diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml index 4a46258..5ec898e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml @@ -1,171 +1,171 @@ This perspective contains all views necessary to post process fibers. diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp index fd58e0d..217b618 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.cpp @@ -1,1828 +1,1935 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 #include #include #include // Qmitk #include "QmitkInteractiveFiberDissectionView.h" #include //Pointset #include //Pointset #include #include #include #include #include #include #include #include "mitkNodePredicateDataType.h" #include #include #include #include +#include +#include +#include +#include +#include +#include //#include #include #include "usModuleRegistry.h" //#include #include #include #include #include #include #include #include #include #include #include #include #include #include + + +#include +#include +#include +#include +#include +#include +#include +#include +#include + const std::string QmitkInteractiveFiberDissectionView::VIEW_ID = "org.mitk.views.interactivefiberdissection"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkInteractiveFiberDissectionView::QmitkInteractiveFiberDissectionView() : QmitkAbstractView() , m_Controls( 0 ) , m_IterationCounter(0) , m_RandomExtractionCounter(0) , m_activeCycleCounter(0) , m_createdStreamlineCounter(0) , m_StreamlineInteractor(nullptr) { } // Destructor QmitkInteractiveFiberDissectionView::~QmitkInteractiveFiberDissectionView() { //disable interactor if (m_StreamlineInteractor != nullptr) { // m_StreamlineInteractor->SetStreamlineNode(nullptr); m_StreamlineInteractor->EnableInteraction(false); } } void QmitkInteractiveFiberDissectionView::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::QmitkInteractiveFiberDissectionViewControls; m_Controls->setupUi( parent ); m_Controls->m_selectedPointSetWidget->SetDataStorage(GetDataStorage());//pointset m_Controls->m_selectedPointSetWidget->SetNodePredicate(mitk::NodePredicateAnd::New(//pointset mitk::TNodePredicateDataType::New(),//pointset mitk::NodePredicateNot::New(mitk::NodePredicateOr::New(//pointset mitk::NodePredicateProperty::New("helper object"),//pointset mitk::NodePredicateProperty::New("hidden object")))));//pointset m_Controls->m_selectedPointSetWidget->SetSelectionIsOptional(true);//pointset m_Controls->m_selectedPointSetWidget->SetAutoSelectNewNodes(true);//pointset m_Controls->m_selectedPointSetWidget->SetEmptyInfo(QString("Please select a point set"));//pointset m_Controls->m_selectedPointSetWidget->SetPopUpTitel(QString("Select point set"));//pointsett m_Controls->m_BundleBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isBundle= mitk::TNodePredicateDataType::New(); m_Controls->m_BundleBox->SetPredicate( isBundle ); m_Controls->m_PrototypeBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isPrototype = mitk::TNodePredicateDataType::New(); m_Controls->m_PrototypeBox->SetPredicate( isPrototype ); m_Controls->m_PredictionBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isPrediction = mitk::TNodePredicateDataType::New(); m_Controls->m_PredictionBox->SetPredicate( isPrediction ); m_Controls->m_GroundtruthBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isGroundtruth = mitk::TNodePredicateDataType::New(); m_Controls->m_GroundtruthBox->SetPredicate( isGroundtruth ); m_Controls->m_TestBundleBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isTestBundle = mitk::TNodePredicateDataType::New(); m_Controls->m_TestBundleBox->SetPredicate( isTestBundle); connect(m_Controls->m_ErazorButton, SIGNAL(toggled(bool)), this, SLOT( RemovefromBundle(bool) ) ); connect(m_Controls->m_BrushButton, SIGNAL(toggled(bool)), this, SLOT( RemovefromBundleBrush(bool) ) ); connect(m_Controls->m_StreamlineCreation, SIGNAL( clicked() ), this, SLOT( CreateStreamline())); connect(m_Controls->m_AddRandomFibers, SIGNAL( clicked() ), this, SLOT( ExtractRandomFibersFromTractogram() ) ); //need connect(m_Controls->m_TrainClassifier, SIGNAL( clicked() ), this, SLOT( StartAlgorithm( ))); connect(m_Controls->m_CreatePrediction, SIGNAL( clicked() ), this, SLOT( CreatePredictionNode( ))); connect(m_Controls->m_certainData, SIGNAL( clicked() ), this, SLOT( CreateCertainNode( ))); connect(m_Controls->m_AddUncertainFibers, SIGNAL( clicked() ), this, SLOT( CreateUncertaintySampleNode( ))); connect(m_Controls->m_AddDistanceFibers, SIGNAL( clicked() ), this, SLOT( CreateDistanceSampleNode( ))); connect(m_Controls->m_unclabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromUncertainty(bool) ) ); //need connect(m_Controls->m_unclabelingBrush, SIGNAL(toggled(bool)), this, SLOT( RemovefromUncertaintyBrush(bool) ) ); //need connect(m_Controls->m_distlabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromDistance(bool) ) ); //need connect(m_Controls->m_predlabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromPrediction(bool) ) ); //need connect(m_Controls->m_predlabelingBrush, SIGNAL(toggled(bool)), this, SLOT( RemovefromPredictionBrush(bool) ) ); //need connect(m_Controls->m_sellabeling, SIGNAL(toggled(bool)), this, SLOT( RemovefromSelection(bool) ) ); //need connect(m_Controls->m_ResampleButton, SIGNAL( clicked() ), this, SLOT( ResampleTractogram( ) ) ); connect(m_Controls->m_RandomPrototypesButton, SIGNAL( clicked() ), this, SLOT( RandomPrototypes( ) ) ); connect(m_Controls->m_SFFPrototypesButton, SIGNAL( clicked() ), this, SLOT( SFFPrototypes( ) ) ); connect(m_Controls->m_validate, SIGNAL( clicked() ), this, SLOT( StartValidation( ) ) ); connect(m_Controls->m_automaticLabelling, SIGNAL( clicked() ), this, SLOT( AutomaticLabelling( ) ) ); connect(m_Controls->m_RemoveCertainData, SIGNAL( clicked() ), this, SLOT( RemoveCertainData( ) ) ); connect(m_Controls->m_resetClassifier, SIGNAL( clicked() ), this, SLOT( ResetClassifier( ) ) ); connect(m_Controls->m_addPointSetPushButton, &QPushButton::clicked,//pointset this, &QmitkInteractiveFiberDissectionView::OnAddPointSetClicked);//pointset connect(m_Controls->m_selectedPointSetWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged,//pointset this, &QmitkInteractiveFiberDissectionView::OnCurrentSelectionChanged);//pointset auto renderWindowPart = this->GetRenderWindowPart();//pointset if (nullptr != renderWindowPart)//pointset this->RenderWindowPartActivated(renderWindowPart);//pointset this->OnCurrentSelectionChanged(m_Controls->m_selectedPointSetWidget->GetSelectedNodes());//pointset } UpdateGui(); } void QmitkInteractiveFiberDissectionView::SetFocus() { m_Controls->toolBoxx->setFocus(); //m_Controls->m_addPointSetPushButton->setFocus();//pointset UpdateGui(); } void QmitkInteractiveFiberDissectionView::UpdateGui() { m_Controls->m_FibLabel->setText("nothing selected"); m_Controls->m_InputData->setTitle("Please Select Input Data"); // disable alle frames