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 10123892ec..4d24c5ffe9 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp @@ -1,441 +1,459 @@ /*=================================================================== 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 // 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"; + "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) + : 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_ButtonBrainMask), SIGNAL(clicked()), this, SLOT(BrainMask()) ); 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()) ); } } void QmitkPreprocessingView::OnSelectionChanged( std::vector nodes ) { bool foundDwiVolume = false; m_DiffusionImage = NULL; m_SelectedDiffusionNodes = mitk::DataStorage::SetOfObjects::New(); // 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_ButtonBrainMask->setEnabled(foundDwiVolume); 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); if (foundDwiVolume) { 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); } - m_Controls->m_GradientsLabel->setText(QString::number(m_DiffusionImage->GetNumDirections())); - if (m_DiffusionImage->IsMultiBval()) - m_Controls->m_BvalLabel->setText("Acquisition with multiple b-values!"); - else - m_Controls->m_BvalLabel->setText(QString::number(m_DiffusionImage->GetB_Value())); + typedef mitk::DiffusionImage::BValueMap BValueMap; + typedef mitk::DiffusionImage::BValueMap::iterator BValueMapIterator; + + BValueMap bValMap = m_DiffusionImage->GetB_ValueMap(); + BValueMapIterator it = bValMap.begin(); + m_Controls->m_BvalueTable->clear(); + m_Controls->m_BvalueTable->setRowCount(bValMap.size() ); + QStringList headerList; + headerList << "b-Value" << "Number of gradients"; + m_Controls->m_BvalueTable->setHorizontalHeaderLabels(headerList); + int i = 0 ; + for(;it != bValMap.end(); it++) + { + m_Controls->m_BvalueTable->setItem(i,0,new QTableWidgetItem(QString::number(it->first))); + m_Controls->m_BvalueTable->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size()))); + i++; + } + } 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_GradientsLabel->setText("-"); - m_Controls->m_BvalLabel->setText("-"); + m_Controls->m_BvalueTable->clear(); + m_Controls->m_BvalueTable->setRowCount(1); + QStringList headerList; + headerList << "b-Value" << "Number of gradients"; + m_Controls->m_BvalueTable->setHorizontalHeaderLabels(headerList); + m_Controls->m_BvalueTable->setItem(0,0,new QTableWidgetItem("-")); + m_Controls->m_BvalueTable->setItem(0,1,new QTableWidgetItem("-")); m_Controls->m_DiffusionImageLabel->setText("-"); } } void QmitkPreprocessingView::Activated() { QmitkFunctionality::Activated(); } void QmitkPreprocessingView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkPreprocessingView::DoHalfSphereGradientDirections() { if (m_DiffusionImage.IsNull()) return; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetOriginalDirections(); for (int j=0; jSize(); j++) if (gradientContainer->at(j)[0]<0) gradientContainer->at(j) = -gradientContainer->at(j); } 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; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetOriginalDirections(); mitk::PointSet::Pointer pointset = mitk::PointSet::New(); for (int j=0; jSize(); j++) { mitk::Point3D p; vnl_vector_fixed< double, 3 > v = gradientContainer->at(j); if (fabs(v[0])>0.001 || fabs(v[1])>0.001 || fabs(v[2])>0.001) { p[0] = v[0]; p[1] = v[1]; p[2] = v[2]; pointset->InsertPoint(j, p); } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(pointset); node->SetName("gradient directions"); node->SetProperty("pointsize", mitk::FloatProperty::New(0.05)); node->SetProperty("color", mitk::ColorProperty::New(1,0,0)); GetDefaultDataStorage()->Add(node); } void QmitkPreprocessingView::DoReduceGradientDirections() { if (m_DiffusionImage.IsNull()) return; typedef mitk::DiffusionImage DiffusionImageType; typedef itk::ReduceDirectionGradientsFilter FilterType; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetOriginalDirections(); FilterType::Pointer filter = FilterType::New(); filter->SetInput(m_DiffusionImage->GetVectorImage()); filter->SetOriginalGradientDirections(gradientContainer); filter->SetNumGradientDirections(m_Controls->m_ReduceGradientsBox->value()); filter->Update(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(m_DiffusionImage->GetB_Value()); image->SetDirections(filter->GetGradientDirections()); image->SetOriginalDirections(filter->GetGradientDirections()); image->SetMeasurementFrame(m_DiffusionImage->GetMeasurementFrame()); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); imageNode->SetName("reduced_image"); 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()); + 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() ); std::vector< mitk::DataNode::Pointer > nodes; while ( itemiter != itemiterend ) // for all items { DiffusionImageType* vols = - static_cast( - (*itemiter)->GetData()); + 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->SetVolume( 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()); + static_cast*>( + (*itemiter)->GetData()); vols->AverageRedundantGradients(m_Controls->m_Blur->value()); ++itemiter; } } void QmitkPreprocessingView::BrainMask() { 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* vols = - static_cast*>( - (*itemiter)->GetData()); + 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()); typedef itk::CastImageFilter, itk::Image > CastFilterType; CastFilterType::Pointer castfilter = CastFilterType::New(); castfilter->SetInput(filter->GetOutput()); typedef itk::BrainMaskExtractionImageFilter MaskFilterType; MaskFilterType::Pointer maskfilter = MaskFilterType::New(); maskfilter->SetInput(castfilter->GetOutput()); maskfilter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( maskfilter->GetOutput() ); mitkImage->SetVolume( maskfilter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_Mask")); GetDefaultDataStorage()->Add(node); ++itemiter; } } 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 c67d78669e..3fe9f46478 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui @@ -1,529 +1,549 @@ QmitkPreprocessingViewControls 0 0 389 - 913 + 984 0 0 - true + false QmitkPreprocessingViewControls + + true + Data Diffusion Image: - Info - - - QFormLayout::AllNonFixedFieldsGrow - + - - - Number of Gradients: - - - - - - - - - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - - - - - b-Value: + + + + 0 + 0 + - - - - - - - + + Qt::ScrollBarAsNeeded - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter + + Qt::ScrollBarAlwaysOff + + true + + + 100 + + + true + + + false + + + true + + + + b-Value + + + + + Number of gradients + + - + false Generate pointset displaying the gradient vectors. Show gradients + + + + Qt::Horizontal + + + + 40 + 20 + + + + Reduce size 0 70 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 anyway by taking into account all directions within a certain radius. true 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 Average redundant gradients false Mirror all gradients around one axis. Mirror gradients to half sphere Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 New number of gradients: 1 30 false Retain only the specified number of gradient directions and according image volumes. The retained directions are spread equally over the half sphere. Reduce number of gradients Non diffusion weighted image 0 30 Average and extract all images that were acquired without diffusion weighting. true false Extract B0 Create a 3D+t data set containing all b0 images as timesteps Extract all B0 without averaging Brain mask false Estimate binary brain mask 0 0 Measurment frame Qt::Horizontal 40 20 false 0 0 10 10 IBeamCursor true Qt::ScrollBarAlwaysOff Qt::ScrollBarAlwaysOff true false false true true false true true New Row New Row New Row New Column New Column New Column false Apply new mesurement frame Qt::Vertical 20 40