diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp index c84f89dbbd..2992c57bd0 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp @@ -1,1256 +1,1274 @@ /*=================================================================== 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 "mitkPartialVolumeAnalysisHistogramCalculator.h" #include "mitkImageAccessByItk.h" #include "mitkExtractImageFilter.h" #include #include #include #include #include #include "itkResampleImageFilter.h" #include "itkGaussianInterpolateImageFunction.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "itkGaussianInterpolateImageFunction.h" #include "itkBSplineInterpolateImageFunction.h" #include "itkNearestNeighborInterpolateImageFunction.h" #include "itkImageMaskSpatialObject.h" #include "itkRegionOfInterestImageFilter.h" #include "itkListSample.h" +#include "mitkAbstractTransformGeometry.h" + #include #include namespace mitk { PartialVolumeAnalysisHistogramCalculator::PartialVolumeAnalysisHistogramCalculator() : m_MaskingMode( MASKING_MODE_NONE ), m_MaskingModeChanged( false ), m_NumberOfBins(256), m_UpsamplingFactor(1), m_GaussianSigma(0), m_ForceUpdate(false), m_PlanarFigureThickness(0) { m_EmptyHistogram = HistogramType::New(); m_EmptyHistogram->SetMeasurementVectorSize(1); HistogramType::SizeType histogramSize(1); histogramSize.Fill( 256 ); m_EmptyHistogram->Initialize( histogramSize ); m_EmptyStatistics.Reset(); } PartialVolumeAnalysisHistogramCalculator::~PartialVolumeAnalysisHistogramCalculator() { } void PartialVolumeAnalysisHistogramCalculator::SetImage( const mitk::Image *image ) { if ( m_Image != image ) { m_Image = image; this->Modified(); m_ImageStatisticsTimeStamp.Modified(); m_ImageStatisticsCalculationTriggerBool = true; } } void PartialVolumeAnalysisHistogramCalculator::AddAdditionalResamplingImage( const mitk::Image *image ) { m_AdditionalResamplingImages.push_back(image); this->Modified(); m_ImageStatisticsTimeStamp.Modified(); m_ImageStatisticsCalculationTriggerBool = true; } void PartialVolumeAnalysisHistogramCalculator::SetModified( ) { this->Modified(); m_ImageStatisticsTimeStamp.Modified(); m_ImageStatisticsCalculationTriggerBool = true; m_MaskedImageStatisticsTimeStamp.Modified(); m_MaskedImageStatisticsCalculationTriggerBool = true; m_PlanarFigureStatisticsTimeStamp.Modified(); m_PlanarFigureStatisticsCalculationTriggerBool = true; } void PartialVolumeAnalysisHistogramCalculator::SetImageMask( const mitk::Image *imageMask ) { if ( m_Image.IsNull() ) { itkExceptionMacro( << "Image needs to be set first!" ); } if ( m_Image->GetTimeSteps() != imageMask->GetTimeSteps() ) { itkExceptionMacro( << "Image and image mask need to have equal number of time steps!" ); } if ( m_ImageMask != imageMask ) { m_ImageMask = imageMask; this->Modified(); m_MaskedImageStatisticsTimeStamp.Modified(); m_MaskedImageStatisticsCalculationTriggerBool = true; } } void PartialVolumeAnalysisHistogramCalculator::SetPlanarFigure( const mitk::PlanarFigure *planarFigure ) { if ( m_Image.IsNull() ) { itkExceptionMacro( << "Image needs to be set first!" ); } if ( m_PlanarFigure != planarFigure ) { m_PlanarFigure = planarFigure; this->Modified(); m_PlanarFigureStatisticsTimeStamp.Modified(); m_PlanarFigureStatisticsCalculationTriggerBool = true; } } void PartialVolumeAnalysisHistogramCalculator::SetMaskingMode( unsigned int mode ) { if ( m_MaskingMode != mode ) { m_MaskingMode = mode; m_MaskingModeChanged = true; this->Modified(); } } void PartialVolumeAnalysisHistogramCalculator::SetMaskingModeToNone() { if ( m_MaskingMode != MASKING_MODE_NONE ) { m_MaskingMode = MASKING_MODE_NONE; m_MaskingModeChanged = true; this->Modified(); } } void PartialVolumeAnalysisHistogramCalculator::SetMaskingModeToImage() { if ( m_MaskingMode != MASKING_MODE_IMAGE ) { m_MaskingMode = MASKING_MODE_IMAGE; m_MaskingModeChanged = true; this->Modified(); } } void PartialVolumeAnalysisHistogramCalculator::SetMaskingModeToPlanarFigure() { if ( m_MaskingMode != MASKING_MODE_PLANARFIGURE ) { m_MaskingMode = MASKING_MODE_PLANARFIGURE; m_MaskingModeChanged = true; this->Modified(); } } bool PartialVolumeAnalysisHistogramCalculator::ComputeStatistics() { MITK_DEBUG << "ComputeStatistics() start"; if ( m_Image.IsNull() ) { itkExceptionMacro( << "Image not set!" ); } if ( m_Image->GetReferenceCount() == 1 ) { MITK_DEBUG << "No Stats calculated; no one else holds a reference on it"; return false; } // If a mask was set but we are the only ones to still hold a reference on // it, delete it. if ( m_ImageMask.IsNotNull() && (m_ImageMask->GetReferenceCount() == 1) ) { m_ImageMask = NULL; } // Check if statistics is already up-to-date unsigned long imageMTime = m_ImageStatisticsTimeStamp.GetMTime(); unsigned long maskedImageMTime = m_MaskedImageStatisticsTimeStamp.GetMTime(); unsigned long planarFigureMTime = m_PlanarFigureStatisticsTimeStamp.GetMTime(); bool imageStatisticsCalculationTrigger = m_ImageStatisticsCalculationTriggerBool; bool maskedImageStatisticsCalculationTrigger = m_MaskedImageStatisticsCalculationTriggerBool; bool planarFigureStatisticsCalculationTrigger = m_PlanarFigureStatisticsCalculationTriggerBool; if ( /*prevent calculation without mask*/!m_ForceUpdate &&( m_MaskingMode == MASKING_MODE_NONE || ( ((m_MaskingMode != MASKING_MODE_NONE) || (imageMTime > m_Image->GetMTime() && !imageStatisticsCalculationTrigger)) && ((m_MaskingMode != MASKING_MODE_IMAGE) || (m_ImageMask.IsNotNull() && maskedImageMTime > m_ImageMask->GetMTime() && !maskedImageStatisticsCalculationTrigger)) && ((m_MaskingMode != MASKING_MODE_PLANARFIGURE) || (m_PlanarFigure.IsNotNull() && planarFigureMTime > m_PlanarFigure->GetMTime() && !planarFigureStatisticsCalculationTrigger)) ) ) ) { MITK_DEBUG << "Returning, statistics already up to date!"; if ( m_MaskingModeChanged ) { m_MaskingModeChanged = false; return true; } else { return false; } } // Reset state changed flag m_MaskingModeChanged = false; // Depending on masking mode, extract and/or generate the required image // and mask data from the user input this->ExtractImageAndMask( ); Statistics *statistics; HistogramType::ConstPointer *histogram; switch ( m_MaskingMode ) { case MASKING_MODE_NONE: default: statistics = &m_ImageStatistics; histogram = &m_ImageHistogram; m_ImageStatisticsTimeStamp.Modified(); m_ImageStatisticsCalculationTriggerBool = false; break; case MASKING_MODE_IMAGE: statistics = &m_MaskedImageStatistics; histogram = &m_MaskedImageHistogram; m_MaskedImageStatisticsTimeStamp.Modified(); m_MaskedImageStatisticsCalculationTriggerBool = false; break; case MASKING_MODE_PLANARFIGURE: statistics = &m_PlanarFigureStatistics; histogram = &m_PlanarFigureHistogram; m_PlanarFigureStatisticsTimeStamp.Modified(); m_PlanarFigureStatisticsCalculationTriggerBool = false; break; } // Calculate statistics and histogram(s) if ( m_InternalImage->GetDimension() == 3 ) { if ( m_MaskingMode == MASKING_MODE_NONE ) { // Reset state changed flag AccessFixedDimensionByItk_2( m_InternalImage, InternalCalculateStatisticsUnmasked, 3, *statistics, histogram ); } else { AccessFixedDimensionByItk_3( m_InternalImage, InternalCalculateStatisticsMasked, 3, m_InternalImageMask3D.GetPointer(), *statistics, histogram ); } } else if ( m_InternalImage->GetDimension() == 2 ) { if ( m_MaskingMode == MASKING_MODE_NONE ) { AccessFixedDimensionByItk_2( m_InternalImage, InternalCalculateStatisticsUnmasked, 2, *statistics, histogram ); } else { AccessFixedDimensionByItk_3( m_InternalImage, InternalCalculateStatisticsMasked, 2, m_InternalImageMask2D.GetPointer(), *statistics, histogram ); } } else { MITK_ERROR << "ImageStatistics: Image dimension not supported!"; } // Release unused image smart pointers to free memory // m_InternalImage = mitk::Image::Pointer(); m_InternalImageMask3D = MaskImage3DType::Pointer(); m_InternalImageMask2D = MaskImage2DType::Pointer(); return true; } const PartialVolumeAnalysisHistogramCalculator::HistogramType * PartialVolumeAnalysisHistogramCalculator::GetHistogram( ) const { if ( m_Image.IsNull() ) { return NULL; } switch ( m_MaskingMode ) { case MASKING_MODE_NONE: default: return m_ImageHistogram; case MASKING_MODE_IMAGE: return m_MaskedImageHistogram; case MASKING_MODE_PLANARFIGURE: return m_PlanarFigureHistogram; } } const PartialVolumeAnalysisHistogramCalculator::Statistics & PartialVolumeAnalysisHistogramCalculator::GetStatistics( ) const { if ( m_Image.IsNull() ) { return m_EmptyStatistics; } switch ( m_MaskingMode ) { case MASKING_MODE_NONE: default: return m_ImageStatistics; case MASKING_MODE_IMAGE: return m_MaskedImageStatistics; case MASKING_MODE_PLANARFIGURE: return m_PlanarFigureStatistics; } } void PartialVolumeAnalysisHistogramCalculator::ExtractImageAndMask( ) { MITK_DEBUG << "ExtractImageAndMask( ) start"; if ( m_Image.IsNull() ) { throw std::runtime_error( "Error: image empty!" ); } mitk::Image *timeSliceImage = const_cast(m_Image.GetPointer());//imageTimeSelector->GetOutput(); switch ( m_MaskingMode ) { case MASKING_MODE_NONE: { m_InternalImage = timeSliceImage; int s = m_AdditionalResamplingImages.size(); m_InternalAdditionalResamplingImages.resize(s); for(int i=0; i(m_AdditionalResamplingImages[i].GetPointer()); } m_InternalImageMask2D = NULL; m_InternalImageMask3D = NULL; break; } case MASKING_MODE_IMAGE: { if ( m_ImageMask.IsNotNull() && (m_ImageMask->GetReferenceCount() > 1) ) { ImageTimeSelector::Pointer maskedImageTimeSelector = ImageTimeSelector::New(); maskedImageTimeSelector->SetInput( m_ImageMask ); maskedImageTimeSelector->SetTimeNr( 0 ); maskedImageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image *timeSliceMaskedImage = maskedImageTimeSelector->GetOutput(); InternalMaskImage(timeSliceMaskedImage); if(m_UpsamplingFactor != 1) { InternalResampleImage(m_InternalImageMask3D); } AccessFixedDimensionByItk_1( timeSliceImage, InternalResampleImageFromMask, 