diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataView.cpp old mode 100644 new mode 100755 index b4cf3217e0..4d83a87d16 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataView.cpp @@ -1,370 +1,388 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // ####### Blueberry includes ####### #include #include // ####### Qmitk includes ####### #include "QmitkConnectomicsDataView.h" #include "QmitkStdMultiWidget.h" // ####### Qt includes ####### #include // ####### ITK includes ####### #include // ####### MITK includes ####### #include #include "mitkConnectomicsSyntheticNetworkGenerator.h" #include "mitkConnectomicsSimulatedAnnealingManager.h" #include "mitkConnectomicsSimulatedAnnealingPermutationModularity.h" #include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h" //#include // Includes for image casting between ITK and MITK #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" +#include const std::string QmitkConnectomicsDataView::VIEW_ID = "org.mitk.views.connectomicsdata"; QmitkConnectomicsDataView::QmitkConnectomicsDataView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_ConnectomicsNetworkCreator( mitk::ConnectomicsNetworkCreator::New() ) , m_demomode( false ) , m_currentIndex( 0 ) { } QmitkConnectomicsDataView::~QmitkConnectomicsDataView() { } void QmitkConnectomicsDataView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkConnectomicsDataViewControls; m_Controls->setupUi( parent ); QObject::connect( m_Controls->networkifyPushButton, SIGNAL(clicked()), this, SLOT(OnNetworkifyPushButtonClicked()) ); QObject::connect( m_Controls->syntheticNetworkCreationPushButton, SIGNAL(clicked()), this, SLOT(OnSyntheticNetworkCreationPushButtonClicked()) ); QObject::connect( (QObject*)( m_Controls->syntheticNetworkComboBox ), SIGNAL(currentIndexChanged (int)), this, SLOT(OnSyntheticNetworkComboBoxCurrentIndexChanged(int)) ); } // GUI is different for developer and demo mode m_demomode = true; if( m_demomode ) { this->m_Controls->networkifyPushButton->show(); this->m_Controls->networkifyPushButton->setText( "Create Network" ); this->m_Controls->syntheticNetworkOptionsGroupBox->show(); //--------------------------- fill comboBox--------------------------- this->m_Controls->syntheticNetworkComboBox->insertItem(0,"Regular lattice"); this->m_Controls->syntheticNetworkComboBox->insertItem(1,"Heterogenic sphere"); this->m_Controls->syntheticNetworkComboBox->insertItem(2,"Random network"); } else { this->m_Controls->networkifyPushButton->show(); this->m_Controls->networkifyPushButton->setText( "Networkify" ); this->m_Controls->syntheticNetworkOptionsGroupBox->show(); //--------------------------- fill comboBox--------------------------- this->m_Controls->syntheticNetworkComboBox->insertItem(0,"Regular lattice"); this->m_Controls->syntheticNetworkComboBox->insertItem(1,"Heterogenic sphere"); this->m_Controls->syntheticNetworkComboBox->insertItem(2,"Random network"); this->m_Controls->syntheticNetworkComboBox->insertItem(3,"Scale free network"); this->m_Controls->syntheticNetworkComboBox->insertItem(4,"Small world network"); } this->WipeDisplay(); } void QmitkConnectomicsDataView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkConnectomicsDataView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkConnectomicsDataView::WipeDisplay() { m_Controls->lblWarning->setVisible( true ); m_Controls->inputImageOneNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->inputImageOneNameLabel->setVisible( false ); m_Controls->inputImageOneLabel->setVisible( false ); m_Controls->inputImageTwoNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->inputImageTwoNameLabel->setVisible( false ); m_Controls->inputImageTwoLabel->setVisible( false ); } void QmitkConnectomicsDataView::OnSelectionChanged( std::vector nodes ) { this->WipeDisplay(); // Valid options are either // 1 image (parcellation) // // 1 image (parcellation) // 1 fiber bundle // // 1 network if( nodes.size() < 2 ) { return; } m_SelectedParcellationImage = NULL; m_SelectedFiberBundles.clear(); bool alreadyImageSelected( false ), currentFormatUnknown( true ); // iterate all selected objects, adjust warning visibility for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; currentFormatUnknown = true; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { currentFormatUnknown = false; if( alreadyImageSelected ) { this->WipeDisplay(); return; } m_SelectedParcellationImage = node; alreadyImageSelected = true; m_Controls->lblWarning->setVisible( false ); m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str()); m_Controls->inputImageOneNameLabel->setVisible( true ); m_Controls->inputImageOneLabel->setVisible( true ); } if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { currentFormatUnknown = false; // a fiber bundle has to be in conjunction with a parcellation if( nodes.size() < 2 ) { this->WipeDisplay(); return; } m_SelectedFiberBundles.push_back(node); m_Controls->lblWarning->setVisible( false ); m_Controls->inputImageTwoNameLabel->setText(node->GetName().c_str()); m_Controls->inputImageTwoNameLabel->setVisible( true ); m_Controls->inputImageTwoLabel->setVisible( true ); } { // network section mitk::ConnectomicsNetwork* network = dynamic_cast( node->GetData() ); if( node.IsNotNull() && network ) { currentFormatUnknown = false; if( nodes.size() != 1 ) { // only valid option is a single network this->WipeDisplay(); return; } m_Controls->lblWarning->setVisible( false ); m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str()); m_Controls->inputImageOneNameLabel->setVisible( true ); m_Controls->inputImageOneLabel->setVisible( true ); } } // end network section if ( currentFormatUnknown ) { this->WipeDisplay(); return; } } // end for loop } void QmitkConnectomicsDataView::OnSyntheticNetworkComboBoxCurrentIndexChanged(int currentIndex) { m_currentIndex = currentIndex; switch (m_currentIndex) { case 0: this->m_Controls->parameterOneLabel->setText( "Nodes per side" ); this->m_Controls->parameterTwoLabel->setText( "Internode distance" ); this->m_Controls->parameterOneSpinBox->setEnabled( true ); this->m_Controls->parameterOneSpinBox->setValue( 5 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true ); this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 999.999 ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 10.0 ); break; case 1: this->m_Controls->parameterOneLabel->setText( "Number of nodes" ); this->m_Controls->parameterTwoLabel->setText( "Radius" ); this->m_Controls->parameterOneSpinBox->setEnabled( true ); this->m_Controls->parameterOneSpinBox->setValue( 1000 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true ); this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 999.999 ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 50.0 ); break; case 2: this->m_Controls->parameterOneLabel->setText( "Number of nodes" ); this->m_Controls->parameterTwoLabel->setText( "Edge percentage" ); this->m_Controls->parameterOneSpinBox->setEnabled( true ); this->m_Controls->parameterOneSpinBox->setValue( 100 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true ); this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 1.0 ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 0.5 ); break; case 3: //GenerateSyntheticScaleFreeNetwork( network, 1000 ); break; case 4: //GenerateSyntheticSmallWorldNetwork( network, 1000 ); break; default: this->m_Controls->parameterOneLabel->setText( "Parameter 1" ); this->m_Controls->parameterTwoLabel->setText( "Paramater 2" ); this->m_Controls->parameterOneSpinBox->setEnabled( false ); this->m_Controls->parameterOneSpinBox->setValue( 0 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( false ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 0.0 ); } } void QmitkConnectomicsDataView::OnSyntheticNetworkCreationPushButtonClicked() { // warn if trying to create a very big network // big network is a network with > 5000 nodes (estimate) // this might fill up the memory to the point it freezes int numberOfNodes( 0 ); switch (m_currentIndex) { case 0: numberOfNodes = this->m_Controls->parameterOneSpinBox->value() * this->m_Controls->parameterOneSpinBox->value() * this->m_Controls->parameterOneSpinBox->value(); break; case 1: numberOfNodes = this->m_Controls->parameterOneSpinBox->value(); break; case 2: numberOfNodes = this->m_Controls->parameterOneSpinBox->value(); break; case 3: // not implemented yet break; case 4: // not implemented yet break; default: break; } if( numberOfNodes > 5000 ) { QMessageBox msgBox; msgBox.setText("Trying to generate very large network."); msgBox.setIcon( QMessageBox::Warning ); msgBox.setInformativeText("You are trying to generate a network with more than 5000 nodes, this is very resource intensive and might lead to program instability. Proceed with network generation?"); msgBox.setStandardButtons(QMessageBox::Yes | QMessageBox::No); msgBox.setDefaultButton(QMessageBox::No); int ret = msgBox.exec(); switch (ret) { case QMessageBox::Yes: // continue break; case QMessageBox::No: // stop return; break; default: // should never be reached break; } } // proceed mitk::ConnectomicsSyntheticNetworkGenerator::Pointer generator = mitk::ConnectomicsSyntheticNetworkGenerator::New(); mitk::DataNode::Pointer networkNode = mitk::DataNode::New(); int parameterOne = this->m_Controls->parameterOneSpinBox->value(); double parameterTwo = this->m_Controls->parameterTwoDoubleSpinBox->value(); //add network to datastorage networkNode->SetData( generator->CreateSyntheticNetwork( m_currentIndex, parameterOne, parameterTwo ) ); networkNode->SetName( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_CNF_NAME ); if( generator->WasGenerationSuccessfull() ) { this->GetDefaultDataStorage()->Add( networkNode ); } else { MITK_WARN << "Problem occured during synthetic network generation."; } return; } +#include + void QmitkConnectomicsDataView::OnNetworkifyPushButtonClicked() { if ( m_SelectedParcellationImage.IsNull() || m_SelectedFiberBundles.empty() ) { QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING); return; } mitk::Image::Pointer image = dynamic_cast< mitk::Image* >(m_SelectedParcellationImage->GetData()); for (int i=0; i( m_SelectedFiberBundles.at(i)->GetData() ); m_ConnectomicsNetworkCreator= mitk::ConnectomicsNetworkCreator::New(); m_ConnectomicsNetworkCreator->SetSegmentation( image ); m_ConnectomicsNetworkCreator->SetFiberBundle( fiberBundle ); m_ConnectomicsNetworkCreator->CalculateCenterOfMass(); m_ConnectomicsNetworkCreator->SetEndPointSearchRadius( 15 ); m_ConnectomicsNetworkCreator->CreateNetworkFromFibersAndSegmentation(); mitk::DataNode::Pointer networkNode = mitk::DataNode::New(); + //add network to datastorage - QString name(m_SelectedFiberBundles.at(i)->GetName().c_str()); - name += "_Connectome"; + QString name("/local/data/Fibercup/connectomics/networks/"); + name += m_SelectedFiberBundles.at(i)->GetName().c_str(); + name += "_Connectome.cnf"; networkNode->SetData( m_ConnectomicsNetworkCreator->GetNetwork() ); networkNode->SetName( name.toStdString().c_str() ); - this->GetDefaultDataStorage()->Add( networkNode, m_SelectedParcellationImage ); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + + mitk::ConnectomicsNetwork::Pointer nw = m_ConnectomicsNetworkCreator->GetNetwork(); + + mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); + for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) + { + if ( (*it)->CanWriteBaseDataType(nw.GetPointer()) ) { + MITK_INFO << "writing " << name.toStdString(); + (*it)->SetFileName( name.toStdString().c_str() ); + (*it)->DoWrite( nw.GetPointer() ); + } + } + + //this->GetDefaultDataStorage()->Add( networkNode, m_SelectedParcellationImage ); + //mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataView.h old mode 100644 new mode 100755 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsDataViewControls.ui old mode 100644 new mode 100755 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.cpp old mode 100644 new mode 100755 index cea47effc9..d5d585637f --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.cpp @@ -1,481 +1,507 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // ####### Blueberry includes ####### #include #include // ####### Qmitk includes ####### #include "QmitkConnectomicsNetworkOperationsView.h" #include "QmitkStdMultiWidget.h" // ####### Qt includes ####### #include // ####### ITK includes ####### #include // ####### MITK includes ####### #include #include "mitkConnectomicsSimulatedAnnealingManager.h" #include "mitkConnectomicsSimulatedAnnealingPermutationModularity.h" #include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h" #include +#include // Includes for image casting between ITK and MITK #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" const std::string QmitkConnectomicsNetworkOperationsView::VIEW_ID = "org.mitk.views.connectomicsnetworkoperations"; QmitkConnectomicsNetworkOperationsView::QmitkConnectomicsNetworkOperationsView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_demomode( false ) , m_currentIndex( 0 ) { } QmitkConnectomicsNetworkOperationsView::~QmitkConnectomicsNetworkOperationsView() { } void QmitkConnectomicsNetworkOperationsView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkConnectomicsNetworkOperationsViewControls; m_Controls->setupUi( parent ); QObject::connect( m_Controls->convertToRGBAImagePushButton, SIGNAL(clicked()), this, SLOT(OnConvertToRGBAImagePushButtonClicked()) ); QObject::connect( (QObject*)( m_Controls->modularizePushButton ), SIGNAL(clicked()), this, SLOT(OnModularizePushButtonClicked()) ); QObject::connect( (QObject*)( m_Controls->prunePushButton ), SIGNAL(clicked()), this, SLOT(OnPrunePushButtonClicked()) ); QObject::connect( (QObject*)( m_Controls->createConnectivityMatrixImagePushButton ), SIGNAL(clicked()), this, SLOT(OnCreateConnectivityMatrixImagePushButtonClicked()) ); } // GUI is different for developer and demo mode m_demomode = true; if( m_demomode ) { this->m_Controls->convertToRGBAImagePushButton->show(); this->m_Controls->modularizePushButton->hide(); this->m_Controls->pruneOptionsGroupBox->hide(); } else { this->m_Controls->convertToRGBAImagePushButton->show(); this->m_Controls->modularizePushButton->show(); this->m_Controls->pruneOptionsGroupBox->show(); } this->WipeDisplay(); } void QmitkConnectomicsNetworkOperationsView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkConnectomicsNetworkOperationsView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkConnectomicsNetworkOperationsView::WipeDisplay() { m_Controls->lblWarning->setVisible( true ); m_Controls->inputImageOneNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->inputImageOneNameLabel->setVisible( false ); m_Controls->inputImageOneLabel->setVisible( false ); } void QmitkConnectomicsNetworkOperationsView::OnSelectionChanged( std::vector nodes ) { this->WipeDisplay(); // Valid options are either if( nodes.size() > 2 ) { return; } bool currentFormatUnknown(true), alreadyImageSelected(false); // iterate all selected objects, adjust warning visibility for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; currentFormatUnknown = true; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { currentFormatUnknown = false; if( alreadyImageSelected ) { this->WipeDisplay(); return; } alreadyImageSelected = true; m_Controls->lblWarning->setVisible( false ); m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str()); m_Controls->inputImageOneNameLabel->setVisible( true ); m_Controls->inputImageOneLabel->setVisible( true ); } if( node.IsNotNull() ) { // network section mitk::ConnectomicsNetwork* network = dynamic_cast( node->GetData() ); if( network ) { currentFormatUnknown = false; if( nodes.size() != 1 ) { // only valid option is a single network this->WipeDisplay(); return; } m_Controls->lblWarning->setVisible( false ); m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str()); m_Controls->inputImageOneNameLabel->setVisible( true ); m_Controls->inputImageOneLabel->setVisible( true ); } } // end network section if ( currentFormatUnknown ) { this->WipeDisplay(); return; } } // end for loop } void QmitkConnectomicsNetworkOperationsView::OnConvertToRGBAImagePushButtonClicked() { std::vector nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode* node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image) mitk::BaseData* data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image* image = dynamic_cast( data ); if (image) { std::stringstream message; std::string name; message << mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_PERFORMING_IMAGE_PROCESSING_FOR_IMAGE; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; } message << "."; MITK_INFO << message.str(); // Convert to RGBA AccessByItk( image, TurnIntoRGBA ); this->GetDefaultDataStorage()->GetNamedNode( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME )->GetData()->SetGeometry( node->GetData()->GetGeometry() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else { QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING); return; } } else { QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING); return; } } template < typename TPixel, unsigned int VImageDimension > void QmitkConnectomicsNetworkOperationsView::TurnIntoRGBA( itk::Image* inputImage) { typedef itk::RGBAPixel< unsigned char > RGBAPixelType; typedef itk::Image< TPixel, VImageDimension > TemplateImageType; typedef itk::Image< RGBAPixelType, VImageDimension > RGBAImageType; itk::ImageRegionIterator it_inputImage(inputImage, inputImage->GetLargestPossibleRegion()); TPixel minimumValue, maximumValue; it_inputImage.GoToBegin(); maximumValue = minimumValue = it_inputImage.Value(); for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage) { if ( it_inputImage.Value() < minimumValue ) { minimumValue = it_inputImage.Value(); } else { if ( it_inputImage.Value() > maximumValue ) { maximumValue = it_inputImage.Value(); } } } int range = int ( maximumValue - minimumValue ); //needs to be castable to int int offset = int ( minimumValue ); if ( range < 0 ) //error { return; } std::vector< unsigned int > histogram; histogram.resize( range + 1, 0 ); for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage) { histogram[ int ( it_inputImage.Value() ) - offset ] += 1; } int gapCounter = 0; //this variable will be used to count the empty labels //stores how much has to be subtracted from the image to remove gaps std::vector< TPixel > subtractionStorage; subtractionStorage.resize( range + 1, 0 ); for( int index = 0; index <= range; index++ ) { if( histogram[ index ] == 0 ) { gapCounter++; //if the label is empty, increase gapCounter } else { subtractionStorage[ index ] = TPixel ( gapCounter ); } } //remove gaps from label image for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage) { it_inputImage.Value() = it_inputImage.Value() - subtractionStorage[int ( it_inputImage.Value() ) - offset ]; } // create colour vector std::vector< RGBAPixelType > lookupTable; { RGBAPixelType backgroundColour; for( int elementIndex = 0; elementIndex < 4; ++elementIndex ) { backgroundColour.SetElement( elementIndex, 0 ); } lookupTable.push_back( backgroundColour ); for(int colourNumber = 0; colourNumber < range ; ++colourNumber) { RGBAPixelType colour; for( int elementIndex = 0; elementIndex < 3; ++elementIndex ) { colour.SetElement( elementIndex, rand() % 256 ); } colour.SetAlpha( 255 ); lookupTable.push_back( colour ); } } // create RGBA image typename RGBAImageType::Pointer rgbaImage = RGBAImageType::New(); rgbaImage->SetRegions(inputImage->GetLargestPossibleRegion().GetSize()); rgbaImage->SetSpacing(inputImage->GetSpacing()); rgbaImage->SetOrigin(inputImage->GetOrigin()); rgbaImage->Allocate(); //fill