage.IsNull()) return; + int b0Index = -1; + for (unsigned int i=0; iGetNumberOfChannels(); i++) + { + GradientDirectionType g = m_DiffusionImage->GetDirections()->GetElement(i); + if (g.magnitude()<0.001) + { + b0Index = i; + break; + } + } + if (b0Index==-1) + return; + typedef mitk::DiffusionImage DiffusionImageType; typedef itk::DwiNormilzationFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(m_DiffusionImage->GetVectorImage()); filter->SetGradientDirections(m_DiffusionImage->GetDirections()); + UcharImageType::Pointer itkImage = NULL; if (m_Controls->m_NormalizationMaskBox->GetSelectedNode().IsNotNull()) { - UcharImageType::Pointer itkImage = UcharImageType::New(); + itkImage = UcharImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()), itkImage); filter->SetMaskImage(itkImage); } + // determin normalization reference + // { + // itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); + // adcFilter->SetInput(m_DiffusionImage->GetVectorImage()); + // adcFilter->SetGradientDirections(m_DiffusionImage->GetDirections()); + // adcFilter->SetB_value(m_DiffusionImage->GetReferenceBValue()); + // adcFilter->Update(); + // ItkDoubleImageType::Pointer adcImage = adcFilter->GetOutput(); + // itk::ImageRegionIterator inIt(adcImage, adcImage->GetLargestPossibleRegion()); + // double max = 0.0030; + // double ref = 0; + // unsigned int count = 0; + // while ( !inIt.IsAtEnd() ) + // { + // if (itkImage.IsNotNull() && itkImage->GetPixel(inIt.GetIndex())<=0) + // { + // ++inIt; + // continue; + // } + // if (inIt.Get()>max && inIt.Get()<0.004) + // { + // ref += m_DiffusionImage->GetVectorImage()->GetPixel(inIt.GetIndex())[b0Index]; + // count++; + // } + // ++inIt; + // } + // if (count>0) + // { + // ref /= count; + // filter->SetUseGlobalReference(true); + // filter->SetReference(ref); + // } + // } + + // normalize relative to mean white matter signal intensity + { + typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; + TensorReconstructionImageFilterType::Pointer dtFilter = TensorReconstructionImageFilterType::New(); + dtFilter->SetGradientImage( m_DiffusionImage->GetDirections(), m_DiffusionImage->GetVectorImage() ); + dtFilter->SetBValue(m_DiffusionImage->GetReferenceBValue()); + dtFilter->Update(); + itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = dtFilter->GetOutput(); + itk::ImageRegionIterator< itk::Image< itk::DiffusionTensor3D< double >, 3 > > inIt(tensorImage, tensorImage->GetLargestPossibleRegion()); + double ref = 0; + unsigned int count = 0; + while ( !inIt.IsAtEnd() ) + { + if (itkImage.IsNotNull() && itkImage->GetPixel(inIt.GetIndex())<=0) + { + ++inIt; + continue; + } + + double FA = inIt.Get().GetFractionalAnisotropy(); + if (FA>0.4 && FA<0.99) + { + ref += m_DiffusionImage->GetVectorImage()->GetPixel(inIt.GetIndex())[b0Index]; + count++; + } + ++inIt; + } + if (count>0) + { + ref /= count; + filter->SetUseGlobalReference(true); + filter->SetReference(ref); + } + } filter->Update(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( filter->GetOutput() ); image->SetReferenceBValue( m_DiffusionImage->GetReferenceBValue() ); image->SetDirections( m_DiffusionImage->GetDirections() ); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_normalized").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); } void QmitkPreprocessingView::DoLengthCorrection() { if (m_DiffusionImage.IsNull()) return; typedef mitk::DiffusionImage DiffusionImageType; typedef itk::DwiGradientLengthCorrectionFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetRoundingValue( m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); filter->SetReferenceBValue(m_DiffusionImage->GetReferenceBValue()); filter->SetReferenceGradientDirectionContainer(m_DiffusionImage->GetDirections()); filter->Update(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( m_DiffusionImage->GetVectorImage()); image->SetReferenceBValue( filter->GetNewBValue() ); image->SetDirections( filter->GetOutputGradientDirectionContainer()); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_rounded").