diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp index 5f269b8134..ffda1ba3b3 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.cpp @@ -1,1767 +1,1494 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // Blueberry #include "berryIWorkbenchWindow.h" #include "berryIWorkbenchPage.h" #include "berryISelectionService.h" #include "berryConstants.h" #include "berryPlatformUI.h" // Qmitk #include "QmitkTractbasedSpatialStatisticsView.h" #include "QmitkStdMultiWidget.h" #include "mitkDataNodeObject.h" #include // Qt #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "vtkFloatArray.h" #include "vtkLinearTransform.h" #include "vtkPoints.h" #include "mitkSurface.h" #include #include "vtkArrowSource.h" #include "vtkUnstructuredGrid.h" #include "vtkPointData.h" #include #include #include #include #include #include "mitkITKImageImport.h" // #include "mitkImageMapperGL2D.h" #include "mitkVolumeDataVtkMapper3D.h" #include "mitkImageAccessByItk.h" #include "mitkTensorImage.h" #include "itkDiffusionTensor3D.h" #define SEARCHSIGMA 10 /* length in linear voxel dimens { // create new ones m_PointSetNode = mitk::PointSet::New();ions */ #define MAXSEARCHLENGTH (3*SEARCHSIGMA) const std::string QmitkTractbasedSpatialStatisticsView::VIEW_ID = "org.mitk.views.tractbasedspatialstatistics"; using namespace berry; struct TbssSelListener : ISelectionListener { berryObjectMacro(TbssSelListener) TbssSelListener(QmitkTractbasedSpatialStatisticsView* view) { m_View = view; } void DoSelectionChanged(ISelection::ConstPointer selection) { // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); // do something with the selected items if(m_View->m_CurrentSelection) { bool foundTbssRoi = false; bool foundTbss = false; bool found3dImage = false; bool found4dImage = false; bool foundFiberBundle = false; mitk::TbssRoiImage* roiImage; mitk::TbssImage* image; mitk::Image* img; mitk::FiberBundleX* fib; // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // only look at interesting types if(QString("TbssRoiImage").compare(node->GetData()->GetNameOfClass())==0) { foundTbssRoi = true; roiImage = static_cast(node->GetData()); } else if (QString("TbssImage").compare(node->GetData()->GetNameOfClass())==0) { foundTbss = true; image = static_cast(node->GetData()); } else if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) { img = static_cast(node->GetData()); if(img->GetDimension() == 3) { found3dImage = true; } else if(img->GetDimension() == 4) { found4dImage = true; } } else if (QString("FiberBundleX").compare(node->GetData()->GetNameOfClass())==0) { foundFiberBundle = true; fib = static_cast(node->GetData()); } } } - - m_View->m_Controls->m_Transform->setEnabled(found3dImage); m_View->m_Controls->m_CreateRoi->setEnabled(found3dImage); m_View->m_Controls->m_ImportFsl->setEnabled(found4dImage); + if(found3dImage) { m_View->InitPointsets(); } if(foundTbss && foundTbssRoi) { m_View->Plot(image, roiImage); } if(found3dImage == true && foundFiberBundle) { m_View->PlotFiberBundle(fib, img); } } } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkTractbasedSpatialStatisticsView* m_View; }; QmitkTractbasedSpatialStatisticsView::QmitkTractbasedSpatialStatisticsView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) { } QmitkTractbasedSpatialStatisticsView::~QmitkTractbasedSpatialStatisticsView() { } void QmitkTractbasedSpatialStatisticsView::OnSelectionChanged(std::vector nodes) { //datamanager selection changed if (!this->IsActivated()) return; // Get DataManagerSelection if (!this->GetDataManagerSelection().empty()) { mitk::DataNode::Pointer sourceImageNode = this->GetDataManagerSelection().front(); mitk::Image::Pointer sourceImage = dynamic_cast(sourceImageNode->GetData()); if (!sourceImage) { m_Controls->m_TbssImageLabel->setText( QString( sourceImageNode->GetName().c_str() ) + " is no image" ); return; } // set Text m_Controls->m_TbssImageLabel->setText( QString( sourceImageNode->GetName().c_str() ) + " (" + QString::number(sourceImage->GetDimension()) + "D)" ); } else { m_Controls->m_TbssImageLabel->setText("Please select an image"); } } void QmitkTractbasedSpatialStatisticsView::InitPointsets() { // Check if PointSetStart exsits, if not create it. m_P1 = this->GetDefaultDataStorage()->GetNamedNode("PointSetNode"); if (m_PointSetNode) { //m_PointSetNode = dynamic_cast(m_P1->GetData()); return; } if ((!m_P1) || (!m_PointSetNode)) { // create new ones m_PointSetNode = mitk::PointSet::New(); m_P1 = mitk::DataNode::New(); m_P1->SetData( m_PointSetNode ); m_P1->SetProperty( "name", mitk::StringProperty::New( "PointSet" ) ); m_P1->SetProperty( "opacity", mitk::FloatProperty::New( 1 ) ); m_P1->SetProperty( "helper object", mitk::BoolProperty::New(false) ); // CHANGE if wanted m_P1->SetProperty( "pointsize", mitk::FloatProperty::New( 0.1 ) ); m_P1->SetColor( 1.0, 0.0, 0.0 ); this->GetDefaultDataStorage()->Add(m_P1); m_Controls->m_PointWidget->SetPointSetNode(m_P1); m_Controls->m_PointWidget->SetMultiWidget(GetActiveStdMultiWidget()); } } void QmitkTractbasedSpatialStatisticsView::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::QmitkTractbasedSpatialStatisticsViewControls; m_Controls->setupUi( parent ); this->CreateConnections(); } m_SelListener = berry::ISelectionListener::Pointer(new TbssSelListener(this)); this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); m_IsInitialized = false; // Table for the FSL TBSS import m_GroupModel = new QmitkTbssTableModel(); m_Controls->m_GroupInfo->setModel(m_GroupModel); } void