3, -1 ); int s = m_AdditionalResamplingImages.size(); m_InternalAdditionalResamplingImages.resize(s); for(int i=0; iIsClosed() ) { throw std::runtime_error( "Masking not possible for non-closed figures" ); } const BaseGeometry *imageGeometry = timeSliceImage->GetUpdatedGeometry(); if ( imageGeometry == NULL ) { throw std::runtime_error( "Image geometry invalid!" ); } const PlaneGeometry *planarFigureGeometry2D = m_PlanarFigure->GetPlaneGeometry(); if ( planarFigureGeometry2D == NULL ) { throw std::runtime_error( "Planar-Figure not yet initialized!" ); } const PlaneGeometry *planarFigureGeometry = dynamic_cast< const PlaneGeometry * >( planarFigureGeometry2D ); - if ( planarFigureGeometry == NULL ) + const AbstractTransformGeometry *abstrTransfGeometry = + dynamic_cast< const AbstractTransformGeometry * >( planarFigureGeometry2D ); + + if ( !planarFigureGeometry || abstrTransfGeometry ) { - throw std::runtime_error( "Non-planar planar figures not supported!" ); + throw std::runtime_error( "Only PlaneGeometry supported." ); } + // unsigned int axis = 2; // unsigned int slice = 0; AccessFixedDimensionByItk_3( timeSliceImage, InternalReorientImagePlane, 3, timeSliceImage->GetGeometry(), m_PlanarFigure->GetGeometry(), -1 ); AccessFixedDimensionByItk_1( m_InternalImage, InternalCalculateMaskFromPlanarFigure, 3, 2 ); int s = m_AdditionalResamplingImages.size(); for(int i=0; iGetGeometry(), m_PlanarFigure->GetGeometry(), i ); AccessFixedDimensionByItk_1( m_InternalAdditionalResamplingImages[i], InternalCropAdditionalImage, 3, i ); } } } } bool PartialVolumeAnalysisHistogramCalculator::GetPrincipalAxis( const Geometry3D *geometry, Vector3D vector, unsigned int &axis ) { vector.Normalize(); for ( unsigned int i = 0; i < 3; ++i ) { Vector3D axisVector = geometry->GetAxisVector( i ); axisVector.Normalize(); if ( fabs( fabs( axisVector * vector ) - 1.0) < mitk::eps ) { axis = i; return true; } } return false; } void PartialVolumeAnalysisHistogramCalculator::InternalMaskImage( mitk::Image *image ) { typedef itk::ImageMaskSpatialObject<3> ImageMaskSpatialObject; typedef itk::Image< unsigned char, 3 > ImageType; typedef itk::ImageRegion<3> RegionType; typedef mitk::ImageToItk CastType; CastType::Pointer caster = CastType::New(); caster->SetInput(image); caster->Update(); ImageMaskSpatialObject::Pointer maskSO = ImageMaskSpatialObject::New(); maskSO->SetImage ( caster->GetOutput() ); m_InternalMask3D = maskSO->GetAxisAlignedBoundingBoxRegion(); // check if bounding box is empty, if so set it to 1,1,1 // to prevent empty mask image if (m_InternalMask3D.GetSize()[0] == 0 ) { m_InternalMask3D.SetSize(0,1); m_InternalMask3D.SetSize(1,1); m_InternalMask3D.SetSize(2,1); } MITK_DEBUG << "Bounding Box Region: " << m_InternalMask3D; typedef itk::RegionOfInterestImageFilter< ImageType, MaskImage3DType > ROIFilterType; ROIFilterType::Pointer roi = ROIFilterType::New(); roi->SetRegionOfInterest(m_InternalMask3D); roi->SetInput(caster->GetOutput()); roi->Update(); m_InternalImageMask3D = roi->GetOutput(); MITK_DEBUG << "Created m_InternalImageMask3D"; } template < typename TPixel, unsigned int VImageDimension > void PartialVolumeAnalysisHistogramCalculator::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::BaseGeometry* , mitk::BaseGeometry* planegeo3D, int additionalIndex ) { MITK_DEBUG << "InternalReorientImagePlane() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< float, VImageDimension > FloatImageType; typedef itk::ResampleImageFilter ResamplerType; typename ResamplerType::Pointer resampler = ResamplerType::New(); mitk::PlaneGeometry* planegeo = dynamic_cast(planegeo3D); + if ( !planegeo ) + { + throw std::runtime_error( "Unexpected null pointer returned for pointer to PlaneGeometry." ); + } + else + { + mitk::AbstractTransformGeometry* abstrGeo = dynamic_cast(planegeo3D); + if ( abstrGeo ) + { + throw std::runtime_error( "Unexpected pointer to AbstractTransformGeometry returned." ); + } + } float upsamp = m_UpsamplingFactor; float gausssigma = m_GaussianSigma; // Spacing typename ResamplerType::SpacingType spacing = planegeo->GetSpacing(); spacing[0] = image->GetSpacing()[0] / upsamp; spacing[1] = image->GetSpacing()[1] / upsamp; spacing[2] = image->GetSpacing()[2]; if(m_PlanarFigureThickness) { spacing[2] = image->GetSpacing()[2] / upsamp; } resampler->SetOutputSpacing( spacing ); // Size typename ResamplerType::SizeType size; size[0] = planegeo->GetExtentInMM(0) / spacing[0]; size[1] = planegeo->GetExtentInMM(1) / spacing[1]; size[2] = 1+2*m_PlanarFigureThickness; // klaus add +2*m_PlanarFigureThickness MITK_DEBUG << "setting size2:="<SetSize( size ); // Origin typename mitk::Point3D orig = planegeo->GetOrigin(); typename mitk::Point3D corrorig; planegeo3D->WorldToIndex(orig,corrorig); corrorig[0] += 0.5/upsamp; corrorig[1] += 0.5/upsamp; if(m_PlanarFigureThickness) { float thickyyy = m_PlanarFigureThickness; thickyyy/=upsamp; corrorig[2] -= thickyyy; // klaus