with appropriate colours itk::ImageRegionIterator it_rgbaImage(rgbaImage, rgbaImage->GetLargestPossibleRegion()); for(it_inputImage.GoToBegin(), it_rgbaImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage, ++it_rgbaImage) { it_rgbaImage.Value() = lookupTable[ int ( it_inputImage.Value() ) - offset ]; } mitk::Image::Pointer mitkRGBAImage = mitk::ImportItkImage( rgbaImage )->Clone(); mitk::DataNode::Pointer rgbaImageNode = mitk::DataNode::New(); rgbaImageNode->SetData(mitkRGBAImage); rgbaImageNode->SetProperty(mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_NAME, mitk::StringProperty::New(mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME)); rgbaImageNode->SetBoolProperty( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_VOLUMERENDERING, true); this->GetDefaultDataStorage()->Add( rgbaImageNode ); } void QmitkConnectomicsNetworkOperationsView::OnModularizePushButtonClicked() { std::vector nodes = this->GetDataManagerSelection(); if ( nodes.empty() ) { QMessageBox::information( NULL, "Modularization calculation", "Please select exactly one network."); return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { return; } { mitk::ConnectomicsNetwork* network = dynamic_cast( node->GetData() ); if( node.IsNotNull() && network ) { typedef mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ToModuleMapType MappingType; int depthOfModuleRecursive( 2 ); double startTemperature( 2.0 ); double stepSize( 4.0 ); mitk::ConnectomicsNetwork::Pointer connectomicsNetwork( network ); mitk::ConnectomicsSimulatedAnnealingManager::Pointer manager = mitk::ConnectomicsSimulatedAnnealingManager::New(); mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Pointer permutation = mitk::ConnectomicsSimulatedAnnealingPermutationModularity::New(); mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::Pointer costFunction = mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::New(); permutation->SetCostFunction( costFunction.GetPointer() ); permutation->SetNetwork( connectomicsNetwork ); permutation->SetDepth( depthOfModuleRecursive ); permutation->SetStepSize( stepSize ); manager->SetPermutation( permutation.GetPointer() ); manager->RunSimulatedAnnealing( startTemperature, stepSize ); MappingType mapping = permutation->GetMapping(); MappingType::iterator iter = mapping.begin(); MappingType::iterator end = mapping.end(); int loop( 0 ); while( iter != end ) { MBI_DEBUG << "Vertex " << iter->first << " belongs to module " << iter->second ; MBI_INFO << "Vertex " << iter->first << " belongs to module " << iter->second ; iter++; } MBI_DEBUG << "Overall number of modules is " << permutation->getNumberOfModules( &mapping ) ; MBI_DEBUG << "Cost is " << costFunction->Evaluate( network, &mapping ) ; MBI_INFO << "Overall number of modules is " << permutation->getNumberOfModules( &mapping ) ; MBI_INFO << "Cost is " << costFunction->Evaluate( network, &mapping ) ; return; } } } } void QmitkConnectomicsNetworkOperationsView::OnPrunePushButtonClicked() { std::vector nodes = this->GetDataManagerSelection(); if ( nodes.empty() ) { QMessageBox::information( NULL, "Network pruning", "Please select one or more networks."); return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { return; } { mitk::ConnectomicsNetwork* network = dynamic_cast( node->GetData() ); if( node.IsNotNull() && network ) { // Edge pruning will also do node pruning network->PruneEdgesBelowWeight( this->m_Controls->pruneEdgeWeightSpinBox->value() ); } } } } void QmitkConnectomicsNetworkOperationsView::OnCreateConnectivityMatrixImagePushButtonClicked() { std::vector nodes = this->GetDataManagerSelection(); if ( nodes.empty() ) { QMessageBox::information( NULL, "Connectivity Matrix Image creation", "Please select one or more networks."); return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast( node->GetData() ) ) { mitk::ConnectomicsNetwork* network = dynamic_cast( node->GetData() ); itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::Pointer filter = itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::New(); filter->SetInputNetwork( network ); filter->SetBinaryConnectivity(m_Controls->binaryCheckBox->isChecked()); filter->SetRescaleConnectivity(m_Controls->rescaleCheckBox->isChecked()); filter->Update(); +// mitk::DataNode::Pointer connectivityMatrixImageNode = mitk::DataNode::New(); +// connectivityMatrixImageNode->SetData ( connectivityMatrixImage ); + +// connectivityMatrixImageNode->SetName( name.toStdString().c_str() ); +// this->GetDefaultDataStorage()->Add(connectivityMatrixImageNode, node ); + mitk::Image::Pointer connectivityMatrixImage = mitk::ImportItkImage( filter->GetOutput())->Clone(); - mitk::DataNode::Pointer connectivityMatrixImageNode = mitk::DataNode::New(); - connectivityMatrixImageNode->SetData ( connectivityMatrixImage ); - QString name(node->GetName().c_str()); - name += "_ConnectivityMatrix"; - connectivityMatrixImageNode->SetName( name.toStdString().c_str() ); - this->GetDefaultDataStorage()->Add(connectivityMatrixImageNode, node ); + if (m_Controls->binaryCheckBox->isChecked()) + { + QString name("/local/data/Fibercup/connectomics/connectivity_matrices/binary/"); + name += node->GetName().c_str(); + name += "_ConnectivityMatrix.nrrd"; + mitk::IOUtil::SaveImage(connectivityMatrixImage, name.toStdString().c_str()); + + QString name2("/local/data/Fibercup/connectomics/pics/binary/"); + name2 += node->GetName().c_str(); + name2 += "_ConnectivityMatrix.png"; + mitk::IOUtil::SaveImage(connectivityMatrixImage, name2.toStdString().c_str()); + } + else + { + QString name("/local/data/Fibercup/connectomics/connectivity_matrices/"); + name += node->GetName().c_str(); + name += "_ConnectivityMatrix.nrrd"; + mitk::IOUtil::SaveImage(connectivityMatrixImage, name.toStdString().c_str()); + + QString name2("/local/data/Fibercup/connectomics/pics/"); + name2 += node->GetName().c_str(); + name2 += "_ConnectivityMatrix.png"; + mitk::IOUtil::SaveImage(connectivityMatrixImage, name2.toStdString().c_str()); + } } } } + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsView.h old mode 100644 new mode 100755 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkConnectomicsNetworkOperationsViewControls.ui old mode 100644 new mode 100755 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp old mode 100644 new mode 100755 index 1ced21f898..340e871f4c --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,1794 +1,1794 