QmitkTractbasedSpatialStatisticsView::Activated() { QmitkFunctionality::Activated(); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkTractbasedSpatialStatisticsView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkTractbasedSpatialStatisticsView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_CreateRoi), SIGNAL(clicked()), this, SLOT(CreateRoi()) ); connect( (QObject*)(m_Controls->m_ImportFsl), SIGNAL(clicked()), this, SLOT(TbssImport()) ); connect( (QObject*)(m_Controls->m_AddGroup), SIGNAL(clicked()), this, SLOT(AddGroup()) ); connect( (QObject*)(m_Controls->m_RemoveGroup), SIGNAL(clicked()), this, SLOT(RemoveGroup()) ); connect( (QObject*)(m_Controls->m_Clipboard), SIGNAL(clicked()), this, SLOT(CopyToClipboard()) ); connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(selected(const QwtDoublePoint&)), SLOT(Clicked(const QwtDoublePoint&) ) ); - connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(moved(const QwtDoublePoint&)), SLOT(Clicked(const QwtDoublePoint&) ) ); - connect( (QObject*)(m_Controls->m_SetDxx), SIGNAL(clicked()), this, SLOT(SetDxx()) ); - connect( (QObject*)(m_Controls->m_SetDxy), SIGNAL(clicked()), this, SLOT(SetDxy()) ); - connect( (QObject*)(m_Controls->m_SetDxz), SIGNAL(clicked()), this, SLOT(SetDxz()) ); - connect( (QObject*)(m_Controls->m_SetDyy), SIGNAL(clicked()), this, SLOT(SetDyy()) ); - connect( (QObject*)(m_Controls->m_SetDyz), SIGNAL(clicked()), this, SLOT(SetDyz()) ); - connect( (QObject*)(m_Controls->m_SetDzz), SIGNAL(clicked()), this, SLOT(SetDzz()) ); - connect( (QObject*)(m_Controls->m_TensorByComps), SIGNAL(clicked()), this, SLOT(ImportTensorByComps()) ); - } -} - -void QmitkTractbasedSpatialStatisticsView::ImportTensorByComps() -{ - if(m_DxxNode.IsNull() || m_DxyNode.IsNull() || m_DxzNode.IsNull() - || m_DyzNode.IsNull() || m_DyyNode.IsNull() || m_DzzNode.IsNull() ) - { - return; - } - - mitk::Image* img = static_cast(m_DxxNode->GetData()); - FloatImageType::Pointer Dxx = FloatImageType::New(); - mitk::CastToItkImage(img, Dxx); - - img = static_cast(m_DxyNode->GetData()); - FloatImageType::Pointer Dxy = FloatImageType::New(); - mitk::CastToItkImage(img, Dxy); - - img = static_cast(m_DxzNode->GetData()); - FloatImageType::Pointer Dxz = FloatImageType::New(); - mitk::CastToItkImage(img, Dxz); - - img = static_cast(m_DyzNode->GetData()); - FloatImageType::Pointer Dyz = FloatImageType::New(); - mitk::CastToItkImage(img, Dyz); - - img = static_cast(m_DyyNode->GetData()); - FloatImageType::Pointer Dyy = FloatImageType::New(); - mitk::CastToItkImage(img, Dyy); - - img = static_cast(m_DzzNode->GetData()); - FloatImageType::Pointer Dzz = FloatImageType::New(); - mitk::CastToItkImage(img, Dzz); - - - - itk::Image, 3>::Pointer tensorImg = itk::Image, 3>::New(); - tensorImg->SetSpacing(Dzz->GetSpacing()); - tensorImg->SetOrigin(Dzz->GetOrigin()); - tensorImg->SetRegions(Dzz->GetLargestPossibleRegion().GetSize()); - tensorImg->Allocate(); - - - mitk::TensorImage::Pointer image = mitk::TensorImage::New(); - - FloatImageType::SizeType size = Dxx->GetLargestPossibleRegion().GetSize(); - - for(int x=0; x ix; - ix[0]=x; - ix[1]=y; - ix[2]=z; - - float dxx = Dxx->GetPixel(ix); - float dxy = Dxy->GetPixel(ix); - float dxz = Dxz->GetPixel(ix); - float dyz = Dyz->GetPixel(ix); - float dyy = Dyy->GetPixel(ix); - float dzz = Dzz->GetPixel(ix); - - - itk::DiffusionTensor3D tensor; - tensor[0] = dxx*1000; - tensor[1] = dxy*1000; - tensor[2] = dxz*1000; - tensor[3] = dyy*1000; - tensor[4] = dyz*1000; - tensor[5] = dzz*1000; - - tensorImg->SetPixel(ix, tensor); - } - } - } - - image->InitializeByItk( tensorImg.GetPointer() ); - image->SetVolume( tensorImg->GetBufferPointer() ); - mitk::DataNode::Pointer node=mitk::DataNode::New(); - node->SetData( image ); - GetDefaultDataStorage()->Add( node ); - - - -} - -void QmitkTractbasedSpatialStatisticsView::SetTensorComponent(QLineEdit* edit, mitk::DataNode::Pointer node) -{ - std::vector nodes = GetDataManagerSelection(); - if (nodes.empty()) - { - node = NULL; - edit->setText("N/A"); - return; - } - - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) - { - mitk::DataNode::Pointer n = *it; - - if (n.IsNotNull() && dynamic_cast(n->GetData())) - { - node = mitk::DataNode::New(); - node = n; - edit->setText(node->GetName().c_str()); - return; - } - } -} - -void QmitkTractbasedSpatialStatisticsView::SetDxx() -{ - std::vector nodes = GetDataManagerSelection(); - if (nodes.empty()) - { - m_DxxNode = NULL; - m_Controls->m_DxxImageEdit->setText("N/A"); - return; - } - - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) - { - mitk::DataNode::Pointer n = *it; - - if (n.IsNotNull() && dynamic_cast(n->GetData())) - { - m_DxxNode = n; - m_Controls->m_DxxImageEdit->setText(n->GetName().c_str()); - return; - } + connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(moved(const QwtDoublePoint&)), SLOT(Clicked(const QwtDoublePoint&) ) ); } } -void QmitkTractbasedSpatialStatisticsView::SetDxy() -{ - std::vector nodes = GetDataManagerSelection(); - if (nodes.empty()) - { - m_DxyNode = NULL; - m_Controls->m_DxyImageEdit->setText("N/A"); - return; - } - - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) - { - mitk::DataNode::Pointer n = *it; - - if (n.IsNotNull() && dynamic_cast(n->GetData())) - { - m_DxyNode = n; - m_Controls->m_DxyImageEdit->setText(n->GetName().c_str()); - return; - } - } -} - -void QmitkTractbasedSpatialStatisticsView::SetDxz() -{ - std::vector nodes = GetDataManagerSelection(); - if (nodes.empty()) - { - m_DxzNode = NULL; - m_Controls->m_DxzImageEdit->setText("N/A"); - return; - } - - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) - { - mitk::DataNode::Pointer n = *it; - - if (n.IsNotNull() && dynamic_cast(n->GetData())) - { - m_DxzNode = n; - m_Controls->m_DxzImageEdit->setText(n->GetName().c_str()); - return; - } - } -} - -void QmitkTractbasedSpatialStatisticsView::SetDyy() -{ - std::vector nodes = GetDataManagerSelection(); - if (nodes.empty()) - { - m_DyyNode = NULL; - m_Controls->m_DyyImageEdit->setText("N/A"); - return; - } - - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) - { - mitk::DataNode::Pointer n = *it; - - if (n.IsNotNull() && dynamic_cast(n->GetData())) - { - m_DyyNode = n; - m_Controls->m_DyyImageEdit->setText(n->GetName().c_str()); - return; - } - } -} - -void QmitkTractbasedSpatialStatisticsView::SetDyz() -{ - std::vector nodes = GetDataManagerSelection(); - if (nodes.empty()) - { - m_DyzNode = NULL; - m_Controls->m_DyzImageEdit->setText("N/A"); - return; - } - - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) - { - mitk::DataNode::Pointer n = *it; - - if (n.IsNotNull() && dynamic_cast(n->GetData())) - { - m_DyzNode = n; - m_Controls->m_DyzImageEdit->setText(n->GetName().c_str()); - return; - } - } -} - -void QmitkTractbasedSpatialStatisticsView::SetDzz() -{ - std::vector nodes = GetDataManagerSelection(); - if (nodes.empty()) - { - m_DzzNode = NULL; - m_Controls->m_DzzImageEdit->setText("N/A"); - return; - } - - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) - { - mitk::DataNode::Pointer n = *it; - - if (n.IsNotNull() && dynamic_cast(n->GetData())) - { - m_DzzNode = n; - m_Controls->m_DzzImageEdit->setText(n->GetName().c_str()); - return; - } - } -} - - - void QmitkTractbasedSpatialStatisticsView::CopyToClipboard() { std::vector > vals = m_Controls->m_RoiPlotWidget->GetVals(); QString clipboardText; for (std::vector >::iterator it = vals.begin(); it != vals.end(); ++it) { for (std::vector::iterator it2 = (*it).begin(); it2 != (*it).end(); ++it2) { clipboardText.append(QString("%1 \t").arg(*it2)); double d = *it2; std::cout << d <setText(clipboardText, QClipboard::Clipboard); } void QmitkTractbasedSpatialStatisticsView::RemoveGroup() { QTableView *temp = static_cast(m_Controls->m_GroupInfo); // QSortFilterProxyModel *proxy = static_cast(temp->model()); QItemSelectionModel *selectionModel = temp->selectionModel(); QModelIndexList indices = selectionModel->selectedRows(); QModelIndex index; foreach(index, indices) { int row = index.row(); m_GroupModel->removeRows(row, 1, QModelIndex()); } } std::string QmitkTractbasedSpatialStatisticsView::ReadFile(std::string whatfile) { std::string s = "Select a" + whatfile; QFileDialog* w = new QFileDialog(this->m_Controls->m_ImportFsl, QString(s.c_str()) ); w->setFileMode(QFileDialog::ExistingFiles); w->setDirectory("/home"); if(whatfile == "gradient image") { w->setNameFilter("Tbss gradient images (*.tgi)"); } // RETRIEVE SELECTION if ( w->exec() != QDialog::Accepted ) { return ""; MITK_INFO << "Failed to load"; } QStringList filenames = w->selectedFiles(); if (filenames.size() > 0) { std::string retval = filenames.at(0).toStdString(); return retval; } return ""; } void QmitkTractbasedSpatialStatisticsView::AddGroup() { QString group("Group"); int number = 0; QPair pair(group, number); QList< QPair >list = m_GroupModel->getList(); if(!list.contains(pair)) { m_GroupModel->insertRows(0, 1, QModelIndex()); QModelIndex index = m_GroupModel->index(0, 0, QModelIndex()); m_GroupModel->setData(index, group, Qt::EditRole); index = m_GroupModel->index(0, 1, QModelIndex()); m_GroupModel->setData(index, number, Qt::EditRole); } else { //QMessageBox::information(this, "Duplicate name"); } } void QmitkTractbasedSpatialStatisticsView::TbssImport() { // Read groups from the interface mitk::TbssImporter::Pointer importer = mitk::TbssImporter::New(); QList< QPair >list = m_GroupModel->getList(); if(list.size() == 0) { QMessageBox msgBox; msgBox.setText("No study group information has been set yet."); msgBox.exec(); return; } std::vector < std::pair > groups; for(int i=0; i pair = list.at(i); std::string s = pair.first.toStdString(); int n = pair.second; std::pair p; p.first = s; p.second = n; groups.push_back(p); } importer->SetGroupInfo(groups); std::string minfo = m_Controls->m_MeasurementInfo->text().toStdString(); importer->SetMeasurementInfo(minfo); std::string name = ""; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) { mitk::Image* img = static_cast(node->GetData()); if(img->GetDimension() == 4) { importer->SetImportVolume(img); name = node->GetName(); } } } } mitk::TbssImage::Pointer tbssImage; tbssImage = importer->Import(); name += "_tbss"; AddTbssToDataStorage(tbssImage, name); } void QmitkTractbasedSpatialStatisticsView::AddTbssToDataStorage(mitk::Image* image, std::string name) { mitk::LevelWindow levelwindow; levelwindow.SetAuto( image ); mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); levWinProp->SetLevelWindow( levelwindow ); mitk::DataNode::Pointer result = mitk::DataNode::New(); result->SetProperty( "name", mitk::StringProperty::New(name) ); result->SetData( image ); result->SetProperty( "levelwindow", levWinProp ); // add new image to data storage and set as active to ease further processing GetDefaultDataStorage()->Add( result ); // show the results mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkTractbasedSpatialStatisticsView::Clicked(const QwtDoublePoint& pos) { if(m_Roi.size() > 0 && m_CurrentGeometry != NULL) { int index = (int)pos.x(); index = std::max(0, index); index = std::min(index, (int)m_Roi.size()); itk::Index<3> ix = m_Roi.at(index); mitk::Vector3D i; i[0] = ix[0]; i[1] = ix[1]; i[2] = ix[2]; mitk::Vector3D w; m_CurrentGeometry->IndexToWorld(i, w); mitk::Point3D origin = m_CurrentGeometry->GetOrigin(); mitk::Point3D p; p[0] = w[0] + origin[0]; p[1] = w[1] + origin[1]; p[2] = w[2] + origin[2]; m_MultiWidget->MoveCrossToPosition(p); m_Controls->m_RoiPlotWidget->drawBar(index); } } void QmitkTractbasedSpatialStatisticsView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkTractbasedSpatialStatisticsView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkTractbasedSpatialStatisticsView::AdjustPlotMeasure(const QString & text) { berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkTractbasedSpatialStatisticsView::Clustering() { /* // Create a mask using the distance map typedef itk::ImageFileReader< VectorImageType > DirectionReader; DirectionReader::Pointer directionReader = DirectionReader::New(); directionReader->SetFileName(m_TbssWorkspaceManager.GetInputDir().toStdString() + "/tbss/" + m_TbssWorkspaceManager.GetGradient().toStdString()); directionReader->Update(); VectorImageType::Pointer directions = directionReader->GetOutput(); FloatReaderType::Pointer distMapReader = FloatReaderType::New(); distMapReader->SetFileName(m_TbssWorkspaceManager.GetInputDir().toStdString() + "/stats/" + m_TbssWorkspaceManager.GetDistanceMap().toStdString()); distMapReader->Update(); FloatImageType::Pointer distanceMap = distMapReader->GetOutput(); std::string line; std::string path = "/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/rois/cc.txt"; std::ifstream file(path.c_str()); std::vector< itk::Index< 3 > > roi; if(file.is_open()) { while(getline(file,line)) { std::vector tokens; Tokenize(line, tokens); itk::Index<3> ix; ix[0] = atoi(tokens[0].c_str()); ix[1] = atoi(tokens[1].c_str()); ix[2] = atoi(tokens[2].c_str()); roi.push_back(ix); } } if(roi.size() == 0) { return; } // Some code from the projection algorithm of tbss to create a mask std::vector< std::vector< itk::Index< 3 > > > rois; for(int j=0; j > indices; FloatImageType::SizeType size = distanceMap->GetLargestPossibleRegion().GetSize(); bool roiDone = false; while(!roiDone && j ix = roi[j]; int x=ix[0]; int y=ix[1]; int z=ix[2]; VectorImageType::PixelType dir = directions->GetPixel(ix); indices.push_back(ix); for(int iters=0;iters<2;iters++) { float distance=0; for(int d=1;d=size[0] && dy<=size[1] && dz<=size[2]) { d=MAXSEARCHLENGTH; } else if(distanceMap->GetPixel(ix)>=distance) { distance = distanceMap->GetPixel(ix); indices.push_back(ix); } else{ d=MAXSEARCHLENGTH; } } } j++; } // Create a mask from indices UCharImageType::Pointer maskItk = UCharImageType::New(); maskItk->SetRegions(distanceMap->GetRequestedRegion()); maskItk->SetDirection(distanceMap->GetDirection()); maskItk->SetSpacing(distanceMap->GetSpacing()); maskItk->SetOrigin(distanceMap->GetOrigin()); maskItk->Allocate(); // For every point on the roi create a mask and feed it to the partial voluming algorithm //maskItk->FillBuffer(0); // Create a bounding box from current ROI int xMin = numeric_limits::max(); int yMin = numeric_limits::max(); int zMin = numeric_limits::max(); int xMax = numeric_limits::min(); int yMax = numeric_limits::min(); int zMax = numeriUCharImageType::Pointer newMask = UCharImageType::New();c_limits::min(); for(int i=0; i ix = indices[i]; if(ix[0] < xMin) xMin=ix[0]; if(ix[1] < yMin) yMin=ix[1]; if(ix[2] < zMin) zMin=ix[2]; if(ix[0] > xMax) xMax=ix[0]; if(ix[1] > yMax) yMax=ix[1]; if(ix[2] > zMax) zMax=ix[2]; } FloatImageType::PointType origin = distanceMap->GetOrigin(); CharImageType::PointType originMask; originMask[0] = origin[0] + xMin; originMask[1] = origin[1] + -yMin; originMask[2] = origin[2] + zMin; CharImageType::RegionType region; CharImageType::RegionType::SizeType s; s[0] = xMax-xMin + 1; s[1] = yMax-yMin + 1; s[2] = zMax-zMin + 1; region.SetSize(s); UCharImageType::Pointer newMask = UCharImageType::New(); newMask->SetSpacing( distanceMap->GetSpacing() ); // Set the image spacing newMask->SetOrigin( originMask ); // Set the image origin newMask->SetDirection( distanceMap->GetDirection() ); // Set the image direction newMask->SetRegions( region ); newMask->Allocate(); newMask->FillBuffer(0); for(int i=0; i ix = indices[i]; itk::Point< double, 3 > point; itk::Index< 3 > index; distanceMap->TransformIndexToPhysicalPoint (ix, point); newMask->TransformPhysicalPointToIndex(point, index); newMask->SetPixel(index, 1); } */ /* UCharImageType::Pointer newMask = UCharImageType::New(); UCharReaderType::Pointer cReader = UCharReaderType::New(); cReader->SetFileName("/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/ClusteringFornix/fornix_central_maxFA_path_Dilated_by_3.nrrd"); cReader->Update(); newMask = cReader->GetOutput(); // mitk::DataNode::Pointer maskNode = readNode("itk image/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/clusterMasks/area2.nii"); // mitk::Image::Pointer mask = dynamic_cast(maskNode->GetData()); mitk::Image::Pointer mask; mitk::CastToMitkImage(newMask, mask); typedef mitk::PartialVolumeAnalysisHistogramCalculator HistorgramCalculator; typedef mitk::PartialVolumeAnalysisClusteringCalculator ClusteringType; typedef HistorgramCalculator::HistogramType HistogramType; HistorgramCalculator::Pointer histogramCalculator = HistorgramCalculator::New(); // Make list of subjects std::vector paths; paths.push_back("/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/FA/SORTEDBYCONDITION/FA/subset"); // paths.push_back("/mnt/E130-Projekte/NeuroDiffusion/BRAM DTI/TBSS/FA/SORTEDBYCONDITION/AXD/"); for(int j=0; j values; for(int i=0; i(node->GetData()); histogramCalculator->SetImage(image); histogramCalculator->SetImageMask( mask ); histogramCalculator->SetMaskingModeToImage(); histogramCalculator->SetNumberOfBins(25); histogramCalculator->SetUpsamplingFactor(5); histogramCalculator->SetGaussianSigma(0.0); histogramCalculator->SetForceUpdate(true); bool statisticsChanged = histogramCalculator->ComputeStatistics( ); ClusteringType::ParamsType *cparams = 0; ClusteringType::ClusterResultType *cresult = 0; ClusteringType::HistType *chist = 0; ClusteringType::HelperStructPerformClusteringRetval *currentPerformClusteringResults; try{ mitk::Image* tmpImg = histogramCalculator->GetInternalImage(); mitk::Image::ConstPointer imgToCluster = tmpImg; if(imgToCluster.IsNotNull()) { // perform clustering const HistogramType *histogram = histogramCalculator->GetHistogram( ); ClusteringType::Pointer clusterer = ClusteringType::New(); clusterer->SetStepsNumIntegration(200); clusterer->SetMaxIt(1000); mitk::Image::Pointer pFiberImg; currentPerformClusteringResults = clusterer->PerformClustering(imgToCluster, histogram, 2); pFiberImg = currentPerformClusteringResults->clusteredImage; cparams = currentPerformClusteringResults->params; cresult = currentPerformClusteringResults->result; chist = currentPerformClusteringResults->hist; // m_Controls->m_HistogramWidget->SetParameters( // cparams, cresult, chist ); std::vector *xVals = chist->GetXVals(); std::vector *fiberVals = new std::vector(cresult->GetFiberVals()); double fiberFA = 0.0; double weights = 0.0; // std::cout << "x, y, fiber, nonFiber, mixed, combi" << std::endl; for(int k=0; ksize(); ++k) { fiberFA += xVals->at(k) * fiberVals->at(k); weights += fiberVals->at(k); } fiberFA = fiberFA / weights; std::cout << "FA: " << fiberFA << std::endl; values.push_back(fiberFA); } } catch ( const std::runtime_error &e ) { std::cout << "noooooooooooooooooooooooooooooooo!"; } //MITK_INFO << "number of voxels: " << indices.size(); } std::vector::iterator it = values.begin(); while(it!