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); } void QmitkPreprocessingView::UpdateDwiBValueMapRounder(int i) { if (m_DiffusionImage.IsNull()) return; //m_DiffusionImage->UpdateBValueMap(); UpdateBValueTableWidget(i); } void QmitkPreprocessingView::CallMultishellToSingleShellFilter(itk::DWIVoxelFunctor * functor, mitk::DiffusionImage::Pointer ImPtr, QString imageName, mitk::DataNode* parent) { typedef itk::RadialMultishellToSingleshellImageFilter FilterType; // filter input parameter const mitk::DiffusionImage::BValueMap &originalShellMap = ImPtr->GetBValueMap(); const mitk::DiffusionImage::ImageType *vectorImage = ImPtr->GetVectorImage(); const mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientContainer = ImPtr->GetDirections(); const unsigned int &bValue = ImPtr->GetReferenceBValue(); mitk::DataNode::Pointer imageNode = 0; // filter call FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::DiffusionImage::Pointer outImage = mitk::DiffusionImage::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( m_Controls->m_targetBValueSpinBox->value() ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); imageNode = mitk::DataNode::New(); imageNode->SetData( outImage ); imageNode->SetName(imageName.toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, parent); // if(m_Controls->m_OutputRMSErrorImage->isChecked()){ // // create new Error image // FilterType::ErrorImageType::Pointer errImage = filter->GetErrorImage(); // mitk::Image::Pointer mitkErrImage = mitk::Image::New(); // mitkErrImage->InitializeByItk(errImage); // mitkErrImage->SetVolume(errImage->GetBufferPointer()); // imageNode = mitk::DataNode::New(); // imageNode->SetData( mitkErrImage ); // imageNode->SetName((imageName+"_Error").toStdString().c_str()); // GetDefaultDataStorage()->Add(imageNode); // } } void QmitkPreprocessingView::DoBiExpFit() { itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New(); for (unsigned int i=0; i::Pointer inImage = dynamic_cast< mitk::DiffusionImage* >(m_SelectedDiffusionNodes.at(i)->GetData()); QString name(m_SelectedDiffusionNodes.at(i)->GetName().c_str()); const mitk::DiffusionImage::BValueMap & originalShellMap = inImage->GetBValueMap(); mitk::DiffusionImage::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,inImage,name + "_BiExp", m_SelectedDiffusionNodes.at(i)); } } void QmitkPreprocessingView::DoAKCFit() { itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New(); for (unsigned int i=0; i::Pointer inImage = dynamic_cast< mitk::DiffusionImage* >(m_SelectedDiffusionNodes.at(i)->GetData()); QString name(m_SelectedDiffusionNodes.at(i)->GetName().c_str()); const mitk::DiffusionImage::BValueMap & originalShellMap = inImage->GetBValueMap(); mitk::DiffusionImage::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,inImage,name + "_AKC", m_SelectedDiffusionNodes.at(i)); } } void QmitkPreprocessingView::DoADCFit() { // later } void QmitkPreprocessingView::DoADCAverage() { itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New(); for (unsigned int i=0; i::Pointer inImage = dynamic_cast< mitk::DiffusionImage* >(m_SelectedDiffusionNodes.at(i)->GetData()); QString name(m_SelectedDiffusionNodes.at(i)->GetName().c_str()); const mitk::DiffusionImage::BValueMap & originalShellMap = inImage->GetBValueMap(); mitk::DiffusionImage::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,inImage,name + "_ADC", m_SelectedDiffusionNodes.at(i)); } } void QmitkPreprocessingView::DoAdcCalculation() { if (m_DiffusionImage.IsNull()) return; typedef mitk::DiffusionImage< DiffusionPixelType > DiffusionImageType; typedef itk::AdcImageFilter< DiffusionPixelType, double > FilterType; for (unsigned int i=0; i(m_SelectedDiffusionNodes.at(i)->GetData()); FilterType::Pointer filter = FilterType::New(); filter->SetInput(inImage->GetVectorImage()); filter->SetGradientDirections(inImage->GetDirections()); filter->SetB_value(inImage->GetReferenceBValue()); filter->Update(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.at(i)->GetName().c_str(); imageNode->SetName((name+"_ADC").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.at(i)); } } void QmitkPreprocessingView::UpdateBValueTableWidget(int i) { if (m_DiffusionImage.IsNull()) { m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(1); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); m_Controls->m_B_ValueMap_TableWidget->setItem(0,0,new QTableWidgetItem("-")); m_Controls->m_B_ValueMap_TableWidget->setItem(0,1,new QTableWidgetItem("-")); }else{ typedef mitk::DiffusionImage::BValueMap BValueMap; typedef mitk::DiffusionImage::BValueMap::iterator BValueMapIterator; BValueMapIterator it; BValueMap roundedBValueMap = m_DiffusionImage->GetBValueMap(); m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(roundedBValueMap.size() ); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); int i = 0 ; for(it = roundedBValueMap.begin() ;it != roundedBValueMap.end(); it++) { m_Controls->m_B_ValueMap_TableWidget->setItem(i,0,new