m_Controls->m_ErazorButton->setCheckable(true); m_Controls->m_ErazorButton->setEnabled(false); m_Controls->m_BrushButton->setCheckable(true); m_Controls->m_BrushButton->setEnabled(false); m_Controls->m_unclabeling->setCheckable(true); m_Controls->m_unclabeling->setEnabled(false); m_Controls->m_predlabeling->setCheckable(true); m_Controls->m_predlabeling->setEnabled(false); m_Controls->m_unclabelingBrush->setCheckable(true); m_Controls->m_unclabelingBrush->setEnabled(false); m_Controls->m_predlabelingBrush->setCheckable(true); m_Controls->m_predlabelingBrush->setEnabled(false); m_Controls->m_distlabeling->setCheckable(true); m_Controls->m_distlabeling->setEnabled(false); m_Controls->m_sellabeling->setCheckable(true); m_Controls->m_sellabeling->setEnabled(false); m_Controls->m_addPointSetPushButton->setEnabled(false); - m_Controls->m_StreamlineCreation->setEnabled(false); + m_Controls->m_StreamlineCreation->setEnabled(true); m_Controls->m_TrainClassifier->setEnabled(false); m_Controls->m_CreatePrediction->setEnabled(false); m_Controls->m_CreateUncertantyMap->setEnabled(false); m_Controls->m_Numtolabel->setEnabled(false); m_Controls->m_Numtolabel2->setEnabled(false); m_Controls->m_addPointSetPushButton->setEnabled(false); m_Controls->m_AddRandomFibers->setEnabled(false); m_Controls->m_AddDistanceFibers->setEnabled(false); m_Controls->m_AddUncertainFibers->setEnabled(false); // m_Controls->m_PrototypeBox->setEditable(false); // m_Controls->m_useStandardP-> mitk::DataNode::Pointer curtestnode = m_Controls->m_TestBundleBox->GetSelectedNode(); bool testnodeSelected = curtestnode.IsNotNull(); MITK_INFO << testnodeSelected; bool fibSelected = !m_SelectedFB.empty(); bool multipleFibsSelected = (m_SelectedFB.size()>1); bool sthSelected = m_SelectedImageNode.IsNotNull(); bool psSelected = m_SelectedPS.IsNotNull(); // bool nfibSelected = !m_newfibersBundleNode.empty(); // bool posSelected = !m_positiveBundleNode.empty(); bool nfibSelected = m_newfibersBundleNode.IsNotNull(); // bool posSelected = !m_positiveBundleNode.IsNotNull(); // bool negSelected = !m_negativeBundleNode.IsNotNull(); bool posSelected = this->GetDataStorage()->Exists(m_positiveBundleNode); bool negSelected = this->GetDataStorage()->Exists(m_negativeBundleNode); bool indexSelected = !m_index.empty(); bool uncertaintySelected = this->GetDataStorage()->Exists(m_UncertaintyLabelNode); // bool distanceSelected = this->GetDataStorage()->Exists(m_DistanceLabelNode); bool predictionSelected = this->GetDataStorage()->Exists(m_PredictionNode); // toggle visibility of elements according to selected method // are fiber bundles selected? if ( testnodeSelected ) { m_Controls->m_addPointSetPushButton->setEnabled(true); m_Controls->m_AddRandomFibers->setEnabled(true); m_Controls->m_sellabeling->setEnabled(true); } if (fibSelected) { m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str())); // more than two bundles needed to join/subtract if (multipleFibsSelected ) { m_Controls->m_FibLabel->setText("multiple bundles selected"); } } // is image selected if ((sthSelected) || (testnodeSelected)) { m_Controls->m_addPointSetPushButton->setEnabled(true); } if (psSelected) { m_Controls->m_StreamlineCreation->setEnabled(true); } if (nfibSelected && posSelected) { m_Controls->m_ErazorButton->setEnabled(true); m_Controls->m_BrushButton->setEnabled(true); } if (posSelected && negSelected) { m_Controls->m_TrainClassifier->setEnabled(true); } if (indexSelected) { m_Controls->m_CreatePrediction->setEnabled(true); m_Controls->m_AddUncertainFibers->setEnabled(true); m_Controls->m_Numtolabel->setEnabled(true); m_Controls->m_AddDistanceFibers->setEnabled(true); m_Controls->m_Numtolabel2->setEnabled(true); } if (uncertaintySelected) { m_Controls->m_unclabeling->setEnabled(true); m_Controls->m_unclabelingBrush->setEnabled(true); } if (predictionSelected) { m_Controls->m_predlabeling->setEnabled(true); m_Controls->m_predlabelingBrush->setEnabled(true); } // if (distanceSelected) // { m_Controls->m_distlabeling->setEnabled(true); // } // if (m_Controls->m_useStandardP->isChecked()) // { // m_Controls->m_PrototypeBox->setEditable(true); // } } void QmitkInteractiveFiberDissectionView::OnEndInteraction() { } void QmitkInteractiveFiberDissectionView::ResampleTractogram() { mitk::DataNode::Pointer node = m_Controls->m_BundleBox->GetSelectedNode(); auto tractogram = dynamic_cast(node->GetData()); mitk::FiberBundle::Pointer tempfib = tractogram->GetDeepCopy(); std::vector myvec; for (unsigned int k=0; kGetNumFibers(); k++) { myvec.push_back(k); } // auto rng = std::default_random_engine {}; std::random_shuffle(std::begin(myvec), std::end(myvec)); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ unsigned int counter = 0; for (unsigned int i=0; iGetNumFibers(); i++) { vtkCell* cell = tempfib->GetFiberPolyData()->GetCell(myvec.at(i)); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, tempfib->GetFiberWeight(myvec.at(i))); vNewLines->InsertNextCell(container); counter++; } vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); mitk::FiberBundle::Pointer ShuffledBundle = mitk::FiberBundle::New(vNewPolyData); ShuffledBundle->SetFiberWeights(weights); ShuffledBundle->ResampleToNumPoints(40); MITK_INFO << "Resampling Done"; mitk::DataNode::Pointer newnode = mitk::DataNode::New(); newnode->SetData( ShuffledBundle ); newnode->SetName( node->GetName() + "_" + std::to_string(40) ); this->GetDataStorage()->Add(newnode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::RandomPrototypes() { // MITK_INFO << "Number of Fibers to use as Prototypes: "; // MITK_INFO << m_Controls->m_NumPrototypes->value(); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_BundleBox->GetSelectedNode()->GetData()); // MITK_INFO << fib->GetNumFibers(); // std::vector myvec; // for (unsigned int k=0; kGetNumFibers(); k++) // { // myvec.push_back(k); // } // std::random_shuffle(std::begin(myvec), std::end(myvec)); // vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); // vtkSmartPointer vNewLines = vtkSmartPointer::New(); // vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // vtkSmartPointer weights = vtkSmartPointer::New(); // /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ // unsigned int counter = 0; // for (int i=0; im_NumPrototypes->value(); i++) // { // vtkCell* cell = fib->GetFiberPolyData()->GetCell(myvec.at(i)); // auto numPoints = cell->GetNumberOfPoints(); // vtkPoints* points = cell->GetPoints(); // vtkSmartPointer container = vtkSmartPointer::New(); // for (unsigned int j=0; jGetPoint(j, p); // vtkIdType id = vNewPoints->InsertNextPoint(p); // container->GetPointIds()->InsertNextId(id); // } // weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); // vNewLines->InsertNextCell(container); // counter++; // } // vNewPolyData->SetLines(vNewLines); // vNewPolyData->SetPoints(vNewPoints); // mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData); // PrototypesBundle->SetFiberWeights(weights); // mitk::DataNode::Pointer node = mitk::DataNode::New(); // node->SetData(PrototypesBundle); // node->SetName("Random_Prototypes"); //// MITK_INFO << "Number of Streamlines in first function"; //// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); // m_Controls->m_PrototypeBox->SetAutoSelectNewItems (true); // this->GetDataStorage()->Add(node); // m_Controls->m_PrototypeBox->SetAutoSelectNewItems (false); // m_Controls->m_useStandardP->setChecked(false); // node->SetVisibility(false); // Get the number of fibers to use as prototypes from the user interface const int numPrototypes = m_Controls->m_NumPrototypes->value(); MITK_INFO << "Number of Fibers to use as Prototypes: " << numPrototypes; // Get the bundle of fibers to extract prototypes from mitk::DataNode::Pointer selectedNode = m_Controls->m_BundleBox->GetSelectedNode(); if (!selectedNode) { MITK_ERROR << "No fiber bundle selected"; return; } mitk::FiberBundle::Pointer fiberBundle = dynamic_cast(selectedNode->GetData()); if (!fiberBundle) { MITK_ERROR << "Selected node does not contain a fiber bundle"; return; } MITK_INFO << "Number of fibers in the selected bundle: " << fiberBundle->GetNumFibers(); // Randomly