=values.end()) { std::cout << *it << std::endl; ++it; } }*/ } void QmitkTractbasedSpatialStatisticsView::CreateRoi() { // It is important to load the MeanFASkeletonMask image in MITK to make sure that point selection and // pathfinding is done on the same image //string filename = m_TbssWorkspaceManager.GetInputDir().toStdString() + "/stats/" + m_TbssWorkspaceManager.GetMeanFASkeletonMask().toStdString(); // Implement a way to obtain skeleton and skeletonFA without sml workspace double threshold = QInputDialog::getDouble(m_Controls->m_CreateRoi, tr("Set an FA threshold"), tr("Threshold:"), QLineEdit::Normal, 0.2); mitk::Image::Pointer image; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) { mitk::Image* img = static_cast(node->GetData()); if(img->GetDimension() == 3) { image = img; } } } } if(image.IsNull()) { return; } mitk::TractAnalyzer analyzer; analyzer.SetInputImage(image); analyzer.SetThreshold(threshold); int n = 0; if(m_PointSetNode.IsNotNull()) { n = m_PointSetNode->GetSize(); if(n==0) { QMessageBox msgBox; msgBox.setText("No points have been set yet."); msgBox.exec(); } } else{ QMessageBox msgBox; msgBox.setText("No points have been set yet."); msgBox.exec(); } std::string pathDescription = ""; std::vector< itk::Index<3> > totalPath; if(n>0) { for(int i=0; iGetPoint(i); mitk::Point3D p2 = m_PointSetNode->GetPoint(i+1); itk::Index<3> StartPoint; mitk::ProgressBar::GetInstance()->Progress(); itk::Index<3> EndPoint; image->GetGeometry()->WorldToIndex(p,StartPoint); image->GetGeometry()->WorldToIndex(p2,EndPoint); MITK_INFO << "create roi"; analyzer.BuildGraph(StartPoint, EndPoint); std::vector< itk::Index<3> > path = analyzer.GetPath(); for(std::vector< itk::Index<3> >::iterator it = path.begin(); it != path.end(); it++) { itk::Index<3> ix = *it; if (!(ix==EndPoint)) { mitk::ProgressBar::GetInstance()->Progress(); totalPath.push_back(ix); std::stringstream ss; ss << ix[0] << " " << ix[1] << " " << ix[2] << "\n"; pathDescription += ss.str(); } else { // Only when dealing with the last segment the last point should be added. This one will not occur // as the first point of the next roi segment. if(i == (n-2)) { totalPath.push_back(EndPoint); std::stringstream ss; ss << EndPoint[0] << " " << EndPoint[1] << " " << EndPoint[2] << "\n"; pathDescription += ss.str(); } } } } m_Controls->m_PathTextEdit->setPlainText(QString(pathDescription.c_str())); FloatImageType::Pointer itkImg = FloatImageType::New(); mitk::CastToItkImage(image, itkImg); CharImageType::Pointer roiImg = CharImageType::New(); roiImg->SetRegions(itkImg->GetLargestPossibleRegion().GetSize()); roiImg->SetOrigin(itkImg->GetOrigin()); roiImg->SetSpacing(itkImg->GetSpacing()); roiImg->SetDirection(itkImg->GetDirection()); roiImg->Allocate(); roiImg->FillBuffer(0); std::vector< itk::Index<3> > roi; std::vector< itk::Index<3> >::iterator it; for(it = totalPath.begin(); it != totalPath.end(); it++) { itk::Index<3> ix = *it; roiImg->SetPixel(ix, 1); roi.push_back(ix); } mitk::TbssRoiImage::Pointer tbssRoi = mitk::TbssRoiImage::New(); //mitk::CastToTbssImage(m_CurrentRoi.GetPointer(), tbssRoi); tbssRoi->SetRoi(roi); tbssRoi->SetImage(roiImg); tbssRoi->SetStructure(m_Controls->m_Structure->text().toStdString()); tbssRoi->InitializeFromImage(); // mitk::Image::Pointer tbssRoi = mitk::Image::New(); //mitk::CastToTbssImage(m_CurrentRoi.GetPointer(), tbssRoi); // mitk::CastToMitkImage(roiImg, tbssRoi); AddTbssToDataStorage(tbssRoi, m_Controls->m_RoiName->text().toStdString()); } } void QmitkTractbasedSpatialStatisticsView::PlotFiberBundle(mitk::FiberBundleX *fib, mitk::Image* img) { int num = fib->GetNumFibers(); std::cout << "number of fibers: " << num << std::endl; vtkSmartPointer fiberPolyData = fib->GetFiberPolyData(); vtkCellArray* lines = fiberPolyData->GetLines(); lines->InitTraversal(); int lineSize = lines->GetSize(); std::cout << "line size: " << lineSize << std::cout; typedef itk::Point PointType; typedef std::vector< PointType> TractType; typedef std::vector< TractType > TractContainerType; TractContainerType tracts; for( int fiberID( 0 ); fiberID < num; fiberID++ ) { vtkIdType numPointsInCell(0); vtkIdType* pointsInCell(NULL); lines->GetNextCell ( numPointsInCell, pointsInCell ); TractType singleTract; for( int pointInCellID( 0 ); pointInCellID < numPointsInCell ; pointInCellID++) { // push back point double *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] ); PointType point; point[0] = p[0]; point[1] = p[1]; point[2] = p[2]; singleTract.push_back( point ); } tracts.push_back(singleTract); } m_Controls->m_RoiPlotWidget->PlotFiberBundles(tracts, img); } void QmitkTractbasedSpatialStatisticsView::Plot(mitk::TbssImage* image, mitk::TbssRoiImage* roiImage) { if(m_Controls->m_TabWidget->currentWidget() == m_Controls->m_MeasureTAB) { std::vector< itk::Index<3> > roi = roiImage->GetRoi(); m_Roi = roi; m_CurrentGeometry = image->GetGeometry(); std::string resultfile = ""; /* if(image->GetPreprocessedFA()) { resultFile = image->GetPreprocessedFAFile(); } */ std::string structure = roiImage->GetStructure(); //m_View->m_CurrentGeometry = image->GetGeometry(); m_Controls->m_RoiPlotWidget->SetGroups(image->GetGroupInfo()); // Check for preprocessed results to save time //if(resultfile == "") // { // Need to calculate the results using the 4D volume // Can save the time this takes if there are results available already //std::string type = m_Controls->m_MeasureType->itemText(m_Controls->m_MeasureType->currentIndex()).toStdString(); m_Controls->m_RoiPlotWidget->SetProjections(image->GetImage()); // } m_Controls->m_RoiPlotWidget->SetRoi(roi); m_Controls->m_RoiPlotWidget->SetStructure(structure); m_Controls->m_RoiPlotWidget->SetMeasure( image->GetMeasurementInfo() ); m_Controls->m_RoiPlotWidget->DrawProfiles(resultfile); } } void QmitkTractbasedSpatialStatisticsView::Masking() { //QString filename = m_Controls->m_WorkingDirectory->text(); QString filename = "E:/Experiments/tbss"; QString faFiles = filename + "/AxD"; QString maskFiles = filename + "/bin_masks"; QDirIterator faDirIt(faFiles, QDir::Files | QDir::NoSymLinks, QDirIterator::Subdirectories); QDirIterator maskDirIt(maskFiles, QDir::Files | QDir::NoSymLinks, QDirIterator::Subdirectories); std::vector faFilenames; std::vector maskFilenames; std::vector outputFilenames; while(faDirIt.hasNext() && maskDirIt.hasNext()) { faDirIt.next(); maskDirIt.next(); if((faDirIt.fileInfo().completeSuffix() == "nii" || faDirIt.fileInfo().completeSuffix() == "mhd" || faDirIt.fileInfo().completeSuffix() == "nii.gz") && (maskDirIt.fileInfo().completeSuffix() == "nii" || maskDirIt.fileInfo().completeSuffix() == "mhd" || maskDirIt.fileInfo().completeSuffix() == "nii.gz")) { faFilenames.push_back(faDirIt.filePath().toStdString()); outputFilenames.push_back(faDirIt.fileName().toStdString()); maskFilenames.push_back(maskDirIt.filePath().toStdString()); } } std::vector::iterator faIt = faFilenames.begin(); std::vector::iterator maskIt = maskFilenames.begin(); std::vector::iterator outputIt = outputFilenames.begin(); // Now multiply all FA images with their corresponding masks QString outputDir = filename; while(faIt != faFilenames.end() && maskIt != maskFilenames.end() && outputIt != outputFilenames.end()) { std::cout << "Mask " << *faIt << " with " << *maskIt << std::endl; typedef itk::MultiplyImageFilter MultiplicationFilterType; FloatReaderType::Pointer floatReader = FloatReaderType::New(); CharReaderType::Pointer charReader = CharReaderType::New(); floatReader->SetFileName(*faIt); //floatReader->Update(); //FloatImageType::Pointer faImage = floatReader->GetOutput(); charReader->SetFileName(*maskIt); //charReader->Update(); // CharImageType::Pointer maskImage = charReader->GetOutput(); MultiplicationFilterType::Pointer multiplicationFilter = MultiplicationFilterType::New(); multiplicationFilter->SetInput1(floatReader->GetOutput()); multiplicationFilter->SetInput2(charReader->GetOutput()); multiplicationFilter->Update(); //FloatImageType::Pointer maskedImage = FloatImageType::New(); //maskedImage = MultiplicationFilter->GetOutput(); FloatWriterType::Pointer floatWriter = FloatWriterType::New(); std::string s = faFiles.toStdString().append("/"+*outputIt); floatWriter->SetFileName(s.c_str()); floatWriter->SetInput(multiplicationFilter->GetOutput()); floatWriter->Update(); ++faIt; ++maskIt; ++outputIt; } } VectorImageType::Pointer QmitkTractbasedSpatialStatisticsView::ConvertToVectorImage(mitk::Image::Pointer mitkImage) { VectorImageType::Pointer vecImg = VectorImageType::New(); mitk::Geometry3D* geo = mitkImage->GetGeometry(); mitk::Vector3D spacing = geo->GetSpacing(); mitk::Point3D origin = geo->GetOrigin(); VectorImageType::SpacingType vecSpacing; vecSpacing[0] = spacing[0]; vecSpacing[1] = spacing[1]; vecSpacing[2] = spacing[2]; VectorImageType::PointType vecOrigin; vecOrigin[0] = origin[0]; vecOrigin[1] = origin[1]; vecOrigin[2] = origin[2]; VectorImageType::SizeType size; size[0] = mitkImage->GetDimension(0); size[1] = mitkImage->GetDimension(1); size[2] = mitkImage->GetDimension(2); vecImg->SetSpacing(vecSpacing); vecImg->SetOrigin(vecOrigin); vecImg->SetRegions(size); vecImg->SetVectorLength(mitkImage->GetDimension(3)); vecImg->Allocate(); for(int x=0; x pixel = vecImg->GetPixel(ix); for (int t=0; tGetPixelValueByIndex(ix, t); pixel.SetElement(t, f); } vecImg->SetPixel(ix, pixel); } } } return vecImg; } /* void QmitkTractbasedSpatialStatisticsView::InitializeGridByVectorImage() { // Read vector image from file typedef itk::ImageFileReader< FloatVectorImageType > VectorReaderType; VectorReaderType::Pointer vectorReader = VectorReaderType::New(); vectorReader->SetFileName("E:\\tbss\\testing\\Gradient.mhd"); vectorReader->Update(); FloatVectorImageType::Pointer directions = vectorReader->GetOutput(); // Read roi from file. CharReaderType::Pointer roiReader = CharReaderType::New(); roiReader->SetFileName("E:\\tbss\\testing\\debugging skeletonization\\segment2.mhd"); roiReader->Update(); CharImageType::Pointer roi = roiReader->GetOutput(); DoInitializeGridByVectorImage(directions, roi, std::string("directions")); } void QmitkTractbasedSpatialStatisticsView::DoInitializeGridByVectorImage(FloatVectorImageType::Pointer vectorpic, CharImageType::Pointer roi, std::string name) { //vtkStructuredGrid* grid = vtkStructuredGrid::New(); itk::Matrix itkdirection = vectorpic->GetDirection(); itk::Matrix itkinversedirection = itk::Matrix(itkdirection.GetInverse()); std::vector GridPoints; vtkPoints *points = vtkPoints::New(); mitk::Geometry3D::Pointer geom = mitk::Geometry3D::New(); vtkLinearTransform *vtktransform; vtkLinearTransform *inverse; mitk::Image::Pointer geomget = mitk::Image::New(); geomget->InitializeByItk(vectorpic.GetPointer()); geom = geomget->GetGeometry(); vtktransform = geom->GetVtkTransform(); inverse = vtktransform->GetLinearInverse(); vtkFloatArray * directions = vtkFloatArray::New(); directions->SetName("Vectors"); directions->SetNumberOfComponents(3); // Iterator for the vector image itk::ImageRegionIterator it_input(vectorpic, vectorpic->GetLargestPossibleRegion()); FloatVectorType nullvector; nullvector.Fill(0); double lengthsum = 0; int id = 0; // Iterator for the roi itk::ImageRegionIterator roiIt(roi, roi->GetLargestPossibleRegion()); roiIt.GoToBegin(); for(it_input.GoToBegin(); !