QTableWidgetItem(QString::number(it->first))); QTableWidgetItem* item = m_Controls->m_B_ValueMap_TableWidget->item(i,0); item->setFlags(item->flags() & ~Qt::ItemIsEditable); m_Controls->m_B_ValueMap_TableWidget->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size()))); i++; } } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedUpdateGui( itk::Image* itkImage) { for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); item->setText(QString::number(itkImage->GetDirection()[r][c])); m_Controls->m_DirectionMatrixTable->setItem(r,c,item); } } void QmitkPreprocessingView::OnSelectionChanged( std::vector nodes ) { bool foundDwiVolume = false; bool foundImageVolume = false; m_DiffusionImage = NULL; m_SelectedImage = NULL; m_SelectedImageNode = NULL; m_SelectedDiffusionNodes.clear(); // iterate selection for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast*>(node->GetData()) ) { foundDwiVolume = true; foundImageVolume = true; m_DiffusionImage = dynamic_cast*>(node->GetData()); m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); m_SelectedDiffusionNodes.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { foundImageVolume = true; m_SelectedImage = dynamic_cast(node->GetData()); m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); m_SelectedImageNode = node; } } m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); m_Controls->m_CheckExtractAll->setEnabled(foundDwiVolume); m_Controls->m_ModifyMeasurementFrame->setEnabled(foundDwiVolume); m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume); m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume); m_Controls->m_MergeDwisButton->setEnabled(foundDwiVolume); m_Controls->m_B_ValueMap_Rounder_SpinBox->setEnabled(foundDwiVolume); m_Controls->m_ProjectSignalButton->setEnabled(foundDwiVolume); m_Controls->m_CreateLengthCorrectedDwi->setEnabled(foundDwiVolume); m_Controls->m_CalcAdcButton->setEnabled(foundDwiVolume); m_Controls->m_targetBValueSpinBox->setEnabled(foundDwiVolume); m_Controls->m_NormalizeImageValuesButton->setEnabled(foundDwiVolume); m_Controls->m_DirectionMatrixTable->setEnabled(foundImageVolume); m_Controls->m_ModifyDirection->setEnabled(foundImageVolume); m_Controls->m_ExtractBrainMask->setEnabled(foundImageVolume); m_Controls->m_ResampleImageButton->setEnabled(foundImageVolume); m_Controls->m_ModifySpacingButton->setEnabled(foundImageVolume); m_Controls->m_ModifyOriginButton->setEnabled(foundImageVolume); m_Controls->m_CropImageButton->setEnabled(foundImageVolume); + m_Controls->m_RemoveGradientButton->setEnabled(foundDwiVolume); + m_Controls->m_ExtractGradientButton->setEnabled(foundDwiVolume); // reset sampling frame to 1 and update all ealted components m_Controls->m_B_ValueMap_Rounder_SpinBox->setValue(1); UpdateBValueTableWidget(m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); DoUpdateInterpolationGui(m_Controls->m_ResampleTypeBox->currentIndex()); if (foundDwiVolume) { m_Controls->m_InputData->setTitle("Input Data"); vnl_matrix_fixed< double, 3, 3 > mf = m_DiffusionImage->GetMeasurementFrame(); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { // Measurement frame { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); item->setText(QString::number(mf.get(r,c))); m_Controls->m_MeasurementFrameTable->setItem(r,c,item); } // Direction matrix { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); item->setText(QString::number(m_DiffusionImage->GetVectorImage()->GetDirection()[r][c])); m_Controls->m_DirectionMatrixTable->setItem(r,c,item); } } //calculate target bValue for MultishellToSingleShellfilter const mitk::DiffusionImage::BValueMap & bValMap = m_DiffusionImage->GetBValueMap(); mitk::DiffusionImage::BValueMap::const_iterator it = bValMap.begin(); unsigned int targetBVal = 0; while(it != bValMap.end()) targetBVal += (it++)->first; targetBVal /= (float)bValMap.size()-1; m_Controls->m_targetBValueSpinBox->setValue(targetBVal); m_Controls->m_HeaderSpacingX->setValue(m_DiffusionImage->GetGeometry()->GetSpacing()[0]); m_Controls->m_HeaderSpacingY->setValue(m_DiffusionImage->GetGeometry()->GetSpacing()[1]); m_Controls->m_HeaderSpacingZ->setValue(m_DiffusionImage->GetGeometry()->GetSpacing()[2]); m_Controls->m_HeaderOriginX->setValue(m_DiffusionImage->GetGeometry()->GetOrigin()[0]); m_Controls->m_HeaderOriginY->setValue(m_DiffusionImage->GetGeometry()->GetOrigin()[1]); m_Controls->m_HeaderOriginZ->setValue(m_DiffusionImage->GetGeometry()->GetOrigin()[2]); m_Controls->m_XstartBox->setMaximum(m_DiffusionImage->GetGeometry()->GetExtent(0)-1); m_Controls->m_YstartBox->setMaximum(m_DiffusionImage->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZstartBox->setMaximum(m_DiffusionImage->GetGeometry()->GetExtent(2)-1); m_Controls->m_XendBox->setMaximum(m_DiffusionImage->GetGeometry()->GetExtent(0)-1); m_Controls->m_YendBox->setMaximum(m_DiffusionImage->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZendBox->setMaximum(m_DiffusionImage->GetGeometry()->GetExtent(2)-1); + m_Controls->m_RemoveGradientBox->setMaximum(m_DiffusionImage->GetDirections()->Size()-1); + m_Controls->m_ExtractGradientBox->setMaximum(m_DiffusionImage->GetDirections()->Size()-1); } else