shuffle the indices of fibers in the bundle std::vector indices(fiberBundle->GetNumFibers()); std::iota(std::begin(indices), std::end(indices), 0); // fill the vector with 0 to n-1 std::random_shuffle(std::begin(indices), std::end(indices)); // Create new PolyData to hold the prototype fibers vtkSmartPointer prototypePolyData = vtkSmartPointer::New(); vtkSmartPointer prototypeLines = vtkSmartPointer::New(); vtkSmartPointer prototypePoints = vtkSmartPointer::New(); vtkSmartPointer prototypeWeights = vtkSmartPointer::New(); // Extract a subset of fibers as prototypes for (int i = 0; i < numPrototypes; i++) { if (indices.empty()) break; const int index = indices.back(); indices.pop_back(); vtkCell* cell = fiberBundle->GetFiberPolyData()->GetCell(index); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j = 0; j < numPoints; j++) { double p[3]; points->GetPoint(j, p); vtkIdType id = prototypePoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } prototypeWeights->InsertNextValue(fiberBundle->GetFiberWeight(index)); prototypeLines->InsertNextCell(container); } // Create a new FiberBundle containing the prototype fibers prototypePolyData->SetLines(prototypeLines); prototypePolyData->SetPoints(prototypePoints); mitk::FiberBundle::Pointer prototypesBundle = mitk::FiberBundle::New(prototypePolyData); prototypesBundle->SetFiberWeights(prototypeWeights); auto node = mitk::DataNode::New(); node->SetData(prototypesBundle); node->SetName("Random_Prototypes"); node->SetVisibility(false); GetDataStorage()->Add(node); m_Controls->m_PrototypeBox->SetAutoSelectNewItems(true); m_Controls->m_PrototypeBox->SetSelectedNode(node); m_Controls->m_PrototypeBox->SetAutoSelectNewItems(false); m_Controls->m_useStandardP->setChecked(false); MITK_INFO << "Created new node with " << numPrototypes << " random prototypes"; } void QmitkInteractiveFiberDissectionView::SFFPrototypes() { MITK_INFO << "Number of Fibers to use as Prototypes: "; MITK_INFO << m_Controls->m_NumPrototypes->value(); MITK_INFO << "Start Creating Prototypes based on SFF"; mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_BundleBox->GetSelectedNode()->GetData()); /* Get Subset of Tractogram*/ int size_subset = std::max(1.0, ceil(3.0 * m_Controls->m_NumPrototypes->value() * std::log(m_Controls->m_NumPrototypes->value()))); MITK_INFO << fib->GetNumFibers(); std::vector myvec; for (unsigned int k=0; kGetNumFibers(); k++) { myvec.push_back(k); } // std::random_shuffle(std::begin(myvec), std::end(myvec)); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); unsigned int counter = 0; for (int i=0; iGetFiberPolyData()->GetCell(myvec.at(i)); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); vNewLines->InsertNextCell(container); counter++; } vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); mitk::FiberBundle::Pointer temp_fib = mitk::FiberBundle::New(vNewPolyData); temp_fib->SetFiberWeights(weights); MITK_INFO << temp_fib->GetFiberPolyData()->GetNumberOfCells(); /* Create std::vector of the SubsetBundle*/ std::vector< vnl_matrix > out_fib(temp_fib->GetFiberPolyData()->GetNumberOfCells()); for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vnl_matrix streamline; streamline.set_size(3, cell->GetNumberOfPoints()); streamline.fill(0.0); for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< float, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; streamline.set_column(j, candV); } // out_fib.push_back(streamline); out_fib.at(i)=streamline; } /* Calculate the distancematrix of Subset*/ std::vector< vnl_matrix > dist_vec(out_fib.size());// cv::parallel_for_(cv::Range(0, out_fib.size()), [&](const cv::Range &range) { for (int i = range.start; i < range.end; i++) // for (unsigned int i=0; i distances; distances.set_size(1, out_fib.size()); distances.fill(0.0); for (unsigned int j=0; j single_distances; single_distances.set_size(1, out_fib.at(0).cols()); single_distances.fill(0.0); vnl_matrix single_distances_flip; single_distances_flip.set_size(1, out_fib.at(0).cols()); single_distances_flip.fill(0.0); for (unsigned int ik=0; ik single_distances.mean()) { distances.put(0,j, single_distances.mean()); } else { distances.put(0,j, single_distances_flip.mean()); } } // dist_vec.push_back(distances); dist_vec.at(i) = distances; } }); /*Index to find values in distancematrix*/ std::vector myidx; /*Index to find actual streamlines using indexUnc*/ std::vector indexUncDist; /*Start with the Streamline of the highest entropy, which is in distance_matrix at idx 0*/ myidx.push_back(0); /*Vecotr that stores minvalues of current iteration*/ vnl_matrix cur_vec; cur_vec.set_size(1, size_subset); cur_vec.fill(0.0); for (int i=0; im_NumPrototypes->value(); i++) { // unsigned int cur_i = indexUnc.at(myidx.at(i)); /*Save mean distance of all used Samples*/ vnl_matrix sum_matrix; sum_matrix.set_size(myidx.size(), size_subset); sum_matrix.fill(0); for (unsigned int ii=0; ii vNewPolyData2 = vtkSmartPointer::New(); vtkSmartPointer vNewLines2 = vtkSmartPointer::New(); vtkSmartPointer vNewPoints2 = vtkSmartPointer::New(); vtkSmartPointer weights2 = vtkSmartPointer::New(); /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ counter = 0; for (int i=0; im_NumPrototypes->value(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(myidx.at(i)); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints2->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights2->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); vNewLines2->InsertNextCell(container); counter++; } vNewPolyData2->SetLines(vNewLines2); vNewPolyData2->SetPoints(vNewPoints2); mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData2); PrototypesBundle->SetFiberWeights(weights2); MITK_INFO << PrototypesBundle->GetFiberPolyData()->GetNumberOfCells(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(PrototypesBundle); node->SetName("SFF_Prototypes"); //// MITK_INFO << "Number of Streamlines in first function"; //// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); m_Controls->m_PrototypeBox->SetAutoSelectNewItems (true); this->GetDataStorage()->Add(node); m_Controls->m_PrototypeBox->SetAutoSelectNewItems (false); m_Controls->m_useStandardP->setChecked(false); node->SetVisibility(false); } void QmitkInteractiveFiberDissectionView::OnAddPointSetClicked()//pointset { // ask for the name of the point set bool ok = false; QString name = QInputDialog::getText(QApplication::activeWindow(), tr("Add point set..."), tr("Enter name for the new point set"), QLineEdit::Normal, tr("PointSet").arg(++m_IterationCounter), &ok); // QString name = "PointSet"; if (!ok || name.isEmpty()) { return; } mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); mitk::DataNode::Pointer pointSetNode = mitk::DataNode::New(); pointSetNode->SetData(pointSet); pointSetNode->SetProperty("name", mitk::StringProperty::New(name.toStdString())); pointSetNode->SetProperty("opacity", mitk::FloatProperty::New(1)); pointSetNode->SetColor(1.0, 1.0, 0.0); m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode(); this->GetDataStorage()->Add(pointSetNode, m_testnode); m_Controls->m_selectedPointSetWidget->SetCurrentSelectedNode(pointSetNode); } void QmitkInteractiveFiberDissectionView::OnCurrentSelectionChanged(QmitkSingleNodeSelectionWidget::NodeList /*nodes*/)//pointset { m_Controls->m_poinSetListWidget->SetPointSetNode(m_Controls->m_selectedPointSetWidget->GetSelectedNode()); m_SelectedPS = m_Controls->m_selectedPointSetWidget->GetSelectedNode(); // m_Controls->m_trainbundleWidget->SetPointSetNode(m_Controls->m_trainbundleWidget->GetSelectedNode()); // m_trainbundle = m_Controls->m_trainbundleWidget->GetSelectedNode(); UpdateGui(); } void QmitkInteractiveFiberDissectionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { m_SelectedFB.clear(); if (nodes.empty() || nodes.front().IsNull()) { m_SelectedImageNode = nullptr; } else { m_SelectedImageNode = nodes.front(); } for (auto node: nodes) { if (dynamic_cast(node->GetData())) m_SelectedImage = dynamic_cast(node->GetData()); else if ( dynamic_cast(node->GetData()) ) m_SelectedFB.push_back(node); } UpdateGui(); } void QmitkInteractiveFiberDissectionView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart)//pointset { if (nullptr != m_Controls) { m_Controls->m_poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); m_Controls->m_poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); m_Controls->m_poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); } } void QmitkInteractiveFiberDissectionView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart)//pointset { if (nullptr != m_Controls) { m_Controls->m_poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); m_Controls->m_poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); m_Controls->m_poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); } } void QmitkInteractiveFiberDissectionView::CreateStreamline() { - if (m_positiveBundleNode.IsNull()) - { - mitk::DataNode::Pointer node = mitk::DataNode::New(); - - m_positiveFibersData = vtkSmartPointer::New(); - m_positiveFibersData->SetPoints(vtkSmartPointer::New()); - m_positiveFibersData->SetLines(vtkSmartPointer::New()); - m_positiveBundle = mitk::FiberBundle:: New(m_positiveFibersData); - - node->SetData( m_positiveBundle ); - node->SetData(m_negativeBundle); -// node->SetFloatProperty("shape.tuberadius", 0.5); -// mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - m_positiveBundleNode = node; - this->GetDataStorage()->Add(m_positiveBundleNode); - MITK_INFO << "Create Bundle"; - } +// if (m_positiveBundleNode.IsNull()) +// { +// mitk::DataNode::Pointer node = mitk::DataNode::New(); + +// m_positiveFibersData = vtkSmartPointer::New(); +// m_positiveFibersData->SetPoints(vtkSmartPointer::New()); +// m_positiveFibersData->SetLines(vtkSmartPointer::New()); +// m_positiveBundle = mitk::FiberBundle:: New(m_positiveFibersData); + +// node->SetData( m_positiveBundle ); +// node->SetData(m_negativeBundle); +//// node->SetFloatProperty("shape.tuberadius", 0.5); +//// mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +// m_positiveBundleNode = node; +// this->GetDataStorage()->Add(m_positiveBundleNode); +// MITK_INFO << "Create Bundle"; +// } - if (!m_positiveBundleNode.IsNull()) - { +// if (!m_positiveBundleNode.IsNull()) +// { - this->GetDataStorage()->Remove(m_positiveBundleNode); - MITK_INFO << "Adding fibers"; - MITK_INFO << m_positiveBundle->GetFiberPolyData()->GetNumberOfCells(); - m_positiveFibersData = m_positiveBundle->GetFiberPolyData(); - } +// this->GetDataStorage()->Remove(m_positiveBundleNode); +// MITK_INFO << "Adding fibers"; +// MITK_INFO << m_positiveBundle->GetFiberPolyData()->GetNumberOfCells(); +// m_positiveFibersData = m_positiveBundle->GetFiberPolyData(); +// } - vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); - vtkSmartPointer vNewLines = vtkSmartPointer::New(); - vtkSmartPointer vNewPoints = vtkSmartPointer::New(); +// vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); +// vtkSmartPointer vNewLines = vtkSmartPointer::New(); +// vtkSmartPointer vNewPoints = vtkSmartPointer::New(); - unsigned int counter = 0; - for (unsigned int i=0; iGetNumberOfCells(); ++i) - { - MITK_INFO<< "New Line"; - vtkCell* cell = m_positiveFibersData->GetCell(i); - auto numPoints = cell->GetNumberOfPoints(); - vtkPoints* points = cell->GetPoints(); +// unsigned int counter = 0; +// for (unsigned int i=0; iGetNumberOfCells(); ++i) +// { +// MITK_INFO<< "New Line"; +// vtkCell* cell = m_positiveFibersData->GetCell(i); +// auto numPoints = cell->GetNumberOfPoints(); +// vtkPoints* points = cell->GetPoints(); - vtkSmartPointer container = vtkSmartPointer::New(); - for (unsigned int j=0; jGetPoint(j, p); +// vtkSmartPointer container = vtkSmartPointer::New(); +// for (unsigned int j=0; jGetPoint(j, p); - vtkIdType id = vNewPoints->InsertNextPoint(p); - container->GetPointIds()->InsertNextId(id); - } +// vtkIdType id = vNewPoints->InsertNextPoint(p); +// container->GetPointIds()->InsertNextId(id); +// } - vNewLines->InsertNextCell(container); - counter++; - } +// vNewLines->InsertNextCell(container); +// counter++; +// } + +// mitk::PointSet::Pointer pointSet = dynamic_cast(m_SelectedPS->GetData()); + + +// vnl_matrix streamline; +// streamline.set_size(3, pointSet->GetSize()); +// streamline.fill(0.0); - mitk::PointSet::Pointer pointSet = dynamic_cast(m_SelectedPS->GetData()); +// mitk::PointSet::PointsIterator begin = pointSet->Begin(); +// mitk::PointSet::PointsIterator end = pointSet->End(); +// unsigned int i; +// mitk::PointSet::PointsContainer::Iterator it; - vnl_matrix streamline; - streamline.set_size(3, pointSet->GetSize()); - streamline.fill(0.0); +// for (it = begin, i = 0; it != end; ++it, ++i) +// { +// PointSet::PointType pt = pointSet->GetPoint(it->Index()); +// vnl_vector_fixed< float, 3 > candV; +// candV[0]=pt[0]; candV[1]=pt[1]; candV[2]=pt[2]; +// streamline.set_column(i, candV); +// } + +// // build Fiber +// vtkSmartPointer container = vtkSmartPointer::New(); + + +// for (unsigned int j=0; jInsertNextPoint(p); +// container->GetPointIds()->InsertNextId(id); +// } +// MITK_INFO<< "Last Line from current pointset"; +// vNewLines->InsertNextCell(container); + +// vNewPolyData->SetPoints(vNewPoints); +// vNewPolyData->SetLines(vNewLines); + +// m_positiveFibersData = vtkSmartPointer::New(); +// m_positiveFibersData->SetPoints(vtkSmartPointer::New()); +// m_positiveFibersData->SetLines(vtkSmartPointer::New()); +// m_positiveFibersData->SetPoints(vNewPoints); +// m_positiveFibersData->SetLines(vNewLines); + +// m_positiveBundle = mitk::FiberBundle::New(vNewPolyData); +// m_positiveBundle->ResampleToNumPoints(40); +// MITK_INFO << "Resampling Done"; + + +// m_positiveBundle->SetFiberColors(0, 255, 0); + + + +// mitk::DataNode::Pointer node = mitk::DataNode::New(); +// node->SetData(m_positiveBundle); +// node->SetName("+Bundle"); +//// node->SetFloatProperty("shape.tuberadius", 0.5); +//// mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + +// m_positiveBundleNode= node; + + + +// MITK_INFO << "The + Bundle has Streamlines:"; +// auto m_PosStreamline= dynamic_cast(m_positiveBundleNode->GetData()); +// MITK_INFO << m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); +// this->GetDataStorage()->Add(m_positiveBundleNode); +//// m_Controls->m_selectedPointSetWidget->m_ToggleAddPoint->setEnabled(false); - mitk::PointSet::PointsIterator begin = pointSet->Begin(); - mitk::PointSet::PointsIterator end = pointSet->End(); - unsigned int i; - mitk::PointSet::PointsContainer::Iterator it; +// UpdateGui(); +// m_createdStreamlineCounter +=1; + // initialize figure's geometry with empty geometry + mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); + mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New(); + figure->SetPlaneGeometry( emptygeometry ); - for (it = begin, i = 0; it != end; ++it, ++i) + //set desired data to DataNode where Planarfigure is stored + mitk::DataNode::Pointer newNode = mitk::DataNode::New(); + newNode->SetName(QString("Ball").toStdString()); + newNode->SetData(figure); + newNode->SetBoolProperty("planarfigure.3drendering", true); + newNode->SetBoolProperty("planarfigure.3drendering.fill", true); + + mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(newNode->GetDataInteractor().GetPointer()); + if(figureInteractor.IsNull()) { - PointSet::PointType pt = pointSet->GetPoint(it->Index()); - vnl_vector_fixed< float, 3 > candV; - candV[0]=pt[0]; candV[1]=pt[1]; candV[2]=pt[2]; - streamline.set_column(i, candV); + figureInteractor = mitk::PlanarFigureInteractor::New(); + us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); + figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); + figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); + figureInteractor->SetDataNode(newNode); } - // build Fiber - vtkSmartPointer container = vtkSmartPointer::New(); + // figure drawn on the topmost layer / image + GetDataStorage()->Add(newNode ); - for (unsigned int j=0; jSetSelected(true); - vtkIdType id = vNewPoints->InsertNextPoint(p); - container->GetPointIds()->InsertNextId(id); - } - MITK_INFO<< "Last Line from current pointset"; - vNewLines->InsertNextCell(container); + vtkSmartPointer sphereSource = vtkSmartPointer::New(); + sphereSource->SetRadius(10); + sphereSource->SetPhiResolution(30); + sphereSource->SetThetaResolution(30); + sphereSource->Update(); - vNewPolyData->SetPoints(vNewPoints); - vNewPolyData->SetLines(vNewLines); + // Convert the VTK sphere to a MITK surface + mitk::Surface::Pointer sphereSurface = mitk::Surface::New(); + sphereSurface->SetVtkPolyData(sphereSource->GetOutput()); - m_positiveFibersData = vtkSmartPointer::New(); - m_positiveFibersData->SetPoints(vtkSmartPointer::New()); - m_positiveFibersData->SetLines(vtkSmartPointer::New()); - m_positiveFibersData->SetPoints(vNewPoints); - m_positiveFibersData->SetLines(vNewLines); + // Add the surface to the DataStorage + mitk::DataNode::Pointer sphereNode = mitk::DataNode::New(); + sphereNode->SetData(sphereSurface); + sphereNode->SetName("Sphere"); + GetDataStorage()->Add(sphereNode); - m_positiveBundle = mitk::FiberBundle::New(vNewPolyData); - m_positiveBundle->ResampleToNumPoints(40); - MITK_INFO << "Resampling Done"; +// vtkSmartPointer sphereSource = vtkSmartPointer::New(); +// sphereSource->SetCenter(0, 0, 0); +// sphereSource->SetRadius(5.0); - m_positiveBundle->SetFiberColors(0, 255, 0); +// auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D); +// vtkSmartPointer mapper = vtkSmartPointer::New(); +// vtkmapper->SetInputConnection(sphereSource->GetOutputPort()); - mitk::DataNode::Pointer node = mitk::DataNode::New(); - node->SetData(m_positiveBundle); - node->SetName("+Bundle"); -// node->SetFloatProperty("shape.tuberadius", 0.5); -// mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +// vtkSmartPointer actor = vtkSmartPointer::New(); +// actor->SetMapper(mapper); +// actor->GetProperty()->SetColor(1,0,0); - m_positiveBundleNode= node; +// mitk::Surface::Pointer sphereSurface = mitk::Surface::New(); +// sphereSurface->SetVtkPolyData(sphereSource->GetOutput()); +// mitk::DataNode::Pointer m_SphereNode = mitk::DataNode::New(); +// m_SphereNode->SetName("Sphere"); +// m_SphereNode->SetData(sphereSurface); +// m_SphereNode->SetOpacity(1.0); +// m_SphereNode->SetColor(1.0, 0.0, 0.0); +// m_SphereNode->SetVisibility(true); - MITK_INFO << "The + Bundle has Streamlines:"; - auto m_PosStreamline= dynamic_cast(m_positiveBundleNode->GetData()); - MITK_INFO << m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); +// GetDataStorage()->Add(m_SphereNode); +// mitk::RenderingManager::GetInstance()->RequestUpdateAll(); +// mitk::VtkPropRenderer::Pointer m_Renderer = mitk::VtkPropRenderer::New(); +// m_Renderer->SetMapperID(mitk::BaseRenderer::Standard3D); +// m_Renderer->SetDataStorage(GetDataStorage()); +// m_Renderer->SetDataNode(m_SphereNode); - this->GetDataStorage()->Add(m_positiveBundleNode); -// m_Controls->m_selectedPointSetWidget->m_ToggleAddPoint->setEnabled(false); +// GetDataStorage()->Add(m_Renderer->GetRendererAsDataNode()); +// mitk::DataNode::Pointer rendererNode = mitk::DataNode::New(); +// rendererNode->SetData(m_Renderer); - UpdateGui(); - m_createdStreamlineCounter +=1; +// m_SphereNode->SetData(sphereSurface); +// m_SphereNode->SetVisibility(true); +// // Set a name for the renderer node +// rendererNode->SetName("RendererNode"); +// // Add the renderer node to the DataStorage +// GetDataStorage()->Add(rendererNode); +// RenderingManager::GetInstance()->RequestUpdateAll(); + UpdateGui(); } void QmitkInteractiveFiberDissectionView::ExtractRandomFibersFromTractogram() { m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode(); m_testnode->SetVisibility(false); // m_SelectedFB.at(0)->SetVisibility(false); m_Controls->m_ErazorButton->setChecked(false); m_Controls->m_BrushButton->setChecked(false); MITK_INFO << "Number of Fibers to extract from Tractogram: "; MITK_INFO << m_Controls->m_NumRandomFibers->value(); if (this->GetDataStorage()->Exists(m_newfibersBundleNode)) { MITK_INFO << "To Label Bundle Exists"; mitk::FiberBundle::Pointer Stack = dynamic_cast(m_newfibersBundleNode->GetData()); this->GetDataStorage()->Remove(m_newfibersBundleNode); mitk::DataNode::Pointer node = mitk::DataNode::New(); m_newfibersFibersData = vtkSmartPointer::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer::New()); m_newfibersBundle = mitk::FiberBundle:: New(m_newfibersFibersData); m_newfibersFibersData->SetLines(vtkSmartPointer::New()); // node->SetData( m_newfibersBundle ); // m_newfibersBundleNode = node ; MITK_INFO << "Create Bundle"; } mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_trainbundle->GetData()); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); // weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers()); // MITK_INFO << fib->GetNumFibers(); // std::vector myvec; // for (unsigned int k=0; kGetNumFibers(); k++) // { // myvec.push_back(k); // } // std::random_shuffle(std::begin(myvec), std::end(myvec)); /* Check weather all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ unsigned int counter = 0; // int thresh1; // int thresh2; // thresh2 = m_Controls->m_NumRandomFibers->value()*(m_RandomExtractionCounter+1); // thresh1 = m_Controls->m_NumRandomFibers->value()*(m_RandomExtractionCounter); // if (thresh1>fib->GetFiberPolyData()->GetNumberOfCells()) // { // thresh1=fib->GetFiberPolyData()->GetNumberOfCells(); // } // if (thresh2>fib->GetFiberPolyData()->GetNumberOfCells()) // { // thresh2=fib->GetFiberPolyData()->GetNumberOfCells(); // } // if (thresh1!=fib->GetFiberPolyData()->GetNumberOfCells()) if (m_Controls->m_NumRandomFibers->value()!