add -= (float)m_PlanarFigureThickness/upsamp statt += 0 } planegeo3D->IndexToWorld(corrorig,corrorig); resampler->SetOutputOrigin(corrorig ); // Direction typename ResamplerType::DirectionType direction; typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix(); for(int c=0; cSetOutputDirection( direction ); // Gaussian interpolation if(gausssigma != 0) { double sigma[3]; for( unsigned int d = 0; d < 3; d++ ) { sigma[d] = gausssigma * image->GetSpacing()[d]; } double alpha = 2.0; typedef itk::GaussianInterpolateImageFunction GaussianInterpolatorType; typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New(); interpolator->SetInputImage( image ); interpolator->SetParameters( sigma, alpha ); resampler->SetInterpolator( interpolator ); } else { // typedef typename itk::BSplineInterpolateImageFunction // InterpolatorType; typedef typename itk::LinearInterpolateImageFunction InterpolatorType; typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); interpolator->SetInputImage( image ); resampler->SetInterpolator( interpolator ); } // Other resampling options resampler->SetInput( image ); resampler->SetDefaultPixelValue(0); MITK_DEBUG << "Resampling requested image plane ... "; resampler->Update(); MITK_DEBUG << " ... done"; if(additionalIndex < 0) { this->m_InternalImage = mitk::Image::New(); this->m_InternalImage->InitializeByItk( resampler->GetOutput() ); this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() ); } else { unsigned int myIndex = additionalIndex; this->m_InternalAdditionalResamplingImages.push_back(mitk::Image::New()); this->m_InternalAdditionalResamplingImages[myIndex]->InitializeByItk( resampler->GetOutput() ); this->m_InternalAdditionalResamplingImages[myIndex]->SetVolume( resampler->GetOutput()->GetBufferPointer() ); } } template < typename TPixel, unsigned int VImageDimension > void PartialVolumeAnalysisHistogramCalculator::InternalResampleImageFromMask( const itk::Image< TPixel, VImageDimension > *image, int additionalIndex ) { typedef itk::Image< TPixel, VImageDimension > ImageType; typename ImageType::Pointer outImage = ImageType::New(); outImage->SetSpacing( m_InternalImageMask3D->GetSpacing() ); // Set the image spacing outImage->SetOrigin( m_InternalImageMask3D->GetOrigin() ); // Set the image origin outImage->SetDirection( m_InternalImageMask3D->GetDirection() ); // Set the image direction outImage->SetRegions( m_InternalImageMask3D->GetLargestPossibleRegion() ); outImage->Allocate(); outImage->FillBuffer(0); typedef itk::InterpolateImageFunction BaseInterpType; typedef itk::GaussianInterpolateImageFunction GaussianInterpolatorType; typedef itk::LinearInterpolateImageFunction LinearInterpolatorType; typename BaseInterpType::Pointer interpolator; if(m_GaussianSigma != 0) { double sigma[3]; for( unsigned int d = 0; d < 3; d++ ) { sigma[d] = m_GaussianSigma * image->GetSpacing()[d]; } double alpha = 2.0; interpolator = GaussianInterpolatorType::New(); dynamic_cast(interpolator.GetPointer())->SetParameters( sigma, alpha ); } else { interpolator = LinearInterpolatorType::New(); } interpolator->SetInputImage( image ); itk::ImageRegionConstIterator itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itk::ImageRegionIterator itimage(outImage, outImage->GetLargestPossibleRegion()); itmask.GoToBegin(); itimage.GoToBegin(); itk::Point< double, 3 > point; itk::ContinuousIndex< double, 3 > index; while( !itmask.IsAtEnd() ) { if(itmask.Get() != 0) { outImage->TransformIndexToPhysicalPoint (itimage.GetIndex(), point); image->TransformPhysicalPointToContinuousIndex(point, index); itimage.Set(interpolator->EvaluateAtContinuousIndex(index)); } ++itmask; ++itimage; } if(additionalIndex < 0) { this->m_InternalImage = mitk::Image::New(); this->m_InternalImage->InitializeByItk( outImage.GetPointer() ); this->m_InternalImage->SetVolume( outImage->GetBufferPointer() ); } else { this->m_InternalAdditionalResamplingImages[additionalIndex] = mitk::Image::New(); this->m_InternalAdditionalResamplingImages[additionalIndex]->InitializeByItk( outImage.GetPointer() ); this->m_InternalAdditionalResamplingImages[additionalIndex]->SetVolume( outImage->GetBufferPointer() ); } } void PartialVolumeAnalysisHistogramCalculator::InternalResampleImage( const MaskImage3DType *image ) { typedef itk::ResampleImageFilter ResamplerType; ResamplerType::Pointer resampler = ResamplerType::New(); // Size ResamplerType::SizeType size; size[0] = m_UpsamplingFactor * image->GetLargestPossibleRegion().GetSize()[0]; size[1] = m_UpsamplingFactor * image->GetLargestPossibleRegion().GetSize()[1]; size[2] = m_UpsamplingFactor * image->GetLargestPossibleRegion().GetSize()[2];; resampler->SetSize( size ); // Origin mitk::Point3D orig = image->GetOrigin(); resampler->SetOutputOrigin(orig ); // Spacing ResamplerType::SpacingType