( it_input.IsAtEnd() || roiIt.IsAtEnd() ); ++it_input) { //VectorType val = it_input.Value(); if(it_input.Value() != nullvector && roiIt.Get() != 0) { //itk::Point point; mitk::Point3D mitkpoint, mitkworldpoint; mitk::Point3D mitkendpoint, mitkworldendpoint; mitk::Vector3D mitkvector, mitktransvector; itk::Point direction = it_input.Value().GetDataPointer(); //itk::Index<3> in_input = it_input.GetIndex(); //itk::ContinuousIndex cindirection; FloatVectorType transvec = it_input.Value(); mitkvector[0] = transvec[0]; mitkvector[1] = transvec[1]; mitkvector[2] = transvec[2]; //mitkvector[2] = 0.0; mitkpoint[0] = it_input.GetIndex()[0]; mitkpoint[1] = it_input.GetIndex()[1]; mitkpoint[2] = it_input.GetIndex()[2]; mitkendpoint[0] = mitkpoint[0] + mitkvector[0]; mitkendpoint[1] = mitkpoint[1] + mitkvector[1]; mitkendpoint[2] = mitkpoint[2] + mitkvector[2]; //mitkpoint.setXYZ((ScalarType)point[0],(ScalarType)point[1],(ScalarType)point[2]); geom->IndexToWorld(mitkpoint, mitkworldpoint); geom->IndexToWorld(mitkendpoint, mitkworldendpoint); mitktransvector[0] = mitkworldendpoint[0] - mitkworldpoint[0]; mitktransvector[1] = mitkworldendpoint[1] - mitkworldpoint[1]; mitktransvector[2] = mitkworldendpoint[2] - mitkworldpoint[2]; lengthsum += mitktransvector.GetNorm(); directions->InsertTuple3(id,mitktransvector[0],mitktransvector[1],mitktransvector[2]); points->InsertPoint(id,mitkworldpoint[0],mitkworldpoint[1],mitkworldpoint[2]); id++; //for (unsigned short loop = 0; (loop < 20) && (!it_input.IsAtEnd()); loop++) //{ // ++it_input; //} if(it_input.IsAtEnd()) { break; } } ++roiIt; } double meanlength = lengthsum / id; vtkGlyph3D* glyph = vtkGlyph3D::New(); vtkUnstructuredGrid* ugrid = vtkUnstructuredGrid::New(); ugrid->SetPoints(points); ugrid->GetPointData()->SetVectors(directions); glyph->SetInput(ugrid); glyph->SetScaleModeToScaleByVector(); glyph->SetScaleFactor(0.5); glyph->SetColorModeToColorByScalar(); //glyph->ClampingOn(); vtkArrowSource* arrow = vtkArrowSource::New(); if(meanlength > 5) {arrow->SetTipLength(0);arrow->SetTipRadius(0);} arrow->SetShaftRadius(0.03/meanlength); //arrow->SetTipRadius(0.05/meanlength); glyph->SetSource(arrow->GetOutput()); glyph->Update(); mitk::Surface::Pointer glyph_surface = mitk::Surface::New(); glyph_surface->SetVtkPolyData(glyph->GetOutput()); glyph_surface->UpdateOutputInformation(); mitk::DataNode::Pointer gridNode = mitk::DataNode::New(); gridNode->SetProperty( "name", mitk::StringProperty::New(name.c_str()) ); //m_GridNode->SetProperty( "color" , m_GridColor); gridNode->SetProperty( "visible", mitk::BoolProperty::New(true) ); gridNode->SetProperty( "segmentation", mitk::BoolProperty::New(true) ); gridNode->SetProperty( "ID-Tag", mitk::StringProperty::New("grid") ); gridNode->SetProperty( "shader", mitk::StringProperty::New("mitkShaderLightning") ); gridNode->SetData( glyph_surface ); GetDefaultDataStorage()->Add(gridNode); } */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h index 1cde1ffe59..b1fe665ff6 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsView.h @@ -1,272 +1,260 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef QmitkTractbasedSpatialStatisticsView_h #define QmitkTractbasedSpatialStatisticsView_h #include #include #include #include #include "ui_QmitkTractbasedSpatialStatisticsViewControls.h" #include #include #include #include #include #include #include #include #include #include "QmitkTbssTableModel.h" #include "QmitkTbssMetaTableModel.h" #include typedef short DiffusionPixelType; typedef itk::Image CharImageType; typedef itk::Image UCharImageType; typedef itk::Image Float4DImageType; typedef itk::Image FloatImageType; typedef itk::Vector IntVectorType; //typedef itk::VectorImage DirectionImageType; typedef itk::VectorImage VectorImageType; typedef itk::ImageFileReader< CharImageType > CharReaderType; typedef itk::ImageFileReader< UCharImageType > UCharReaderType; typedef itk::ImageFileWriter< CharImageType > CharWriterType; typedef itk::ImageFileReader< FloatImageType > FloatReaderType; typedef itk::ImageFileWriter< FloatImageType > FloatWriterType; typedef itk::ImageFileReader< Float4DImageType > Float4DReaderType; typedef itk::ImageFileWriter< Float4DImageType > Float4DWriterType; struct TbssSelListener; /*! \brief QmitkTractbasedSpatialStatisticsView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. \sa QmitkFunctionalitymitkTbssWorkspaceManager \ingroup Functionalities */ class QmitkTractbasedSpatialStatisticsView : public QmitkFunctionality { friend struct TbssSelListener; // this is needed for all Qt objesetupUicts that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkTractbasedSpatialStatisticsView(); virtual ~QmitkTractbasedSpatialStatisticsView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); protected slots: //void OutputValues(); // void InitializeGridByVectorImage(); void Masking(); void CreateRoi(); void Clustering(); void AdjustPlotMeasure(const QString & text); void Clicked(const QwtDoublePoint& pos); void TbssImport(); void AddGroup(); void RemoveGroup(); void CopyToClipboard(); - void SetDxx(); - void SetDyy(); - void SetDzz(); - void SetDxy(); - void SetDxz(); - void SetDyz(); - void ImportTensorByComps(); + protected: - void SetTensorComponent(QLineEdit* edit, mitk::DataNode::Pointer node); /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); void Plot(mitk::TbssImage*, mitk::TbssRoiImage*); void