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( NULL ) { } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { } void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_GibbsRingingFrame->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberSamplingChanged(int))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); connect((QObject*) m_Controls->m_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGibbsRinging(int))); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGibbsRinging(int value) { if (value>0) m_Controls->m_GibbsRingingFrame->setVisible(true); else m_Controls->m_GibbsRingingFrame->setVisible(false); } void QmitkFiberfoxView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(int value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double value) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for( int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for( int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Geometry3D::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::OnAddBundle() { if (m_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImage); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); UpdateGui(); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; vector< vector< unsigned int > > fliplist; for (int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { fiducials.push_back(fib); fliplist.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetFiducials(fiducials); filter->SetFlipList(fliplist); switch(m_Controls->m_DistributionBox->currentIndex()){ case 0: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); break; case 1: filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); filter->SetVariance(m_Controls->m_VarianceBox->value()); break; } filter->SetDensity(m_Controls->m_FiberDensityBox->value()); filter->SetTension(m_Controls->m_TensionBox->value()); filter->SetContinuity(m_Controls->m_ContinuityBox->value()); filter->SetBias(m_Controls->m_BiasBox->value()); filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); for (int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::GenerateImage() { itk::ImageRegion<3> imageRegion; imageRegion.SetSize(0, m_Controls->m_SizeX->value()); imageRegion.SetSize(1, m_Controls->m_SizeY->value()); imageRegion.SetSize(2, m_Controls->m_SizeZ->value()); mitk::Vector3D spacing; spacing[0] = m_Controls->m_SpacingX->value(); spacing[1] = m_Controls->m_SpacingY->value(); spacing[2] = m_Controls->m_SpacingZ->value(); mitk::Point3D origin; origin[0] = spacing[0]/2; origin[1] = spacing[1]/2; origin[2] = spacing[2]/2; itk::Matrix directionMatrix; directionMatrix.SetIdentity(); if (m_SelectedImage.IsNotNull()) { mitk::Image* img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); imageRegion = itkImg->GetLargestPossibleRegion(); spacing = itkImg->GetSpacing(); origin = itkImg->GetOrigin(); directionMatrix = itkImg->GetDirection(); } DiffusionSignalModel::GradientListType gradientList; double bVal = 1000; if (m_SelectedDWI.IsNull()) { gradientList = GenerateHalfShell(m_Controls->m_NumGradientsBox->value());; bVal = m_Controls->m_BvalueBox->value(); } else { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); imageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); spacing = dwi->GetVectorImage()->GetSpacing(); origin = dwi->GetVectorImage()->GetOrigin(); directionMatrix = dwi->GetVectorImage()->GetDirection(); bVal = dwi->GetB_Value(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = dwi->GetDirections(); for (int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; gradientList.push_back(g); } } if (m_SelectedBundles.empty()) { if (m_SelectedDWI.IsNotNull()) // add artifacts to existing diffusion weighted image { for (int i=0; i*>(m_SelectedImages.at(i)->GetData())) continue; mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedImages.at(i)->GetData()); double noiseVariance = 0; if (m_Controls->m_AddNoise->isChecked()) { noiseVariance = m_Controls->m_NoiseLevel->value(); artifactModelString += "_NOISE"; artifactModelString += QString::number(noiseVariance); } mitk::RicianNoiseModel noiseModel; noiseModel.SetNoiseVariance(noiseVariance); if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } double lineReadoutTime = m_Controls->m_LineReadoutTimeBox->value(); // add N/2 ghosting double kOffset = 0; if (m_Controls->m_AddGhosts->isChecked()) { artifactModelString += "_GHOST"; kOffset = m_Controls->m_kOffsetBox->value(); } if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } itk::AddArtifactsToDwiImageFilter< short >::Pointer filter = itk::AddArtifactsToDwiImageFilter< short >::New(); filter->SetInput(diffImg->GetVectorImage()); filter->SettLine(lineReadoutTime); filter->SetkOffset(kOffset); filter->SetNoiseModel(&noiseModel); filter->SetGradientList(gradientList); filter->SetTE(this->m_Controls->m_TEbox->value()); if (m_Controls->m_AddEddy->isChecked()) { filter->SetSimulateEddyCurrents(true); filter->SetEddyGradientStrength(m_Controls->m_EddyGradientStrength->value()); artifactModelString += "_EDDY"; } mitk::GibbsRingingArtifact gibbsModel; if (m_Controls->m_AddGibbsRinging->isChecked()) { - resultNode->AddProperty("Fiberfox.k-Space-Undersampling", IntProperty::New(m_Controls->m_KspaceUndersamplingBox->currentText().toInt())); - gibbsModel.SetKspaceCropping((double)m_Controls->m_KspaceUndersamplingBox->currentText().toInt()); + resultNode->AddProperty("Fiberfox.k-Space-Undersampling", DoubleProperty::New(m_Controls->m_KspaceUndersamplingBox->value())); + gibbsModel.SetKspaceCropping(m_Controls->m_KspaceUndersamplingBox->value()); filter->SetRingingModel(&gibbsModel); } if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); if (imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { filter->SetFrequencyMap(itkImg); artifactModelString += "_DISTORTED"; } } filter->Update(); resultNode->AddProperty("Fiberfox.Line-Offset", DoubleProperty::New(kOffset)); resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); resultNode->AddProperty("Fiberfox.Tinhom", IntProperty::New(m_Controls->m_T2starBox->value())); resultNode->AddProperty("binary", BoolProperty::New(false)); mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(diffImg->GetB_Value()); image->SetDirections(diffImg->GetDirections()); image->InitializeFromVectorImage(); resultNode->SetData( image ); resultNode->SetName(m_SelectedImages.at(i)->GetName()+artifactModelString.toStdString()); GetDataStorage()->Add(resultNode); } return; } mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::Geometry3D* geom = image->GetGeometry(); geom->SetOrigin(origin); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImage = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); return; } for (int i=0; im_Compartment4Box->currentIndex()>0) { comp4Weight = m_Controls->m_Comp4FractionBox->value(); comp3Weight -= comp4Weight; } mitk::StickModel stickModel1; mitk::StickModel stickModel2; mitk::TensorModel zeppelinModel1; mitk::TensorModel zeppelinModel2; mitk::TensorModel tensorModel1; mitk::TensorModel tensorModel2; mitk::BallModel ballModel1; mitk::BallModel ballModel2; mitk::AstroStickModel astrosticksModel1; mitk::AstroStickModel astrosticksModel2; mitk::DotModel dotModel1; mitk::DotModel dotModel2; // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: MITK_INFO << "Using stick model"; stickModel1.SetGradientList(gradientList); stickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); stickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); fiberModelList.push_back(&stickModel1); signalModelString += "Stick"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); resultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(stickModel1.GetT2()) ); break; case 1: MITK_INFO << "Using zeppelin model"; zeppelinModel1.SetGradientList(gradientList); zeppelinModel1.SetBvalue(bVal); zeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); zeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); zeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); fiberModelList.push_back(&zeppelinModel1); signalModelString += "Zeppelin"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; case 2: MITK_INFO << "Using tensor model"; tensorModel1.SetGradientList(gradientList); tensorModel1.SetBvalue(bVal); tensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); tensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); tensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); tensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); fiberModelList.push_back(&tensorModel1); signalModelString += "Tensor"; resultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); resultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); resultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(zeppelinModel1.GetT2()) ); break; } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: stickModel2.SetGradientList(gradientList); stickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); stickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); fiberModelList.push_back(&stickModel2); signalModelString += "Stick"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); resultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(stickModel2.GetT2()) ); break; case 2: zeppelinModel2.SetGradientList(gradientList); zeppelinModel2.SetBvalue(bVal); zeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); zeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); zeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); fiberModelList.push_back(&zeppelinModel2); signalModelString += "Zeppelin"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; case 3: tensorModel2.SetGradientList(gradientList); tensorModel2.SetBvalue(bVal); tensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); tensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); tensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); tensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); fiberModelList.push_back(&tensorModel2); signalModelString += "Tensor"; resultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); resultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); resultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); resultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); resultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); resultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(zeppelinModel2.GetT2()) ); break; } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: ballModel1.SetGradientList(gradientList); ballModel1.SetBvalue(bVal); ballModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); ballModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); ballModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&ballModel1); signalModelString += "Ball"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(ballModel1.GetT2()) ); break; case 1: astrosticksModel1.SetGradientList(gradientList); astrosticksModel1.SetBvalue(bVal); astrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); astrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); astrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); astrosticksModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&astrosticksModel1); signalModelString += "Astrosticks"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); resultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(astrosticksModel1.GetT2()) ); resultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; case 2: dotModel1.SetGradientList(gradientList); dotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); dotModel1.SetWeight(comp3Weight); nonFiberModelList.push_back(&dotModel1); signalModelString += "Dot"; resultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); resultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); resultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(dotModel1.GetT2()) ); break; } // compartment 4 switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: ballModel2.SetGradientList(gradientList); ballModel2.SetBvalue(bVal); ballModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); ballModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); ballModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&ballModel2); signalModelString += "Ball"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(ballModel2.GetT2()) ); break; case 2: astrosticksModel2.SetGradientList(gradientList); astrosticksModel2.SetBvalue(bVal); astrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); astrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); astrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); astrosticksModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&astrosticksModel2); signalModelString += "Astrosticks"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); resultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(astrosticksModel2.GetT2()) ); resultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; case 3: dotModel2.SetGradientList(gradientList); dotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); dotModel2.SetWeight(comp4Weight); nonFiberModelList.push_back(&dotModel2); signalModelString += "Dot"; resultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); resultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); resultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(dotModel2.GetT2()) ); break; } itk::TractsToDWIImageFilter::KspaceArtifactList artifactList; // artifact models QString artifactModelString(""); double noiseVariance = 0; if (m_Controls->m_AddNoise->isChecked()) { noiseVariance = m_Controls->m_NoiseLevel->value(); artifactModelString += "_NOISE"; artifactModelString += QString::number(noiseVariance); resultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } mitk::RicianNoiseModel noiseModel; noiseModel.SetNoiseVariance(noiseVariance); mitk::GibbsRingingArtifact gibbsModel; if (m_Controls->m_AddGibbsRinging->isChecked()) { artifactModelString += "_RINGING"; - resultNode->AddProperty("Fiberfox.k-Space-Undersampling", IntProperty::New(m_Controls->m_KspaceUndersamplingBox->currentText().toInt())); - gibbsModel.SetKspaceCropping((double)m_Controls->m_KspaceUndersamplingBox->currentText().toInt()); + resultNode->AddProperty("Fiberfox.k-Space-Undersampling", DoubleProperty::New(m_Controls->m_KspaceUndersamplingBox->value())); + gibbsModel.SetKspaceCropping(m_Controls->m_KspaceUndersamplingBox->value()); artifactList.push_back(&gibbsModel); } if ( this->m_Controls->m_TEbox->value() < imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ) { this->m_Controls->m_TEbox->setValue( imageRegion.GetSize(1)*m_Controls->m_LineReadoutTimeBox->value() ); QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(this->m_Controls->m_TEbox->value())+" ms"); } double lineReadoutTime = m_Controls->m_LineReadoutTimeBox->value(); // adjusting line readout time to the adapted image size needed for the DFT int y = imageRegion.GetSize(1); if ( y%2 == 1 ) y += 1; if ( y>imageRegion.GetSize(1) ) lineReadoutTime *= (double)imageRegion.GetSize(1)/y; // add N/2 ghosting double kOffset = 0; if (m_Controls->m_AddGhosts->isChecked()) { artifactModelString += "_GHOST"; kOffset = m_Controls->m_kOffsetBox->value(); resultNode->AddProperty("Fiberfox.Line-Offset", DoubleProperty::New(kOffset)); } // add distortions if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); if (imageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && imageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && imageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { tractsToDwiFilter->SetFrequencyMap(itkImg); artifactModelString += "_DISTORTED"; } } if (m_Controls->m_AddEddy->isChecked()) { tractsToDwiFilter->SetSimulateEddyCurrents(true); tractsToDwiFilter->SetEddyGradientStrength(m_Controls->m_EddyGradientStrength->value()); artifactModelString += "_EDDY"; } mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(m_SelectedBundles.at(i)->GetData()); if (fiberBundle->GetNumFibers()<=0) continue; if (m_Controls->m_RelaxationBox->isChecked()) artifactModelString += "_RELAX"; tractsToDwiFilter->SetSimulateRelaxation(m_Controls->m_RelaxationBox->isChecked()); tractsToDwiFilter->SetImageRegion(imageRegion); tractsToDwiFilter->SetSpacing(spacing); tractsToDwiFilter->SetOrigin(origin); tractsToDwiFilter->SetDirectionMatrix(directionMatrix); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->SetFiberModels(fiberModelList); tractsToDwiFilter->SetNonFiberModels(nonFiberModelList); tractsToDwiFilter->SetNoiseModel(&noiseModel); tractsToDwiFilter->SetKspaceArtifacts(artifactList); tractsToDwiFilter->SetkOffset(kOffset); tractsToDwiFilter->SettLine(m_Controls->m_LineReadoutTimeBox->value()); tractsToDwiFilter->SettInhom(this->m_Controls->m_T2starBox->value()); tractsToDwiFilter->SetTE(this->m_Controls->m_TEbox->value()); tractsToDwiFilter->SetNumberOfRepetitions(m_Controls->m_RepetitionsBox->value()); tractsToDwiFilter->SetEnforcePureFiberVoxels(m_Controls->m_EnforcePureFiberVoxelsBox->isChecked()); tractsToDwiFilter->SetInterpolationShrink(m_Controls->m_InterpolationShrink->value()); tractsToDwiFilter->SetFiberRadius(m_Controls->m_FiberRadius->value()); tractsToDwiFilter->SetSignalScale(m_Controls->m_SignalScaleBox->value()); if (m_Controls->m_InterpolationShrink->value()<1000) tractsToDwiFilter->SetUseInterpolation(true); if (m_TissueMask.IsNotNull()) { ItkUcharImgType::Pointer mask = ItkUcharImgType::New(); mitk::CastToItkImage(m_TissueMask, mask); tractsToDwiFilter->SetTissueMask(mask); } tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( tractsToDwiFilter->GetOutput() ); image->SetB_Value(bVal); image->SetDirections(gradientList); image->InitializeFromVectorImage(); resultNode->SetData( image ); resultNode->SetName(m_SelectedBundles.at(i)->GetName() +"_D"+QString::number(imageRegion.GetSize(0)).toStdString() +"-"+QString::number(imageRegion.GetSize(1)).toStdString() +"-"+QString::number(imageRegion.GetSize(2)).toStdString() +"_S"+QString::number(spacing[0]).toStdString() +"-"+QString::number(spacing[1]).toStdString() +"-"+QString::number(spacing[2]).toStdString() +"_b"+QString::number(bVal).toStdString() +"_"+signalModelString.toStdString() +artifactModelString.toStdString()); GetDataStorage()->Add(resultNode, m_SelectedBundles.at(i)); resultNode->AddProperty("Fiberfox.InterpolationShrink", IntProperty::New(m_Controls->m_InterpolationShrink->value())); resultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_Controls->m_SignalScaleBox->value())); resultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_Controls->m_FiberRadius->value())); resultNode->AddProperty("Fiberfox.Tinhom", IntProperty::New(m_Controls->m_T2starBox->value())); resultNode->AddProperty("Fiberfox.Repetitions", IntProperty::New(m_Controls->m_RepetitionsBox->value())); resultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(bVal)); resultNode->AddProperty("Fiberfox.Model", StringProperty::New(signalModelString.toStdString())); resultNode->AddProperty("Fiberfox.PureFiberVoxels", BoolProperty::New(m_Controls->m_EnforcePureFiberVoxelsBox->isChecked())); resultNode->AddProperty("binary", BoolProperty::New(false)); resultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(tractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { std::vector< itk::TractsToDWIImageFilter::ItkDoubleImgType::Pointer > volumeFractions = tractsToDwiFilter->GetVolumeFractions(); for (int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName(m_SelectedBundles.at(i)->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, m_SelectedBundles.at(i)); } } mitk::BaseData::Pointer basedata = resultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for( int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { std::vector::const_iterator it = selectedBundles.begin(); for (it; it!