spacing; spacing[0] = image->GetSpacing()[0] / m_UpsamplingFactor; spacing[1] = image->GetSpacing()[1] / m_UpsamplingFactor; spacing[2] = image->GetSpacing()[2] / m_UpsamplingFactor; resampler->SetOutputSpacing( spacing ); resampler->SetOutputDirection( image->GetDirection() ); typedef itk::NearestNeighborInterpolateImageFunction InterpolatorType; InterpolatorType::Pointer interpolator = InterpolatorType::New(); interpolator->SetInputImage( image ); resampler->SetInterpolator( interpolator ); // Other resampling options resampler->SetInput( image ); resampler->SetDefaultPixelValue(0); resampler->Update(); m_InternalImageMask3D = resampler->GetOutput(); } template < typename TPixel, unsigned int VImageDimension > void PartialVolumeAnalysisHistogramCalculator::InternalCalculateStatisticsUnmasked( const itk::Image< TPixel, VImageDimension > *image, Statistics &statistics, typename HistogramType::ConstPointer *histogram ) { MITK_DEBUG << "InternalCalculateStatisticsUnmasked()"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< unsigned char, VImageDimension > MaskImageType; typedef typename ImageType::IndexType IndexType; // Progress listening... typedef itk::SimpleMemberCommand< PartialVolumeAnalysisHistogramCalculator > ITKCommandType; ITKCommandType::Pointer progressListener; progressListener = ITKCommandType::New(); progressListener->SetCallbackFunction( this, &PartialVolumeAnalysisHistogramCalculator::UnmaskedStatisticsProgressUpdate ); // Issue 100 artificial progress events since ScalarIMageToHistogramGenerator // does not (yet?) support progress reporting this->InvokeEvent( itk::StartEvent() ); for ( unsigned int i = 0; i < 100; ++i ) { this->UnmaskedStatisticsProgressUpdate(); } // Calculate statistics (separate filter) typedef itk::StatisticsImageFilter< ImageType > StatisticsFilterType; typename StatisticsFilterType::Pointer statisticsFilter = StatisticsFilterType::New(); statisticsFilter->SetInput( image ); unsigned long observerTag = statisticsFilter->AddObserver( itk::ProgressEvent(), progressListener ); statisticsFilter->Update(); statisticsFilter->RemoveObserver( observerTag ); this->InvokeEvent( itk::EndEvent() ); statistics.N = image->GetBufferedRegion().GetNumberOfPixels(); statistics.Min = statisticsFilter->GetMinimum(); statistics.Max = statisticsFilter->GetMaximum(); statistics.Mean = statisticsFilter->GetMean(); statistics.Median = 0.0; statistics.Sigma = statisticsFilter->GetSigma(); statistics.RMS = sqrt( statistics.Mean * statistics.Mean + statistics.Sigma * statistics.Sigma ); typename ImageType::Pointer inImage = const_cast(image); // Calculate histogram typedef itk::Statistics::ScalarImageToHistogramGenerator< ImageType > HistogramGeneratorType; typename HistogramGeneratorType::Pointer histogramGenerator = HistogramGeneratorType::New(); histogramGenerator->SetInput( inImage ); histogramGenerator->SetMarginalScale( 10 ); // Defines y-margin width of histogram histogramGenerator->SetNumberOfBins( m_NumberOfBins ); // CT range [-1024, +2048] --> bin size 4 values histogramGenerator->SetHistogramMin( statistics.Min ); histogramGenerator->SetHistogramMax( statistics.Max ); histogramGenerator->Compute(); *histogram = histogramGenerator->GetOutput(); } template < typename TPixel, unsigned int VImageDimension > void PartialVolumeAnalysisHistogramCalculator::InternalCalculateStatisticsMasked( const itk::Image< TPixel, VImageDimension > *image, itk::Image< unsigned char, VImageDimension > *maskImage, Statistics &, typename HistogramType::ConstPointer *histogram ) { MITK_DEBUG << "InternalCalculateStatisticsMasked() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< unsigned char, VImageDimension > MaskImageType; typedef typename ImageType::IndexType IndexType; // generate a list sample of angles at positions // where the fiber-prob is higher than .2*maxprob typedef TPixel MeasurementType; const unsigned int MeasurementVectorLength = 1; typedef itk::Vector< MeasurementType , MeasurementVectorLength > MeasurementVectorType; typedef itk::Statistics::ListSample< MeasurementVectorType > ListSampleType; typename ListSampleType::Pointer listSample = ListSampleType::New(); listSample->SetMeasurementVectorSize( MeasurementVectorLength ); itk::ImageRegionConstIterator itmask(maskImage, maskImage->GetLargestPossibleRegion()); itk::ImageRegionConstIterator itimage(image, image->GetLargestPossibleRegion()); itmask.GoToBegin(); itimage.GoToBegin(); while( !itmask.IsAtEnd() ) { if(itmask.Get() != 0) { // apend to list MeasurementVectorType mv; mv[0] = ( MeasurementType ) itimage.Get(); listSample->PushBack(mv); } ++itmask; ++itimage; } // generate a histogram from the list sample typedef double HistogramMeasurementType; typedef itk::Statistics::Histogram< HistogramMeasurementType, itk::Statistics::DenseFrequencyContainer2 > HistogramType; typedef itk::Statistics::SampleToHistogramFilter< ListSampleType, HistogramType > GeneratorType; typename GeneratorType::Pointer generator = GeneratorType::New(); typename GeneratorType::HistogramType::SizeType