if (foundImageVolume) { for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); delete item; item = new QTableWidgetItem(); m_Controls->m_MeasurementFrameTable->setItem(r,c,item); } m_Controls->m_HeaderSpacingX->setValue(m_SelectedImage->GetGeometry()->GetSpacing()[0]); m_Controls->m_HeaderSpacingY->setValue(m_SelectedImage->GetGeometry()->GetSpacing()[1]); m_Controls->m_HeaderSpacingZ->setValue(m_SelectedImage->GetGeometry()->GetSpacing()[2]); m_Controls->m_HeaderOriginX->setValue(m_SelectedImage->GetGeometry()->GetOrigin()[0]); m_Controls->m_HeaderOriginY->setValue(m_SelectedImage->GetGeometry()->GetOrigin()[1]); m_Controls->m_HeaderOriginZ->setValue(m_SelectedImage->GetGeometry()->GetOrigin()[2]); m_Controls->m_XstartBox->setMaximum(m_SelectedImage->GetGeometry()->GetExtent(0)-1); m_Controls->m_YstartBox->setMaximum(m_SelectedImage->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZstartBox->setMaximum(m_SelectedImage->GetGeometry()->GetExtent(2)-1); m_Controls->m_XendBox->setMaximum(m_SelectedImage->GetGeometry()->GetExtent(0)-1); m_Controls->m_YendBox->setMaximum(m_SelectedImage->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZendBox->setMaximum(m_SelectedImage->GetGeometry()->GetExtent(2)-1); AccessFixedDimensionByItk(m_SelectedImage, TemplatedUpdateGui,3); } else { for (int r=0; r<3; r++) for (int c=0; c<3; c++) { { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); delete item; item = new QTableWidgetItem(); m_Controls->m_MeasurementFrameTable->setItem(r,c,item); } { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); delete item; item = new QTableWidgetItem(); m_Controls->m_DirectionMatrixTable->setItem(r,c,item); } } m_Controls->m_DiffusionImageLabel->setText("mandatory"); m_Controls->m_InputData->setTitle("Please Select Input Data"); } } void QmitkPreprocessingView::Activated() { QmitkFunctionality::Activated(); } void QmitkPreprocessingView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkPreprocessingView::DoHalfSphereGradientDirections() { MitkDwiType::Pointer newDwi = m_DiffusionImage->Clone(); GradientDirectionContainerType::Pointer gradientContainer = newDwi->GetDirections(); for (unsigned int j=0; jSize(); j++) if (gradientContainer->at(j)[0]<0) gradientContainer->at(j) = -gradientContainer->at(j); newDwi->SetDirections(gradientContainer); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_halfsphere").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); } void QmitkPreprocessingView::DoApplyMesurementFrame() { if (m_DiffusionImage.IsNull()) return; vnl_matrix_fixed< double, 3, 3 > mf; for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); if (!item) return; mf[r][c] = item->text().toDouble(); } MitkDwiType::Pointer newDwi = m_DiffusionImage->Clone(); newDwi->SetMeasurementFrame(mf); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = m_SelectedDiffusionNodes.back()->GetName().c_str(); imageNode->SetName((name+"_new-MF").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); } void QmitkPreprocessingView::DoShowGradientDirections() { if (m_DiffusionImage.IsNull()) return; int maxIndex = 0; unsigned int maxSize = m_DiffusionImage->GetDimension(0); if (maxSizeGetDimension(1)) { maxSize = m_DiffusionImage->GetDimension(1); maxIndex = 1; } if (maxSizeGetDimension(2)) { maxSize = m_DiffusionImage->GetDimension(2); maxIndex = 2; } mitk::Point3D origin = m_DiffusionImage->GetGeometry()->GetOrigin(); mitk::PointSet::Pointer originSet = mitk::PointSet::New(); typedef mitk::DiffusionImage::BValueMap BValueMap; typedef mitk::DiffusionImage::BValueMap::iterator BValueMapIterator; BValueMap bValMap = m_DiffusionImage->GetBValueMap(); GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); mitk::BaseGeometry::Pointer geometry = m_DiffusionImage->GetGeometry(); int shellCount = 1; for(BValueMapIterator it = bValMap.begin(); it!