=selectedBundles.end(); ++it) { mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< float, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< float, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); } } } } } else { for (int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Geometry3D* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< float, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< float, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< float, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< float, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); for (it; it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (it; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_FiberBundleLabel->setText("mandatory"); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_TissueMask.IsNotNull() || m_SelectedImage.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (!m_SelectedBundles.empty()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_TissueMask = NULL; m_SelectedBundles.clear(); m_SelectedImage = NULL; m_SelectedDWI = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_TissueMask = dynamic_cast(node->GetData()); m_Controls->m_TissueMaskLabel->setText(node->GetName().c_str()); } } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundleX::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", nonConstNode); } else { // just to be sure that the interactor is not added twice mitk::GlobalInteraction::GetInstance()->RemoveInteractor(figureInteractor); } MITK_DEBUG << "adding interactor to globalinteraction"; mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h old mode 100644 new mode 100755 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui old mode 100644 new mode 100755 index 9b378012bd..d8fbe2ec33 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,2227 +1,2198 @@ QmitkFiberfoxViewControls 0 0 493 1565 Form 0 Fiber Definition Qt::Vertical 20 40 color: rgb(255, 0, 0); Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the "Signal Generation" tab. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. Align With Grid Operations false Copy Bundles false Transform Selection QFrame::NoFrame QFrame::Raised 0 Y false Rotation angle (in degree) around x-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false Join Bundles If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Fiber sampling points (per cm) 1 100 1 10 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 QFrame::NoFrame QFrame::Raised 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false Generate Fibers QFrame::NoFrame QFrame::Raised 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QFrame::NoFrame QFrame::Raised 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation Intra-axonal Compartment Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model Data Fiber Bundle: false <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Tissue Mask: false <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Extra-axonal Compartments Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 Weighting factor between the two extra-axonal compartments. 1.000000000000000 0.100000000000000 0.300000000000000 Compartment Fraction: true Start DWI generation from selected fiebr bundle. If no fiber bundle is selected, a grayscale image containing a simple gradient is generated. Generate Image Image Settings QFrame::NoFrame QFrame::Raised 0 6 <html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html> Simulate Signal Relaxation true Repetitions: T2* relaxation time (in milliseconds). 100.000000000000000 0.100000000000000 1.000000000000000 Fiber Radius: Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 TE in milliseconds 1 10000 1 100 Interpolation Shrink: Line Readout Time: false <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Output one image per compartment containing the corresponding volume fractions per voxel. Output Volume Fractions false <html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html> false Number of signal averages. Increase to reduce noise. 1 100 1 1 Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 TE in milliseconds 1 10000 1 100 <html><head/><body><p>Large values shrink (towards nearest neighbour interpolation), small values strech interpolation function (towards linear interpolation). 1000 equals nearest neighbour interpolation.</p></body></html> 1 1000 1000 Signal Scale: color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 11 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 QFrame::NoFrame QFrame::Raised 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 b-Value: false b-value in mm/s² 0 10000 100 1000 Advanced Options Qt::Vertical 20 40 Noise and other Artifacts + + + + Add N/2 Ghosts + + + false + + + true QFrame::NoFrame QFrame::Raised 6 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 Variance: Variance of Rician noise model. 4 0.000000000000000 100000.000000000000000 0.001000000000000 25.000000000000000 Add Gibbs Ringing false Add Rician Noise false - + true QFrame::NoFrame QFrame::Raised 6 0 k-Space Undersampling: false - + - Image is upsampled using this factor, afterwards fourier transformed, cropped to the original size and then inverse fourier transformed. + A larger offset increases the inensity of the ghost image. - - 0 + + 2 + + + 1.000000000000000 + + + 4.000000000000000 + + + 0.100000000000000 + + + 1.100000000000000 - - - 2 - - - - - 4 - - - - - 8 - - - - - 16 - - - - - 32 - - - - - 64 - - - - - 128 - - - - - 256 - - Add Distortions false true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 Gradient Strength: false A larger offset increases the inensity of the ghost image. 5 1000.000000000000000 0.001000000000000 0.015000000000000 true QFrame::NoFrame QFrame::Raised 6 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). - - - - Add N/2 Ghosts - - - false - - - Add Eddy Current Effects false Inter-axonal Compartment Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_AlignOnGrid m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_RepetitionsBox m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_InterpolationShrink m_EnforcePureFiberVoxelsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_Comp4FractionBox m_AddNoise m_NoiseLevel m_AddGhosts m_kOffsetBox m_AddDistortions m_FrequencyMapBox m_AddGibbsRinging - m_KspaceUndersamplingBox tabWidget