size(MeasurementVectorLength); size.Fill(m_NumberOfBins); generator->SetHistogramSize( size ); generator->SetInput( listSample ); generator->SetMarginalScale( 10.0 ); generator->Update(); *histogram = generator->GetOutput(); } template < typename TPixel, unsigned int VImageDimension > void PartialVolumeAnalysisHistogramCalculator::InternalCropAdditionalImage( itk::Image< TPixel, VImageDimension > *image, int additionalIndex ) { typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::RegionOfInterestImageFilter< ImageType, ImageType > ROIFilterType; typename ROIFilterType::Pointer roi = ROIFilterType::New(); roi->SetRegionOfInterest(m_CropRegion); roi->SetInput(image); roi->Update(); m_InternalAdditionalResamplingImages[additionalIndex] = mitk::Image::New(); m_InternalAdditionalResamplingImages[additionalIndex]->InitializeByItk(roi->GetOutput()); m_InternalAdditionalResamplingImages[additionalIndex]->SetVolume(roi->GetOutput()->GetBufferPointer()); } template < typename TPixel, unsigned int VImageDimension > void PartialVolumeAnalysisHistogramCalculator::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis ) { MITK_DEBUG << "InternalCalculateMaskFromPlanarFigure() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::CastImageFilter< ImageType, MaskImage3DType > CastFilterType; // Generate mask image as new image with same header as input image and // initialize with "1". MaskImage3DType::Pointer newMaskImage = MaskImage3DType::New(); newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction newMaskImage->SetRegions( image->GetLargestPossibleRegion() ); newMaskImage->Allocate(); newMaskImage->FillBuffer( 1 ); // Generate VTK polygon from (closed) PlanarFigure polyline // (The polyline points are shifted by -0.5 in z-direction to make sure // that the extrusion filter, which afterwards elevates all points by +0.5 // in z-direction, creates a 3D object which is cut by the the plane z=0) const mitk::PlaneGeometry *planarFigureGeometry2D = m_PlanarFigure->GetPlaneGeometry(); const typename PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const mitk::BaseGeometry *imageGeometry3D = m_InternalImage->GetGeometry( 0 ); vtkPolyData *polyline = vtkPolyData::New(); polyline->Allocate( 1, 1 ); // Determine x- and y-dimensions depending on principal axis int i0, i1; switch ( axis ) { case 0: i0 = 1; i1 = 2; break; case 1: i0 = 0; i1 = 2; break; case 2: default: i0 = 0; i1 = 1; break; } // Create VTK polydata object of polyline contour bool outOfBounds = false; vtkPoints *points = vtkPoints::New(); typename PlanarFigure::PolyLineType::const_iterator it; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; // Convert 2D point back to the local index coordinates of the selected // image mitk::Point2D point2D = *it; planarFigureGeometry2D->WorldToIndex(point2D, point2D); point2D[0] -= 0.5/m_UpsamplingFactor; point2D[1] -= 0.5/m_UpsamplingFactor; planarFigureGeometry2D->IndexToWorld(point2D, point2D); planarFigureGeometry2D->Map( point2D, point3D ); // Polygons (partially) outside of the image bounds can not be processed // further due to a bug in vtkPolyDataToImageStencil if ( !imageGeometry3D->IsInside( point3D ) ) { outOfBounds = true; } imageGeometry3D->WorldToIndex( point3D, point3D ); point3D[i0] += 0.5; point3D[i1] += 0.5; // Add point to polyline array points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); } polyline->SetPoints( points ); points->Delete(); if ( outOfBounds ) { polyline->Delete(); throw std::runtime_error( "Figure at least partially outside of image bounds!" ); } std::size_t numberOfPoints = planarFigurePolyline.size(); vtkIdType *ptIds = new vtkIdType[numberOfPoints]; for ( std::size_t i = 0; i < numberOfPoints; ++i ) { ptIds[i] = i; } polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds ); // Extrude the generated contour polygon vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New(); extrudeFilter->SetInputData( polyline ); extrudeFilter->SetScaleFactor( 1 ); extrudeFilter->SetExtrusionTypeToNormalExtrusion(); extrudeFilter->SetVector( 0.0, 0.0, 1.0 ); // Make a stencil from the extruded polygon vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New(); polyDataToImageStencil->SetInputConnection( extrudeFilter->GetOutputPort() ); // Export from ITK to VTK (to use a VTK filter) typedef itk::VTKImageImport< MaskImage3DType > ImageImportType; typedef itk::VTKImageExport< MaskImage3DType > ImageExportType; typename ImageExportType::Pointer itkExporter = ImageExportType::New(); itkExporter->SetInput( newMaskImage ); vtkImageImport *vtkImporter = vtkImageImport::New(); this->ConnectPipelines( itkExporter, vtkImporter ); vtkImporter->Update(); // Apply the generated image stencil to the input image vtkImageStencil *imageStencilFilter = vtkImageStencil::New(); imageStencilFilter->SetInputData( vtkImporter->GetOutput() ); imageStencilFilter->SetStencilConnection(polyDataToImageStencil->GetOutputPort() ); imageStencilFilter->ReverseStencilOff(); imageStencilFilter->SetBackgroundValue( 