diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp new file mode 100644 index 0000000000..343210387b --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp @@ -0,0 +1,67 @@ +/*=================================================================== + +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. + +===================================================================*/ +/*========================================================================= + +Program: Tensor ToolKit - TTK +Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx $ +Language: C++ +Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $ +Version: $Revision: 68 $ + +Copyright (c) INRIA 2010. All rights reserved. +See LICENSE.txt for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#include "itkDwiGradientLengthCorrectionFilter.h" + +itk::DwiGradientLengthCorrectionFilter::DwiGradientLengthCorrectionFilter() + : m_ReferenceBValue(0) + , m_RoundingValue(0) + , m_ReferenceGradientDirectionContainer(0) + , m_OutputGradientDirectionContainer(0) +{ +} + +itk::DwiGradientLengthCorrectionFilter::~DwiGradientLengthCorrectionFilter() +{ +} + +void itk::DwiGradientLengthCorrectionFilter::GenerateData() +{ + + if(m_ReferenceBValue == 0 || m_RoundingValue == 0 || m_ReferenceGradientDirectionContainer.IsNull()) + itkExceptionMacro("Wrong initialization"); + + m_OutputGradientDirectionContainer = GradientDirectionContainerType::New(); + + std::cout << m_ReferenceBValue << std::endl; + + GradientDirectionContainerType::ConstIterator it = m_ReferenceGradientDirectionContainer->Begin(); + for(; it != m_ReferenceGradientDirectionContainer->End(); ++it) + { + const double twonorm = it.Value().two_norm(); + const double currentBValue = m_ReferenceBValue*twonorm*twonorm ; + const double roundedBValue = int((currentBValue + 0.5 * m_RoundingValue)/m_RoundingValue)*m_RoundingValue; + const double f = roundedBValue/m_ReferenceBValue; + GradientDirectionType grad = it.Value(); + m_OutputGradientDirectionContainer->push_back( grad.normalize() * f ); + } +} diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.h b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.h new file mode 100644 index 0000000000..1c38483c00 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkDwiGradientLengthCorrectionFilter.h @@ -0,0 +1,71 @@ +/*=================================================================== + +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 _itk_DwiGradientLengthCorrectionFilter_h_ +#define _itk_DwiGradientLengthCorrectionFilter_h_ + +#include +#include +#include + +namespace itk +{ + + class DwiGradientLengthCorrectionFilter : public ProcessObject + { + + public: + typedef DwiGradientLengthCorrectionFilter Self; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef ProcessObject Superclass; + + typedef vnl_vector_fixed< double, 3 > GradientDirectionType; + typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType; + + /** Method for creation through the object factory. */ + itkNewMacro(Self) + itkTypeMacro(DwiGradientLengthCorrectionFilter,ProcessObject) + + void GenerateData(); + + virtual void Update(){ + this->GenerateData(); + } + + // input + itkSetMacro(RoundingValue, int) + itkSetMacro(ReferenceBValue, double) + itkSetMacro(ReferenceGradientDirectionContainer, GradientDirectionContainerType::Pointer) + + // output + itkGetMacro(OutputGradientDirectionContainer, GradientDirectionContainerType::Pointer) + + protected: + DwiGradientLengthCorrectionFilter(); + ~DwiGradientLengthCorrectionFilter(); + + double m_ReferenceBValue; + int m_RoundingValue; + + GradientDirectionContainerType::Pointer m_ReferenceGradientDirectionContainer; + GradientDirectionContainerType::Pointer m_OutputGradientDirectionContainer; + }; + + +} // end of namespace + +#endif diff --git a/Modules/DiffusionImaging/DiffusionCore/files.cmake b/Modules/DiffusionImaging/DiffusionCore/files.cmake index 44d1bfa51a..1e12041845 100644 --- a/Modules/DiffusionImaging/DiffusionCore/files.cmake +++ b/Modules/DiffusionImaging/DiffusionCore/files.cmake @@ -1,117 +1,119 @@ 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 IODataStructures/mitkDiffusionCoreObjectFactory.cpp # DataStructures -> DWI IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSource.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageReader.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageIOFactory.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriterFactory.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSerializer.cpp # DataStructures -> QBall IODataStructures/QBallImages/mitkQBallImageSource.cpp IODataStructures/QBallImages/mitkNrrdQBallImageReader.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriter.cpp IODataStructures/QBallImages/mitkNrrdQBallImageIOFactory.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriterFactory.cpp IODataStructures/QBallImages/mitkQBallImage.cpp IODataStructures/QBallImages/mitkQBallImageSerializer.cpp # DataStructures -> Tensor IODataStructures/TensorImages/mitkTensorImageSource.cpp IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriter.cpp IODataStructures/TensorImages/mitkNrrdTensorImageIOFactory.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriterFactory.cpp IODataStructures/TensorImages/mitkTensorImage.cpp IODataStructures/TensorImages/mitkTensorImageSerializer.cpp # Rendering Rendering/vtkMaskedProgrammableGlyphFilter.cpp Rendering/mitkCompositeMapper.cpp Rendering/mitkVectorImageVtkGlyphMapper3D.cpp Rendering/vtkOdfSource.cxx Rendering/vtkThickPlane.cxx Rendering/mitkOdfNormalizationMethodProperty.cpp Rendering/mitkOdfScaleByProperty.cpp Rendering/mitkPlanarFigureMapper3D.cpp # Algorithms Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp + Algorithms/itkDwiGradientLengthCorrectionFilter.cpp # Function Collection mitkDiffusionFunctionCollection.cpp ) set(H_FILES # function Collection mitkDiffusionFunctionCollection.h # Rendering Rendering/mitkDiffusionImageMapper.h Rendering/mitkOdfVtkMapper2D.h Rendering/mitkPlanarFigureMapper3D.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 Algorithms/Reconstruction/itkMultiShellAdcAverageReconstructionImageFilter.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/itkOdfMaximaExtractionFilter.h Algorithms/itkResampleDwiImageFilter.h + Algorithms/itkDwiGradientLengthCorrectionFilter.h ) set( TOOL_FILES ) 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 8fed48bf35..ee60f561c9 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp @@ -1,662 +1,688 @@ /*=================================================================== 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 // 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 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(const QmitkPreprocessingView& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } 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); } } void QmitkPreprocessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkPreprocessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { 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_AdcAverage), SIGNAL(clicked()), this, SLOT(DoAdcAverage()) ); 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()) ); } } +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->GetB_Value()); + filter->SetReferenceGradientDirectionContainer(m_DiffusionImage->GetDirections()); + filter->Update(); + + DiffusionImageType::Pointer image = DiffusionImageType::New(); + image->SetVectorImage( m_DiffusionImage->GetVectorImage()); + image->SetB_Value( m_DiffusionImage->GetB_Value() ); + image->SetDirections( filter->GetOutputGradientDirectionContainer()); + image->InitializeFromVectorImage(); + + mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); + imageNode->SetData( image ); + QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); + + imageNode->SetName((name+"_rounded").toStdString().c_str()); + GetDefaultDataStorage()->Add(imageNode); +} void QmitkPreprocessingView::UpdateDwiBValueMapRounder(int i) { if (m_DiffusionImage.IsNull()) return; m_DiffusionImage->SetB_ValueMap_Rounder(i); m_DiffusionImage->UpdateBValueMap(); UpdateBValueTableWidget(); } void QmitkPreprocessingView::DoAdcAverage() { if (m_DiffusionImage.IsNull()) return; typedef mitk::DiffusionImage DiffusionImageType; typedef itk::MultiShellAdcAverageReconstructionImageFilter FilterType; typedef DiffusionImageType::BValueMap BValueMap; BValueMap originalShellMap = m_DiffusionImage->GetB_ValueMap(); GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); FilterType::Pointer filter = FilterType::New(); filter->SetInput(m_DiffusionImage->GetVectorImage()); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); - filter->SetBValue(m_DiffusionImage->GetB_Value()); + filter->SetB_Value(m_DiffusionImage->GetB_Value()); filter->Update(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( filter->GetOutput() ); - image->SetB_Value( filter->GetTargetBValue() ); + image->SetB_Value( filter->GetTargetB_Value() ); //image->SetOriginalDirections( filter->GetTargetGradientDirections() ); image->SetDirections( filter->GetTargetGradientDirections() ); //image->SetMeasurementFrame( m_DiffusionImage->GetMeasurementFrame() ); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); imageNode->SetName((name+"_averaged").toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode); } void QmitkPreprocessingView::UpdateBValueTableWidget() { + foreach(QCheckBox * box, m_ReduceGradientCheckboxes) + { + m_Controls->m_ReductionFrame->layout()->removeWidget(box); + delete box; + } + foreach(QSpinBox * box, m_ReduceGradientSpinboxes) + { + m_Controls->m_ReductionFrame->layout()->removeWidget(box); + delete box; + } + m_ReduceGradientCheckboxes.clear(); + m_ReduceGradientSpinboxes.clear(); + 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; BValueMap bValMap = m_DiffusionImage->GetB_ValueMap(); BValueMapIterator it = bValMap.begin(); m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(bValMap.size() ); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); QCheckBox* checkBox; QSpinBox* spinBox; int i = 0 ; for(;it != bValMap.end(); it++) { m_Controls->m_B_ValueMap_TableWidget->setItem(i,0,new QTableWidgetItem(QString::number(it->first))); m_Controls->m_B_ValueMap_TableWidget->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size()))); // Reduce Gradients GUI adaption if(it->first != 0 && bValMap.size() > 1){ checkBox = new QCheckBox(QString::number(it->first) + " with " + QString::number(it->second.size()) + " directions"); checkBox->setEnabled(true); checkBox->setChecked(true); checkBox->setCheckable(true); m_ReduceGradientCheckboxes.push_back(checkBox); m_Controls->m_ReductionFrame->layout()->addWidget(checkBox); spinBox = new QSpinBox(); spinBox->setValue(std::ceil((float)it->second.size()/2)); spinBox->setMaximum(it->second.size()); spinBox->setMinimum(0); m_ReduceGradientSpinboxes.push_back(spinBox); m_Controls->m_ReductionFrame->layout()->addWidget(spinBox); } i++; } } } void QmitkPreprocessingView::OnSelectionChanged( std::vector nodes ) { bool foundDwiVolume = false; m_DiffusionImage = 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; m_DiffusionImage = dynamic_cast*>(node->GetData()); m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); m_SelectedDiffusionNodes.push_back(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); if(foundDwiVolume)m_Controls->m_B_ValueMap_Rounder_SpinBox->setValue(m_DiffusionImage->GetB_ValueMap_Rounder()); - - foreach(QCheckBox * box, m_ReduceGradientCheckboxes) - { - m_Controls->m_ReductionFrame->layout()->removeWidget(box); - delete box; - } - foreach(QSpinBox * box, m_ReduceGradientSpinboxes) - { - m_Controls->m_ReductionFrame->layout()->removeWidget(box); - delete box; - } - m_ReduceGradientCheckboxes.clear(); - m_ReduceGradientSpinboxes.clear(); - UpdateBValueTableWidget(); 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++) { 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); } } 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); } 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() { GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); for (int j=0; jSize(); j++) if (gradientContainer->at(j)[0]<0) gradientContainer->at(j) = -gradientContainer->at(j); m_DiffusionImage->SetDirections(gradientContainer); } 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(); } m_DiffusionImage->SetMeasurementFrame(mf); } void QmitkPreprocessingView::DoShowGradientDirections() { if (m_DiffusionImage.IsNull()) return; int maxIndex = 0; 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->GetB_ValueMap(); GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetDirections(); mitk::Geometry3D::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 (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->GetB_ValueMap(); std::vector newNumGradientDirections; int shellCounter = 0; foreach(QCheckBox * box , m_ReduceGradientCheckboxes) { if(box->isChecked()) { double BValue = (box->text().split(' ')).at(0).toDouble(); shellSlectionMap[BValue] = originalShellMap[BValue]; newNumGradientDirections.push_back(m_ReduceGradientSpinboxes.at(shellCounter)->value()); } 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->SetB_Value(m_DiffusionImage->GetB_Value()); image->SetDirections(filter->GetGradientDirections()); image->SetMeasurementFrame(m_DiffusionImage->GetMeasurementFrame()); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = m_SelectedDiffusionNodes.front()->GetName().c_str(); foreach(QSpinBox* box, m_ReduceGradientSpinboxes) { name += "_"; name += QString::number(box->value()); } imageNode->SetName(name.toStdString().c_str()); GetDefaultDataStorage()->Add(imageNode); } 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 (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->GetB_Value()); 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->SetB_Value(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; } } 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; } } 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() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); vols->AverageRedundantGradients(m_Controls->m_Blur->value()); ++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 8741bd1a7f..68fc15c9c7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h @@ -1,113 +1,114 @@ /*=================================================================== 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 "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; QmitkPreprocessingView(); QmitkPreprocessingView(const QmitkPreprocessingView& other); 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 DoApplyMesurementFrame(); void DoReduceGradientDirections(); void DoShowGradientDirections(); void DoHalfSphereGradientDirections(); void DoAdcAverage(); void UpdateDwiBValueMapRounder(int i); + void DoLengthCorrection(); protected: /** Called by ExtractB0 if check-box activated, extracts all b0 images without averaging */ void DoExtractBOWithoutAveraging(); void UpdateBValueTableWidget(); /// \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::DiffusionImage::Pointer m_DiffusionImage; std::vector< mitk::DataNode::Pointer > m_SelectedDiffusionNodes; QList m_ReduceGradientCheckboxes; QList m_ReduceGradientSpinboxes; }; #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 2827d6fc3b..d62a4059ab 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui @@ -1,578 +1,585 @@ QmitkPreprocessingViewControls 0 0 892 - 1114 + 1149 0 0 false QmitkPreprocessingViewControls true Please Select Input Data Raw DWI: <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true 0 0 Info + + + + 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 + + + + <html><head/><body><p>This rounder allowes you to manipulate <a name="result_box"/>the classification of the b-Values to the corresponding shells. But is not manipulating the original b-Values or data.</p></body></html> 1 10000 10 - - - - false - - - Generate pointset displaying the gradient vectors (applied measurement frame). - - - - - - - + + - Show gradients + Create Corrected Diffusion Image - - - - Qt::Horizontal - - - - 40 - 20 - - - - Non diffusion weighted image 0 30 Average and extract all images that were acquired without diffusion weighting. true false If multiple baseline acquisitions are present, the default behaviour is to output an averaged image. Extract B0 Create a 3D+t data set containing all b0 images as timesteps Extract all B0 images without averaging Modify DWI QFrame::NoFrame QFrame::Raised 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 redundant gradients false <html><head/><body><p>Create a new Diffusion Weighted Image (DWI) using an ADC average over all q-shells.</p></body></html> ADC Average (Multi-Shell) Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 9 Specify desired number of gradients per shell: 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 Qt::Horizontal false Sometimes the gradient directions are not located on one half sphere. Mirror gradients to half sphere Merge selected images false Merges selected DWIs of same dimension. If several b-values are present, the resulting image will contain multiple b-shells. Merge selected DWIs 0 0 Measurment frame 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 Apply new measurement frame Qt::Vertical 20 40