=fib->GetFiberPolyData()->GetNumberOfCells()) { // for ( int i=thresh1; im_NumRandomFibers->value(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } for ( int i=0; im_NumRandomFibers->value(); i++) { fib->GetFiberPolyData()->DeleteCell(i); } fib->GetFiberPolyData()->RemoveDeletedCells(); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); // m_SelectedFB.at(0)->SetData(fib); vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); m_newfibersFibersData = vtkSmartPointer::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer::New()); m_newfibersFibersData->SetLines(vtkSmartPointer::New()); m_newfibersFibersData->SetPoints(vNewPoints); m_newfibersFibersData->SetLines(vNewLines); m_newfibersBundle = mitk::FiberBundle::New(vNewPolyData); m_newfibersBundle->SetFiberColors(255, 255, 255); m_newfibersBundle->SetFiberWeights(weights); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_newfibersBundle); node->SetName("ToLabel"); // node->SetData(m_negativeBundle); // node->SetFloatProperty("shape.tuberadius", 0.5); // mitk::RenderingManager::GetInstance()->RequestUpdateAll(); m_newfibersBundleNode = node; // MITK_INFO << "Number of Streamlines in first function"; // MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); this->GetDataStorage()->Add(m_newfibersBundleNode); mitk::FiberBundle::Pointer m_negativeBundle = mitk::FiberBundle::New(); mitk::DataNode::Pointer node2 = mitk::DataNode::New(); node2->SetName("-Bundle"); node2->SetData(m_negativeBundle); // node->SetFloatProperty("shape.tuberadius", 0.5); // mitk::RenderingManager::GetInstance()->RequestUpdateAll(); m_negativeBundleNode = node2; this->GetDataStorage()->Add(m_negativeBundleNode); m_RandomExtractionCounter++; } // m_Controls->m_ErazorButton->setChecked(true); UpdateGui(); } void QmitkInteractiveFiberDissectionView::RemovefromBundle( bool checked ) { if (checked) { m_Controls->m_BrushButton->setChecked(false); // if (m_StreamlineInteractor.IsNull()) // { this->CreateStreamlineInteractorBrush(); this->CreateStreamlineInteractor(); // } m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(false); m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); m_StreamlineInteractor->EnableInteraction(true); // m_StreamlineInteractor->EnableInteraction(true); // m_StreamlineInteractor->LabelfromPrediction(false); // m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); // m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); // } // else // { // m_StreamlineInteractor->EnableInteraction(true); // m_StreamlineInteractor->LabelfromPrediction(false); // m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); // } } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } UpdateGui(); } void QmitkInteractiveFiberDissectionView::RemovefromBundleBrush( bool checked ) { if (checked) { m_Controls->m_ErazorButton->setChecked(false); // if (m_StreamlineInteractorBrush.IsNull()) // { this->CreateStreamlineInteractor(); this->CreateStreamlineInteractorBrush(); // } m_StreamlineInteractorBrush->EnableInteraction(true); m_StreamlineInteractorBrush->LabelfromPrediction(false); m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode); m_StreamlineInteractorBrush->EnableInteraction(true); // m_StreamlineInteractorBrush->EnableInteraction(true); // m_StreamlineInteractorBrush->LabelfromPrediction(false); // m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); // m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode); // } // else // { // m_StreamlineInteractorBrush->EnableInteraction(true); // m_StreamlineInteractorBrush->LabelfromPrediction(false); // m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); // m_StreamlineInteractorBrush->SetToLabelNode(m_newfibersBundleNode); // } } else { m_StreamlineInteractorBrush->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreateStreamlineInteractor() { m_StreamlineInteractor = mitk::StreamlineInteractor::New(); m_StreamlineInteractor->LoadStateMachine("Streamline3DStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); m_StreamlineInteractor->SetEventConfig("Streamline3DConfig.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); // m_StreamlineInteractor->SetRotationEnabled(rotationEnabled); } void QmitkInteractiveFiberDissectionView::CreateStreamlineInteractorBrush() { m_StreamlineInteractorBrush = mitk::StreamlineInteractorBrush::New(); m_StreamlineInteractorBrush->LoadStateMachine("StreamlineBrush3DStates.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); m_StreamlineInteractorBrush->SetEventConfig("StreamlineBrush3DConfig.xml", us::ModuleRegistry::GetModule("MitkFiberDissection")); // m_StreamlineInteractor->SetRotationEnabled(rotationEnabled); } void QmitkInteractiveFiberDissectionView::StartAlgorithm() { m_negativeBundle = dynamic_cast(m_negativeBundleNode->GetData()); m_positiveBundle = dynamic_cast(m_positiveBundleNode->GetData()); this->GetDataStorage()->Remove(m_UncertaintyLabelNode); this->GetDataStorage()->Remove(m_DistanceLabelNode); MITK_INFO << "Clean Test Data"; // this->CleanTestArray(); m_testnode = m_Controls->m_TestBundleBox->GetSelectedNode(); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); fib->GetFiberPolyData()->RemoveDeletedCells(); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); m_Controls->m_unclabeling->setChecked(false); m_Controls->m_distlabeling->setChecked(false); m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_predlabeling->setChecked(false); m_Controls->m_predlabelingBrush->setChecked(false); m_uncCounter = 0; // classifier.reset(); MITK_INFO << "Extract Features"; classifier = std::make_shared(); classifier->SetActiveCycle(m_activeCycleCounter); classifier->SetTractogramPlus(m_positiveBundle); classifier->SetTractogramMinus(m_negativeBundle); classifier->SetTractogramPrototypes(dynamic_cast(m_Controls->m_PrototypeBox->GetSelectedNode()->GetData()), m_Controls->m_useStandardP->isChecked()); // classifier->SetTractogramTest(dynamic_cast(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName()); classifier->SetTractogramTest(dynamic_cast(m_testnode->GetData()), m_testnode->GetName()); // classifier->SetTractogramTest(dynamic_cast(m_trainbundle->GetData()), m_trainbundle->GetName()); classifier->Update(); m_index = classifier->m_index; MITK_INFO << "Number of Cycles"; MITK_INFO << m_activeCycleCounter; m_activeCycleCounter += 1; MITK_INFO << "Algorithm run succesfully"; // mitk::DataNode::Pointer node = mitk::DataNode::New(); // this->GetDataStorage()->Add(node); m_Controls->m_CreatePrediction->setEnabled(true); UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreatePredictionNode() { MITK_INFO << "Create Prediction"; m_Prediction = classifier->CreatePrediction(m_index.at(0), false); // m_Prediction->ColorFibersByFiberWeights(false, mitk::LookupTable::JET); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_Prediction); auto s = std::to_string(m_activeCycleCounter); node->SetName("Prediction"+s); m_PredictionNode = node; this->GetDataStorage()->Add(m_PredictionNode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreateCertainNode() { MITK_INFO << "Create Certain Data"; m_CertainMinus = classifier->CreatePrediction(m_index.at(2), false); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_CertainMinus); auto s = std::to_string(m_activeCycleCounter); node->SetName("m_CertainMinus"+s); m_CertainMinusNode = node; this->GetDataStorage()->Add(m_CertainMinusNode); // m_CertainPlus = classifier->CreatePrediction(m_index.at(4)); // mitk::DataNode::Pointer node2= mitk::DataNode::New(); // node2->SetData(m_CertainPlus); // node2->SetName("m_CertainPlus"+s); // m_CertainPlusNode = node2; // this->GetDataStorage()->Add(m_CertainPlusNode); // m_CertainBetweenMinus = classifier->CreatePrediction(m_index.at(4)); // mitk::DataNode::Pointer node3 = mitk::DataNode::New(); // node3->SetData(m_CertainBetweenMinus); // node3->SetName("m_CertainBetweenMinus"+s); // m_CertainBetweenMinusNode = node3; // this->GetDataStorage()->Add(m_CertainBetweenMinusNode); // m_CertainBetweenPlus = classifier->CreatePrediction(m_index.at(6)); // mitk::DataNode::Pointer node4= mitk::DataNode::New(); // node4->SetData(m_CertainBetweenPlus); // node4->SetName("m_CertainBetweenPlus"+s); // m_CertainBetweenPlusNode = node4; // this->GetDataStorage()->Add(m_CertainBetweenPlusNode); } void