0 ); imageStencilFilter->Update(); // Export from VTK back to ITK vtkImageExport *vtkExporter = vtkImageExport::New(); vtkExporter->SetInputData( imageStencilFilter->GetOutput() ); vtkExporter->Update(); typename ImageImportType::Pointer itkImporter = ImageImportType::New(); this->ConnectPipelines( vtkExporter, itkImporter ); itkImporter->Update(); // calculate cropping bounding box m_InternalImageMask3D = itkImporter->GetOutput(); m_InternalImageMask3D->SetDirection(image->GetDirection()); itk::ImageRegionIterator itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itmask.GoToBegin(); while( !itmask.IsAtEnd() ) { if(itmask.Get() != 0) { typename ImageType::IndexType index = itmask.GetIndex(); for(unsigned int thick=0; thick<2*m_PlanarFigureThickness+1; thick++) { index[axis] = thick; m_InternalImageMask3D->SetPixel(index, itmask.Get()); } } ++itmask; } itmask.GoToBegin(); itk::ImageRegionIterator itimage(image, image->GetLargestPossibleRegion()); itimage.GoToBegin(); typename ImageType::SizeType lowersize; lowersize.Fill(std::numeric_limits::max()); typename ImageType::SizeType uppersize; uppersize.Fill(std::numeric_limits::min()); while( !itmask.IsAtEnd() ) { if(itmask.Get() == 0) { itimage.Set(0); } else { typename ImageType::IndexType index = itimage.GetIndex(); typename ImageType::SizeType signedindex; signedindex[0] = index[0]; signedindex[1] = index[1]; signedindex[2] = index[2]; lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0]; lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1]; lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2]; uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0]; uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1]; uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2]; } ++itmask; ++itimage; } typename ImageType::IndexType index; index[0] = lowersize[0]; index[1] = lowersize[1]; index[2] = lowersize[2]; typename ImageType::SizeType size; size[0] = uppersize[0] - lowersize[0] + 1; size[1] = uppersize[1] - lowersize[1] + 1; size[2] = uppersize[2] - lowersize[2] + 1; m_CropRegion = itk::ImageRegion<3>(index, size); // crop internal image typedef itk::RegionOfInterestImageFilter< ImageType, ImageType > ROIFilterType; typename ROIFilterType::Pointer roi = ROIFilterType::New(); roi->SetRegionOfInterest(m_CropRegion); roi->SetInput(image); roi->Update(); m_InternalImage = mitk::Image::New(); m_InternalImage->InitializeByItk(roi->GetOutput()); m_InternalImage->SetVolume(roi->GetOutput()->GetBufferPointer()); // crop internal mask typedef itk::RegionOfInterestImageFilter< MaskImage3DType, MaskImage3DType > ROIMaskFilterType; typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New(); roi2->SetRegionOfInterest(m_CropRegion); roi2->SetInput(m_InternalImageMask3D); roi2->Update(); m_InternalImageMask3D = roi2->GetOutput(); // Clean up VTK objects polyline->Delete(); extrudeFilter->Delete(); polyDataToImageStencil->Delete(); vtkImporter->Delete(); imageStencilFilter->Delete(); //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak?? delete[] ptIds; } void PartialVolumeAnalysisHistogramCalculator::UnmaskedStatisticsProgressUpdate() { // Need to throw away every second progress event to reach a final count of // 100 since two consecutive filters are used in this case static int updateCounter = 0; if ( updateCounter++ % 2 == 0 ) { this->InvokeEvent( itk::ProgressEvent() ); } } void PartialVolumeAnalysisHistogramCalculator::MaskedStatisticsProgressUpdate() { this->InvokeEvent( itk::ProgressEvent() ); } } diff --git a/Modules/Ext/Algorithms/mitkPointSetToCurvedGeometryFilter.cpp b/Modules/Ext/Algorithms/mitkPointSetToCurvedGeometryFilter.cpp index 5b0941bdf6..77c36f225c 100644 --- a/Modules/Ext/Algorithms/mitkPointSetToCurvedGeometryFilter.cpp +++ b/Modules/Ext/Algorithms/mitkPointSetToCurvedGeometryFilter.cpp @@ -1,165 +1,178 @@ /*=================================================================== 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 "mitkPointSetToCurvedGeometryFilter.h" #include "mitkThinPlateSplineCurvedGeometry.h" #include "mitkPlaneGeometry.h" #include "mitkImage.h" #include "mitkDataNode.h" #include "mitkGeometryData.h" #include "mitkPlaneGeometryData.h" #include "mitkProperties.h" #include "itkMesh.h" #include "itkPointSet.h" mitk::PointSetToCurvedGeometryFilter::PointSetToCurvedGeometryFilter() { m_ProjectionMode = YZPlane; m_PCAPlaneCalculator = mitk::PlaneFit::New(); m_ImageToBeMapped = NULL; m_Sigma = 1000; mitk::PlaneGeometryData::Pointer output = static_cast ( this->MakeOutput ( 0 ).GetPointer() ); output->Initialize(); Superclass::SetNumberOfRequiredOutputs ( 1 ); Superclass::SetNthOutput ( 0, output.GetPointer() ); } mitk::PointSetToCurvedGeometryFilter::~PointSetToCurvedGeometryFilter() {} void mitk::PointSetToCurvedGeometryFilter::GenerateOutputInformation() { mitk::PointSet::ConstPointer