=bValMap.end(); ++it) { mitk::PointSet::Pointer pointset = mitk::PointSet::New(); for (unsigned int j=0; jsecond.size(); j++) { mitk::Point3D ip; vnl_vector_fixed< double, 3 > v = gradientContainer->at(it->second[j]); if (v.magnitude()>mitk::eps) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*m_DiffusionImage->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*m_DiffusionImage->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*m_DiffusionImage->GetDimension(2)/2; pointset->InsertPoint(j, ip); } else if (originSet->IsEmpty()) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*m_DiffusionImage->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*m_DiffusionImage->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*m_DiffusionImage->GetDimension(2)/2; originSet->InsertPoint(j, ip); } } if (it->firstSetData(pointset); QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); name += "_Shell_"; name += QString::number(it->first); node->SetName(name.toStdString().c_str()); node->SetProperty("pointsize", mitk::FloatProperty::New((float)maxSize/50)); int b0 = shellCount%2; int b1 = 0; int b2 = 0; if (shellCount>4) b2 = 1; if (shellCount%4 >= 2) b1 = 1; node->SetProperty("color", mitk::ColorProperty::New(b2, b1, b0)); GetDefaultDataStorage()->Add(node, m_SelectedDiffusionNodes.front()); shellCount++; } // add origin to datastorage mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(originSet); QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); name += "_Origin"; node->SetName(name.toStdString().c_str()); node->SetProperty("pointsize", mitk::FloatProperty::New((float)maxSize/50)); node->SetProperty("color", mitk::ColorProperty::New(1,1,1)); GetDefaultDataStorage()->Add(node, m_SelectedDiffusionNodes.front()); } void QmitkPreprocessingView::DoReduceGradientDirections() { if (m_DiffusionImage.IsNull()) return; typedef mitk::DiffusionImage DiffusionImageType; typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter FilterType; typedef DiffusionImageType::BValueMap BValueMap; // GetShellSelection from GUI BValueMap shellSlectionMap; BValueMap originalShellMap = m_DiffusionImage->GetBValueMap(); std::vector newNumGradientDirections; int shellCounter = 0; QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); for (int i=0; im_B_ValueMap_TableWidget->rowCount(); i++) { double BValue = m_Controls->m_B_ValueMap_TableWidget->item(i,0)->text().toDouble(); shellSlectionMap[BValue] = originalShellMap[BValue]; unsigned int num = m_Controls->m_B_ValueMap_TableWidget->item(i,1)->text().toUInt(); newNumGradientDirections.push_back(num); name += "_"; name += QString::number(num); shellCounter++; } if (newNumGradientDirections.empty()) return; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); FilterType::Pointer filter = FilterType::New(); filter->SetInput(m_DiffusionImage->GetVectorImage()); filter->SetOriginalGradientDirections(gradientContainer); filter->SetNumGradientDirections(newNumGradientDirections); filter->SetOriginalBValueMap(originalShellMap); filter->SetShellSelectionBValueMap(shellSlectionMap); filter->Update(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( filter->GetOutput() ); image->SetReferenceBValue(m_DiffusionImage->GetReferenceBValue()); image->SetDirections(filter->GetGradientDirections()); image->SetMeasurementFrame(m_DiffusionImage->GetMeasurementFrame()); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); imageNode->SetName(name.toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, m_SelectedDiffusionNodes.back()); } void QmitkPreprocessingView::MergeDwis() { typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType; if (m_SelectedDiffusionNodes.size()<2) return; typedef itk::VectorImage DwiImageType; typedef DwiImageType::PixelType DwiPixelType; typedef DwiImageType::RegionType DwiRegionType; typedef std::vector< DwiImageType::Pointer > DwiImageContainerType; typedef std::vector< GradientContainerType::Pointer > GradientListContainerType; DwiImageContainerType imageContainer; GradientListContainerType gradientListContainer; std::vector< double > bValueContainer; QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); for (unsigned int i=0; i* >( m_SelectedDiffusionNodes.at(i)->GetData() ); if ( dwi.IsNotNull() ) { imageContainer.push_back(dwi->GetVectorImage()); gradientListContainer.push_back(dwi->GetDirections()); bValueContainer.push_back(dwi->GetReferenceBValue()); if (i>0) { name += "+"; name += m_SelectedDiffusionNodes.at(i)->GetName().c_str(); } } } typedef