PlotFiberBundle(mitk::FiberBundleX* fib, mitk::Image* img); void InitPointsets(); void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; bool m_IsInitialized; mitk::PointSet::Pointer m_PointSetNode; mitk::DataNode::Pointer m_P1; Ui::QmitkTractbasedSpatialStatisticsViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; std::vector SortPoints(CharImageType::Pointer roi, CharImageType::IndexType currentPoint); bool PointVisited(std::vector points, CharImageType::IndexType point); // Modifies the current point by reference and returns true if no more points need to be visited CharImageType::IndexType FindNextPoint(std::vector pointsVisited, CharImageType::IndexType currentPoint, CharImageType::Pointer roi, bool &ready); //void DoInitializeGridByVectorImage(FloatVectorImageType::Pointer vectorpic, CharImageType::Pointer roi ,std::string name); // Tokenizer needed for the roi files void Tokenize(const std::string& str, std::vector& tokens, const std::string& delimiters = " ") { // Skip delimiters at beginning. std::string::size_type lastPos = str.find_first_not_of(delimiters, 0); // Find first "non-delimiter". std::string::size_type pos = str.find_first_of(delimiters, lastPos); while (std::string::npos != pos || std::string::npos != lastPos) { // Found a token, add it to the vector. tokens.push_back(str.substr(lastPos, pos - lastPos)); // Skip delimiters. Note the "not_of" lastPos = str.find_first_not_of(delimiters, pos); // Find next "non-delimiter" pos = str.find_first_of(delimiters, lastPos); } } mitk::DataNode::Pointer readNode(std::string f) { mitk::DataNode::Pointer node; mitk::DataNodeFactory::Pointer nodeReader = mitk::DataNodeFactory::New(); try { nodeReader->SetFileName(f); nodeReader->Update(); node = nodeReader->GetOutput(); } catch(...) { MITK_ERROR << "Could not read file"; return NULL; } return node; } /*template < typename TPixel, unsigned int VImageDimension > void ToITK4D( itk::Image* inputImage, Float4DImageType::Pointer& outputImage );*/ std::string ReadFile(std::string whatfile); std::vector< itk::Index<3> > m_Roi; std::string m_CurrentStructure; mitk::Geometry3D* m_CurrentGeometry; QmitkTbssTableModel* m_GroupModel; void AddTbssToDataStorage(mitk::Image* image, std::string name); mitk::TbssImage::Pointer m_CurrentTbssMetaImage; VectorImageType::Pointer ConvertToVectorImage(mitk::Image::Pointer mitkImg); - mitk::DataNode::Pointer m_DxxNode; - mitk::DataNode::Pointer m_DxyNode; - mitk::DataNode::Pointer m_DxzNode; - mitk::DataNode::Pointer m_DyzNode; - mitk::DataNode::Pointer m_DyyNode; - mitk::DataNode::Pointer m_DzzNode; + }; #endif // _QMITKTRACTBASEDSPATIALSTATISTICSVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui index c07a46a0bd..b6d1b75c69 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui @@ -1,640 +1,318 @@ QmitkTractbasedSpatialStatisticsViewControls 0 0 431 811 0 0 QmitkTemplate FSL import false false Here subject data and tbss meta data can be imported from FSL into the MITK TBSS module 0 Subject data QFrame::StyledPanel QFrame::Raised Group information QAbstractItemView::SelectRows QFrame::StyledPanel QFrame::Raised Add group entry. After that give the group a name and the correct number Add Remove selected entries Remove false Import a 4D image containing group data after group information has been set Import subject data QFrame::StyledPanel QFrame::Raised Diffusion measure Measurement in the to be imported 4D image Fractional Anisotropy Tract-specific analysis true To create a roi first load a tbss meta image into the datamanager - 3 + 0 ROIs QFormLayout::AllNonFixedFieldsGrow current selection mean FA skeleton: Points on Roi 100 100 0 100 Use this widget to create points on the ROI by shift-leftclick on the right positions on the skeleton. Then click Create Roi. The Roi that will be created will pass through the points in the order of occurence in this list false No suitable tbss meta image selected yet. The meta image needs to contain a mean FA skeleton and a skeleton mask Create ROI 0 0 Points on the ROI Name Give a name to the region of interest roiname Structure info On what anatomical structure lies the ROI? Structure Measuring To plot, load a tbss image with subject information and a region of interest corresponding to the study and select them both Copy to clipboard - - - Transform - - - - - - - - - false - - - Transform - - - - - - - - Import Tensor Image - - - - - - Dxx - - - - - - - Binary mask image to reduce the algorithms search space. - - - QFrame::StyledPanel - - - QFrame::Raised - - - - 0 - - - - - true - - - => - - - - - - - true - - - N/A - - - true - - - - - - - - - - Dxy - - - - - - - Binary mask image to reduce the algorithms search space. - - - QFrame::StyledPanel - - - QFrame::Raised - - - - 0 - - - - - true - - - => - - - - - - - true - - - N/A - - - true - - - - - - - - - - Dxz - - - - - - - Binary mask image to reduce the algorithms search space. - - - QFrame::StyledPanel - - - QFrame::Raised - - - - 0 - - - - - true - - - => - - - - - - - true - - - N/A - - - true - - - - - - - - - - Dyy - - - - - - - Binary mask image to reduce the algorithms search space. - - - QFrame::StyledPanel - - - QFrame::Raised - - - - 0 - - - - - true - - - => - - - - - - - true - - - N/A - - - true - - - - - - - - - - Dyz - - - - - - - Binary mask image to reduce the algorithms search space. - - - QFrame::StyledPanel - - - QFrame::Raised - - - - 0 - - - - - true - - - => - - - - - - - true - - - N/A - - - true - - - - - - - - - - Dzz - - - - - - - Binary mask image to reduce the algorithms search space. - - - QFrame::StyledPanel - - - QFrame::Raised - - - - 0 - - - - - true - - - => - - - - - - - true - - - N/A - - - true - - - - - - - - - - Import - - - - - QmitkPointListWidget QWidget
QmitkPointListWidget.h
 QmitkTbssRoiAnalysisWidget QWidget
QmitkTbssRoiAnalysisWidget.h
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