input = this->GetInput(); mitk::PlaneGeometryData::Pointer output = dynamic_cast ( this->GetOutput() ); if ( input.IsNull() ) itkGenericExceptionMacro ( "Input point set is NULL!" ); if ( input->GetTimeGeometry()->CountTimeSteps() != 1 ) itkWarningMacro ( "More than one time step is not yet supported!" ); if ( output.IsNull() ) itkGenericExceptionMacro ( "Output is NULL!" ); if ( m_ImageToBeMapped.IsNull() ) itkGenericExceptionMacro ( "Image to be mapped is NULL!" ); bool update = false; if ( output->GetGeometry() == NULL || output->GetPlaneGeometry() == NULL || output->GetTimeGeometry() == NULL ) update = true; if ( ( ! update ) && ( output->GetTimeGeometry()->CountTimeSteps() != input->GetTimeGeometry()->CountTimeSteps() ) ) update = true; if ( update ) { mitk::ThinPlateSplineCurvedGeometry::Pointer curvedGeometry = mitk::ThinPlateSplineCurvedGeometry::New(); output->SetGeometry(curvedGeometry); } } void mitk::PointSetToCurvedGeometryFilter::GenerateData() { mitk::PointSet::ConstPointer input = this->GetInput(); mitk::GeometryData::Pointer output = this->GetOutput(); // // check preconditions // if ( input.IsNull() ) itkGenericExceptionMacro ( "Input point set is NULL!" ); if ( output.IsNull() ) itkGenericExceptionMacro ( "output geometry data is NULL!" ); if ( output->GetTimeGeometry() == NULL ) itkGenericExceptionMacro ( "Output time sliced geometry is NULL!" ); if ( output->GetTimeGeometry()->GetGeometryForTimeStep ( 0 ).IsNull() ) itkGenericExceptionMacro ( "Output geometry3d is NULL!" ); mitk::ThinPlateSplineCurvedGeometry::Pointer curvedGeometry = dynamic_cast ( output->GetTimeGeometry()->GetGeometryForTimeStep( 0 ).GetPointer() ); if ( curvedGeometry.IsNull() ) itkGenericExceptionMacro ( "Output geometry3d is not an instance of mitk::ThinPlateSPlineCurvedGeometry!" ); if ( m_ImageToBeMapped.IsNull() ) itkGenericExceptionMacro ( "Image to be mapped is NULL!" ); // // initialize members if needed // if ( m_XYPlane.IsNull() || m_XZPlane.IsNull() || m_YZPlane.IsNull() ) { m_ImageToBeMapped->UpdateOutputInformation(); const mitk::BaseGeometry* imageGeometry = m_ImageToBeMapped->GetUpdatedGeometry(); imageGeometry = m_ImageToBeMapped->GetUpdatedGeometry(); m_XYPlane = mitk::PlaneGeometry::New(); m_XZPlane = mitk::PlaneGeometry::New(); m_YZPlane = mitk::PlaneGeometry::New(); m_XYPlane->InitializeStandardPlane ( imageGeometry, mitk::PlaneGeometry::Axial ); m_YZPlane->InitializeStandardPlane ( imageGeometry, mitk::PlaneGeometry::Sagittal ); m_XZPlane->InitializeStandardPlane ( imageGeometry, mitk::PlaneGeometry::Frontal ); } if ( m_PlaneLandmarkProjector.IsNull() ) { m_PlaneLandmarkProjector = mitk::PlaneLandmarkProjector::New(); m_SphereLandmarkProjector = mitk::SphereLandmarkProjector::New(); } // // set up geometry according to the current settings // if ( m_ProjectionMode == Sphere ) { curvedGeometry->SetLandmarkProjector ( m_SphereLandmarkProjector ); } else { if ( m_ProjectionMode == XYPlane ) m_PlaneLandmarkProjector->SetProjectionPlane ( m_XYPlane ); else if ( m_ProjectionMode == XZPlane ) m_PlaneLandmarkProjector->SetProjectionPlane ( m_XZPlane ); else if ( m_ProjectionMode == YZPlane ) m_PlaneLandmarkProjector->SetProjectionPlane ( m_YZPlane ); else if ( m_ProjectionMode == PCAPlane ) { itkExceptionMacro ( "PCAPlane not yet implemented!" ); m_PCAPlaneCalculator->SetInput ( input ); m_PCAPlaneCalculator->Update(); - m_PlaneLandmarkProjector->SetProjectionPlane ( dynamic_cast ( m_PCAPlaneCalculator->GetOutput() ) ); + + const PlaneGeometry *planarFigureGeometry = + dynamic_cast< const PlaneGeometry * >( m_PCAPlaneCalculator->GetOutput() ); + const AbstractTransformGeometry *abstrTransfGeometry = + dynamic_cast< const AbstractTransformGeometry * >( m_PCAPlaneCalculator->GetOutput() ); + + if ( !planarFigureGeometry || abstrTransfGeometry ) + { + m_PlaneLandmarkProjector->SetProjectionPlane ( NULL ); + } + else + { + m_PlaneLandmarkProjector->SetProjectionPlane ( planarFigureGeometry ); + } } else itkExceptionMacro ( "Unknown projection mode" ); curvedGeometry->SetLandmarkProjector ( m_PlaneLandmarkProjector ); } //curvedGeometry->SetReferenceGeometry( m_ImageToBeMapped->GetGeometry() ); curvedGeometry->SetTargetLandmarks ( input->GetPointSet ( 0 )->GetPoints() ); curvedGeometry->SetSigma ( m_Sigma ); curvedGeometry->ComputeGeometry(); curvedGeometry->SetOversampling ( 1.0 ); } void mitk::PointSetToCurvedGeometryFilter::SetDefaultCurvedGeometryProperties ( mitk::DataNode* node ) { if ( node == NULL ) { itkGenericOutputMacro ( "Warning: node is NULL!" ); return; } node->SetIntProperty ( "xresolution", 50 ); node->SetIntProperty ( "yresolution", 50 ); node->SetProperty ( "name", mitk::StringProperty::New ( "Curved Plane" ) ); // exclude extent of this plane when calculating DataStorage bounding box node->SetProperty ( "includeInBoundingBox", mitk::BoolProperty::New ( false ) ); }