itk::MergeDiffusionImagesFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetImageVolumes(imageContainer); filter->SetGradientLists(gradientListContainer); filter->SetBValues(bValueContainer); filter->Update(); vnl_matrix_fixed< double, 3, 3 > mf; mf.set_identity(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( filter->GetOutput() ); image->SetReferenceBValue(filter->GetB_Value()); image->SetDirections(filter->GetOutputGradients()); image->SetMeasurementFrame(mf); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); imageNode->SetName(name.toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode); } void QmitkPreprocessingView::ExtractB0() { typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType; int nrFiles = m_SelectedDiffusionNodes.size(); if (!nrFiles) return; // call the extraction withou averaging if the check-box is checked if( this->m_Controls->m_CheckExtractAll->isChecked() ) { DoExtractBOWithoutAveraging(); return; } mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { DiffusionImageType* vols = static_cast( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0")); GetDefaultDataStorage()->Add(node, (*itemiter)); ++itemiter; } } void QmitkPreprocessingView::DoExtractBOWithoutAveraging() { // typedefs typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType; typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType; // check number of selected objects, return if empty int nrFiles = m_SelectedDiffusionNodes.size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() ); while ( itemiter != itemiterend ) // for all items { DiffusionImageType* vols = static_cast( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0_ALL")); GetDefaultDataStorage()->Add(node, (*itemiter)); /*A reinitialization is needed to access the time channels via the ImageNavigationController The Global-Geometry can not recognize the time channel without a re-init. (for a new selection in datamanger a automatically updated of the Global-Geometry should be done - if it contains the time channel)*/ mitk::RenderingManager::GetInstance()->InitializeViews(node->GetData()->GetTimeGeometry(),mitk::RenderingManager::REQUEST_UPDATE_ALL, true); ++itemiter; } - - - } void QmitkPreprocessingView::AverageGradients() { int nrFiles = m_SelectedDiffusionNodes.size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes.begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes.end() ); while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* mitkDwi = static_cast*>( (*itemiter)->GetData()); MitkDwiType::Pointer newDwi = mitkDwi->Clone(); newDwi->AverageRedundantGradients(m_Controls->m_Blur->value()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = (*itemiter)->GetName().c_str(); imageNode->SetName((name+"_averaged").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode, (*itemiter)); ++itemiter; } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h index cde0e98156..4c49a9cd63 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h @@ -1,152 +1,155 @@ /*=================================================================== 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 _QMITKPREPROCESSINGVIEW_H_INCLUDED #define _QMITKPREPROCESSINGVIEW_H_INCLUDED #include #include #include "ui_QmitkPreprocessingViewControls.h" #include "itkDWIVoxelFunctor.h" #include "mitkDiffusionImage.h" typedef short DiffusionPixelType; struct PrpSelListener; /*! * \ingroup org_mitk_gui_qt_preprocessing_internal * * \brief QmitkPreprocessingView * * Document your class here. * * \sa QmitkFunctionality */ class QmitkPreprocessingView : public QmitkFunctionality { friend struct PrpSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; typedef vnl_vector_fixed< double, 3 > GradientDirectionType; typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType; typedef mitk::DiffusionImage MitkDwiType; typedef itk::VectorImage< short, 3 > ItkDwiType; typedef itk::Image< unsigned char, 3 > UcharImageType; + typedef itk::Image< double, 3 > ItkDoubleImageType; QmitkPreprocessingView(); virtual ~QmitkPreprocessingView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); static const int nrconvkernels; protected slots: void AverageGradients(); void ExtractB0(); void MergeDwis(); void DoApplySpacing(); void DoApplyOrigin(); void DoApplyDirectionMatrix(); void DoApplyMesurementFrame(); void DoReduceGradientDirections(); void DoShowGradientDirections(); void DoHalfSphereGradientDirections(); void UpdateDwiBValueMapRounder(int i); void DoLengthCorrection(); void DoAdcCalculation(); void DoDwiNormalization(); void DoProjectSignal(); void DoExtractBrainMask(); void DoResampleImage(); void DoCropImage(); void DoUpdateInterpolationGui(int i); + void DoRemoveGradient(); + void DoExtractGradient(); protected: void DoADCFit(); void DoAKCFit(); void DoBiExpFit(); void DoADCAverage(); template < typename TPixel, unsigned int VImageDimension > void TemplatedCropImage( itk::Image* itkImage); template < typename TPixel, unsigned int VImageDimension > void TemplatedApplyRotation( itk::Image* itkImage); template < typename TPixel, unsigned int VImageDimension > void TemplatedUpdateGui( itk::Image* itkImage); template < typename TPixel, unsigned int VImageDimension > void TemplatedResampleImage( itk::Image* itkImage); template < typename TPixel, unsigned int VImageDimension > void TemplatedSetImageSpacing( itk::Image* itkImage); template < typename TPixel, unsigned int VImageDimension > void TemplatedSetImageOrigin( itk::Image* itkImage); /** Called by ExtractB0 if check-box activated, extracts all b0 images without averaging */ void DoExtractBOWithoutAveraging(); void UpdateBValueTableWidget(int i); /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkPreprocessingViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); mitk::DataNode::Pointer m_SelectedImageNode; mitk::Image::Pointer m_SelectedImage; mitk::DiffusionImage::Pointer m_DiffusionImage; std::vector< mitk::DataNode::Pointer > m_SelectedDiffusionNodes; void CallMultishellToSingleShellFilter(itk::DWIVoxelFunctor * functor, mitk::DiffusionImage::Pointer ImPtr, QString imageName, mitk::DataNode* parent); }; #endif // _QMITKPREPROCESSINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui index 620df7063c..feec6d9844 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui @@ -1,1473 +1,1526 @@ QmitkPreprocessingViewControls 0 0 639 1030 0 0 false QmitkPreprocessingViewControls true Please Select Input Data Image: <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true 0 Gradients Qt::Vertical 20 40 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 false Sometimes the gradient directions are not located on one half sphere. Mirror gradients to half sphere false Round b-values false Retain only the specified number of gradient directions and according image volumes. The retained directions are spread equally over the half sphere using an iterative energy repulsion strategy. Reduce number of gradients <html><head/><body><p>Define the sampling frame the b-Values are rounded with.</p></body></html> Sampling frame: false <html><head/><body><p>Round b-values to nearest multiple of this value (click &quot;Round b-value&quot; to create new image with these values).</p></body></html> QAbstractSpinBox::CorrectToNearestValue 1 10000 10 false Generate pointset displaying the gradient vectors (applied measurement frame). Show gradients 0 0 Qt::ScrollBarAsNeeded Qt::ScrollBarAlwaysOff true 100 true false true b-Value Number of gradients Qt::Horizontal 40 20 Image Values Qt::Vertical 20 40 Resample image QFrame::NoFrame QFrame::Raised 0 0 0 0 0 0.010000000000000 2.000000000000000 0.010000000000000 2.000000000000000 0.010000000000000 2.000000000000000 Sampling factor New image spacing New image size QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Interpolator: Nearest neighbour Linear B-spline Windowed sinc false Resample image QFrame::NoFrame QFrame::Raised 0 0 0 0 0 1 10000 1 10000 1 10000 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 false Project image values onto one b-shell. Project onto shell QFrame::NoFrame QFrame::Raised 0 0 0 0 Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. 6 2.000000000000000 0.000100000000000 0.001000000000000 Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Merge radius false Multiple acquistions of one gradient direction can be averaged. Due to rounding errors, similar gradients often differ in the last decimal positions. The Merge radius allows to average them by taking all directions within a certain radius into account. Average repetitions Select projection method. QFrame::NoFrame QFrame::Raised 0 0 0 0 0 false Target b-value 100000 500 Select projection method. ADC Average AKC Bi-Exponential false Each image value is normalized with the corresponding baseline signal value. Normalize image values false Merges selected DWIs of same dimension. If several b-values are present, the resulting image will contain multiple b-shells. Merge selected DWIs Header - - + + - Qt::Horizontal + Qt::Vertical - 40 - 20 + 20 + 40 Voxel size 0 0 0 4 4 4 0.000000000000000 99.989999999999995 false Set new voxel size - - + + + + Image size + + + + 0 + + + 0 + + + 0 + + + + + y: + + + + + + + Number of pixels to remove on lower image bound. + + + 999999999 + + + + + + + Number of pixels to remove on upper image bound. + + + 999999999 + + + + + + + Number of pixels to remove on upper image bound. + + + 999999999 + + + + + + + Number of pixels to remove on lower image bound. + + + 999999999 + + + + + + + x: + + + + + + + Number of pixels to remove on lower image bound. + + + 999999999 + + + + + + + Number of pixels to remove on upper image bound. + + + 999999999 + + + + + + + z: + + + + + + + false + + + + + + + + + + + + Crop image + + + + + + + + + + Origin + + + + 0 + + + 0 + + + 0 + + + + + 4 + + + -999999999.000000000000000 + + + 999999999.000000000000000 + + + + + + + 4 + + + -999999999.000000000000000 + + + 999999999.000000000000000 + + + + + + + 4 + + + -99999999.000000000000000 + + + 999999999.000000000000000 + + + + + + + false + + + + + + + + + + + + Set new origin + + + + + + + + - Qt::Vertical + Qt::Horizontal - 20 - 40 + 40 + 20 - - - - 0 - 0 - - + - Measurment frame + Direction matrix - + 0 + + 9 + 0 0 - - - - Qt::Horizontal - - - - 40 - 20 - - - - - + false 0 0 0 0 IBeamCursor true Qt::ScrollBarAlwaysOff Qt::ScrollBarAlwaysOff true false false true true 0 false true true New Row New Row New Row New Column New Column New Column - + false Diffusion encoding gradient directions are rotated accordingly. - Apply new measurement frame + Apply new direction + + + + Qt::Horizontal + + + + 40 + 20 + + + + - - + + + + + 0 + 0 + + - Direction matrix + Measurment frame - + 0 - - 9 - 0 0 + + + + Qt::Horizontal + + + + 40 + 20 + + + + - + false 0 0 0 0 IBeamCursor true Qt::ScrollBarAlwaysOff Qt::ScrollBarAlwaysOff true false false true true 0 false true true New Row New Row New Row New Column New Column New Column - + false Diffusion encoding gradient directions are rotated accordingly. - Apply new direction + Apply new measurement frame - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - + + - Origin + Remove or extract gradient volumes - - - 0 - - - 0 - - - 0 - + - - - 4 - - - -999999999.000000000000000 - - - 999999999.000000000000000 - - - - - - - 4 - - - -999999999.000000000000000 - - - 999999999.000000000000000 - - - - - - - 4 - - - -99999999.000000000000000 - - - 999999999.000000000000000 - - - - - + false - + Generate pointset displaying the gradient vectors (applied measurement frame). - Set new origin - - - - - - - - - - Image size - - - - 0 - - - 0 - - - 0 - - - - - Number of pixels to remove on upper image bound. - - - 999999999 - - - - - - - Number of pixels to remove on upper image bound. - - - 999999999 - - - - - - - Number of pixels to remove on lower image bound. - - - 999999999 + Remove - - - y: - - - - - - - x: - - - - - - - Number of pixels to remove on lower image bound. - - - 999999999 - - - - - - - Number of pixels to remove on lower image bound. - - - 999999999 - - - - - - - Number of pixels to remove on upper image bound. - - - 999999999 - - - - - - - z: - - - - - + false - + Generate pointset displaying the gradient vectors (applied measurement frame). - Crop image + Extract + + + + + + Other Create a 3D+t data set containing all b0 images as timesteps Disable averaging false If multiple baseline acquisitions are present, the default behaviour is to output an averaged image. Extract baseline image Qt::Vertical 20 40 false If multiple baseline acquisitions are present, the default behaviour is to output an averaged image. Calculate ADC map false If multiple baseline acquisitions are present, the default behaviour is to output an averaged image. Estimate binary brain mask Maximum number of iterations. 10000 10000 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 m_B_ValueMap_Rounder_SpinBox m_Blur m_targetBValueSpinBox m_ProjectionMethodBox m_NormalizationMaskBox m_ResampleTypeBox m_ResampleDoubleX m_ResampleDoubleY m_ResampleDoubleZ m_ResampleIntX m_ResampleIntY m_ResampleIntZ m_InterpolatorBox m_HeaderSpacingX m_HeaderSpacingY m_HeaderSpacingZ m_HeaderOriginX m_HeaderOriginY m_HeaderOriginZ m_DirectionMatrixTable m_MeasurementFrameTable m_CheckExtractAll m_BrainMaskIterationsBox tabWidget m_B_ValueMap_TableWidget m_CreateLengthCorrectedDwi m_ShowGradientsButton m_MirrorGradientToHalfSphereButton m_ReduceGradientsButton m_ButtonAverageGradients m_ProjectSignalButton m_NormalizeImageValuesButton m_MergeDwisButton m_ResampleImageButton m_ModifySpacingButton m_ModifyOriginButton m_ModifyDirection m_ModifyMeasurementFrame m_ButtonExtractB0 m_CalcAdcButton m_ExtractBrainMask