QmitkInteractiveFiberDissectionView::RemoveCertainData() { // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); MITK_INFO << "Length of certain negativ data:"; MITK_INFO << m_index.at(2).size(); MITK_INFO << "Length of Testdata"; MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); for (unsigned int i=0; i< m_index.at(2).size(); i++) { fib->GetFiberPolyData()->DeleteCell(m_index.at(2).at(i)); } // fib->GetFiberPolyData()->RemoveDeletedCells(); MITK_INFO << "Length of Testdata"; MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); } void QmitkInteractiveFiberDissectionView::CreateUncertaintySampleNode() { this->GetDataStorage()->Remove(m_UncertaintyLabelNode); MITK_INFO << "Create Fibers to label based on Uncertainty"; std::vector vec = m_index.at(1); std::vector myvec = {vec.begin() + m_uncCounter, vec.begin() + m_uncCounter + m_Controls->m_Numtolabel->value()}; m_uncCounter = m_uncCounter + m_Controls->m_Numtolabel->value(); MITK_INFO << m_index.at(1).size(); MITK_INFO << myvec.size(); m_UncertaintyLabel = classifier->CreatePrediction(myvec, true); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_UncertaintyLabel); float d = 5.0; auto s = std::to_string(m_activeCycleCounter); node->SetName("UncertaintyLabel"+s); m_UncertaintyLabelNode = node; m_UncertaintyLabelNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(d)); this->GetDataStorage()->Add(m_UncertaintyLabelNode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreateDistanceSampleNode() { // MITK_INFO << "Create Fibers to label based on Distance in Features-Space"; // std::vector myvec = m_index.at(2); // myvec.resize(m_Controls->m_Numtolabel2->value()); // MITK_INFO << m_index.at(2).size(); // MITK_INFO << myvec.size(); float myval = m_Controls->m_subsetfft->value() * 0.01; MITK_INFO << myval; std::vector> curidx; curidx = classifier->GetDistanceData(myval); std::vector myvec = curidx.at(0); myvec.resize(m_Controls->m_Numtolabel2->value()); MITK_INFO << m_index.at(2).size(); MITK_INFO << myvec.size(); m_DistanceLabel = classifier->CreatePrediction(myvec, true); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_DistanceLabel); auto s = std::to_string(m_activeCycleCounter); node->SetName("DistanceLabel"+s); m_DistanceLabelNode = node; this->GetDataStorage()->Add(m_DistanceLabelNode); UpdateGui(); } void QmitkInteractiveFiberDissectionView::RemovefromUncertainty( bool checked ) { if (checked) { m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_predlabelingBrush->setChecked(false); m_Controls->m_predlabeling->setChecked(false); m_UncertaintyLabel->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractor(); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(false); m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractor->SetToLabelNode(m_UncertaintyLabelNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkInteractiveFiberDissectionView::RemovefromUncertaintyBrush( bool checked ) { if (checked) { m_Controls->m_unclabeling->setChecked(false); m_Controls->m_predlabelingBrush->setChecked(false); m_Controls->m_predlabeling->setChecked(false); m_UncertaintyLabel->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractorBrush(); m_StreamlineInteractorBrush->EnableInteraction(true); m_StreamlineInteractorBrush->LabelfromPrediction(false); m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractorBrush->SetToLabelNode(m_UncertaintyLabelNode); } else { m_StreamlineInteractorBrush->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkInteractiveFiberDissectionView::RemovefromDistance( bool checked ) { if (checked) { m_DistanceLabel->SetFiberColors(255, 255, 255); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(false); m_StreamlineInteractor->SetToLabelNode(m_DistanceLabelNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkInteractiveFiberDissectionView::RemovefromPrediction( bool checked ) { if (checked) { m_Controls->m_predlabelingBrush->setChecked(false); m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_unclabeling->setChecked(false); // m_Prediction->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractor(); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(true); m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractor->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractor->SetToLabelNode(m_PredictionNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; // this->CleanTestArray(); } } void QmitkInteractiveFiberDissectionView::RemovefromPredictionBrush( bool checked ) { if (checked) { m_Controls->m_predlabeling->setChecked(false); m_Controls->m_unclabelingBrush->setChecked(false); m_Controls->m_unclabeling->setChecked(false); // m_Prediction->SetFiberColors(255, 255, 255); this->CreateStreamlineInteractorBrush(); m_StreamlineInteractorBrush->EnableInteraction(true); m_StreamlineInteractorBrush->LabelfromPrediction(true); m_StreamlineInteractorBrush->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractorBrush->SetPositiveNode(m_positiveBundleNode); m_StreamlineInteractorBrush->SetToLabelNode(m_PredictionNode); } else { m_StreamlineInteractorBrush->EnableInteraction(false); // m_StreamlineInteractor = nullptr; // this->CleanTestArray(); } } void QmitkInteractiveFiberDissectionView::RemovefromSelection( bool checked ) { if (checked) { // m_Prediction->SetFiberColors(255, 255, 255); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->LabelfromPrediction(true); // m_StreamlineInteractor->SetToLabelNode(m_SelectedFB.at(0)); m_StreamlineInteractor->SetToLabelNode(m_testnode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } } void QmitkInteractiveFiberDissectionView::StartValidation() { validater.reset(); // mitk::DataNode::Pointer prednode = m_Controls->m_BundleBox->GetSelectedNode(); // mitk::FiberBundle::Pointer pred = dynamic_cast(prednode->GetData()); // mitk::DataNode::Pointer gtnode = m_Controls->m_BundleBox->GetSelectedNode(); // mitk::FiberBundle::Pointer gt = dynamic_cast(gtnode->GetData()); // mitk::FiberBundle::Pointer pred = dynamic_cast(m_Controls->m_PredictionBox->GetSelectedNode()->GetData()); // mitk::FiberBundle::Pointer gt = dynamic_cast(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData()); validater= std::make_shared(); validater->SetTractogramPrototypes(dynamic_cast(m_Controls->m_PrototypeBox->GetSelectedNode()->GetData()), m_Controls->m_useStandardP->isChecked()); MITK_INFO << "Prototypes loaded"; validater->SetTractogramPrediction(dynamic_cast(m_Controls->m_PredictionBox->GetSelectedNode()->GetData())); MITK_INFO << "Prediction loaded"; validater->SetTractogramGroundtruth(dynamic_cast(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData())); MITK_INFO << "Groundtruth loaded"; validater->SetActiveCycle(m_activeCycleCounter); // validater->SetTractogramTest(dynamic_cast(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName()); validater->SetTractogramTest(dynamic_cast(m_testnode->GetData()), m_testnode->GetName()); // classifier->SetTractogramTest(dynamic_cast(m_trainbundle->GetData()), m_trainbundle->GetName()); MITK_INFO << "Testdata loaded"; vnl_vector metrics; metrics = validater->ValidationPipe(); m_metrics.push_back(metrics); MITK_INFO << "Validation run succesfully"; UpdateGui(); } void QmitkInteractiveFiberDissectionView::AutomaticLabelling() { // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); // mitk::FiberBundle::Pointer fib_true = dynamic_cast(m_Controls->m_GroundtruthBox->GetSelectedNode()->GetData()); // vtkCell* cell; // vtkCell* cell2; // for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) // { // cell = fib->GetFiberPolyData()->GetCell(i); // for (int k=0; kGetFiberPolyData()->GetNumberOfCells(); k++ ) // { // cell2 = fib_true->GetFiberPolyData()->GetCell(i); // if (cell==cell2) // MITK_INFO << "Same"; // } // } mitk::FiberBundle::Pointer fib = dynamic_cast(m_PredictionNode->GetData()); mitk::FiberBundle::Pointer fib_true = dynamic_cast(m_positiveBundleNode->GetData()); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer weights = vtkSmartPointer::New(); /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ unsigned int counter = 0; for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib_true->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib_true->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); mitk::FiberBundle::Pointer MergedPrediction = mitk::FiberBundle::New(vNewPolyData); MergedPrediction->SetFiberWeights(weights); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(MergedPrediction); node->SetName("MergedPrediction"); this->GetDataStorage()->Add(node); } void QmitkInteractiveFiberDissectionView::CleanTestArray() { mitk::FiberBundle::Pointer fib_pos = dynamic_cast(m_positiveBundleNode->GetData()); mitk::FiberBundle::Pointer fib_neg = dynamic_cast(m_negativeBundleNode->GetData()); // mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); mitk::FiberBundle::Pointer fib = dynamic_cast(m_testnode->GetData()); vtkCell* cur_cell; vtkCell* cur_cell2; MITK_INFO << fib_neg->GetFiberPolyData()->GetNumberOfCells(); MITK_INFO << fib_pos->GetFiberPolyData()->GetNumberOfCells(); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); std::vector array; std::vector array2; // cv::parallel_for_(cv::Range(0, fib->GetFiberPolyData()->GetNumberOfCells()), [&](const cv::Range &range) // { // for (int i = range.start; i < range.end; i++) for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { cur_cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cur_cell->GetNumberOfPoints(); vtkPoints* points = cur_cell->GetPoints(); for (unsigned int j=0; jGetPoint(j, p); array.push_back(*p); } for (int ik=0; ikGetFiberPolyData()->GetNumberOfCells(); ik++) { cur_cell2 = fib_neg->GetFiberPolyData()->GetCell(ik); auto numPoints2 = cur_cell2->GetNumberOfPoints(); vtkPoints* points2 = cur_cell2->GetPoints(); for (unsigned int j2=0; j2GetPoint(j2, p2); array2.push_back(*p2); } if (array==array2) { fib->GetFiberPolyData()->DeleteCell(i); MITK_INFO << "Delete Cell"; } array2.clear(); } for (int ik=0; ikGetFiberPolyData()->GetNumberOfCells(); ik++) { cur_cell2 = fib_pos->GetFiberPolyData()->GetCell(ik); auto numPoints2 = cur_cell2->GetNumberOfPoints(); vtkPoints* points2 = cur_cell2->GetPoints(); for (unsigned int j2=0; j2GetPoint(j2, p2); array2.push_back(*p2); } if (array==array2) { fib->GetFiberPolyData()->DeleteCell(i); MITK_INFO << "Delete Cell"; } array2.clear(); } array.clear(); } // }); // fib->GetFiberPolyData()->RemoveDeletedCells(); MITK_INFO << fib->GetFiberPolyData()->GetNumberOfCells(); } void QmitkInteractiveFiberDissectionView::ResetClassifier() { m_IterationCounter = 0; m_RandomExtractionCounter = 0; m_activeCycleCounter = 0; m_createdStreamlineCounter = 0; classifier.reset(); this->GetDataStorage()->Remove(m_positiveBundleNode); this->GetDataStorage()->Remove(m_negativeBundleNode); this->GetDataStorage()->Remove(m_negativeBundleNode); m_positiveBundleNode = NULL; m_negativeBundleNode = NULL; m_negativeBundleNode = NULL; m_positiveBundle = NULL; m_negativeBundle = NULL; m_negativeBundle = NULL; m_Controls->m_TrainClassifier->setEnabled(false); m_Controls->m_CreatePrediction->setEnabled(false); m_Controls->m_CreateUncertantyMap->setEnabled(false); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h index acab0f6..a93a067 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionView.h @@ -1,191 +1,196 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkInteractiveFiberDissectionView_h #define QmitkInteractiveFiberDissectionView_h #include "ui_QmitkInteractiveFiberDissectionViewControls.h" #include //Pointset #include //Pointset #include //Pointset #include //Pointset #include #include #include //Pointset #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include + +#include +#include + /*! \brief View to process fiber bundles. Supplies methods to extract fibers from the bundle, fiber resampling, mirroring, join and subtract bundles and much more. */ class QmitkInteractiveFiberDissectionView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: typedef itk::Image< unsigned char, 3 > ItkUCharImageType; typedef itk::Image< float, 3 > ItkFloatImageType; static const std::string VIEW_ID; QmitkInteractiveFiberDissectionView(); virtual ~QmitkInteractiveFiberDissectionView(); virtual void CreateQtPartControl(QWidget *parent) override; /// /// Sets the focus to an internal widget. /// virtual void SetFocus() override; protected slots: void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; //Pointset void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; //Pointset void OnAddPointSetClicked();//Pointset void CreateStreamline(); void RemovefromBundle( bool checked ); void RemovefromBundleBrush( bool checked ); void ExtractRandomFibersFromTractogram(); void StartAlgorithm(); void CreatePredictionNode(); void CreateCertainNode(); void CreateUncertaintySampleNode(); void CreateDistanceSampleNode(); void RemovefromUncertainty( bool checked ); void RemovefromUncertaintyBrush( bool checked ); void RemovefromDistance( bool checked ); void RemovefromPrediction( bool checked ); void RemovefromPredictionBrush( bool checked ); void RemovefromSelection( bool checked ); void ResampleTractogram(); void RandomPrototypes(); void SFFPrototypes(); void StartValidation(); void AutomaticLabelling(); void RemoveCertainData(); void ResetClassifier(); void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection protected: void OnCurrentSelectionChanged(QmitkSingleNodeSelectionWidget::NodeList nodes);//Pointset virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; void OnEndInteraction(); void CreateStreamlineInteractor(); void CreateStreamlineInteractorBrush(); void CleanTestArray(); Ui::QmitkInteractiveFiberDissectionViewControls* m_Controls; int m_IterationCounter; ///< used for data node naming int m_RandomExtractionCounter; ///< used for random extracton of different Streamlines int m_activeCycleCounter; int m_newpos; int m_newneg; int m_startneg; int m_createdStreamlineCounter; int m_uncCounter; // int m_thresh2; std::vector m_SelectedFB; ///< selected fiber bundle nodes mitk::DataNode::Pointer m_testnode; // mitk::DataNode::Pointer m_trainbundle; mitk::Image::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedPS; mitk::DataNode::Pointer m_SelectedImageNode; mitk::FiberBundle::Pointer m_positiveBundle; mitk::FiberBundle::Pointer m_newfibersBundle; mitk::FiberBundle::Pointer m_negativeBundle; mitk::FiberBundle::Pointer m_Prediction; mitk::FiberBundle::Pointer m_CertainPlus; mitk::FiberBundle::Pointer m_CertainMinus; mitk::FiberBundle::Pointer m_CertainBetweenPlus; mitk::FiberBundle::Pointer m_CertainBetweenMinus; mitk::FiberBundle::Pointer m_UncertaintyLabel; mitk::FiberBundle::Pointer m_DistanceLabel; mitk::DataNode::Pointer m_positiveBundleNode; mitk::DataNode::Pointer m_newfibersBundleNode; mitk::DataNode::Pointer m_negativeBundleNode; mitk::DataNode::Pointer m_PredictionNode; mitk::DataNode::Pointer m_CertainPlusNode; mitk::DataNode::Pointer m_CertainMinusNode; mitk::DataNode::Pointer m_CertainBetweenPlusNode; mitk::DataNode::Pointer m_CertainBetweenMinusNode; mitk::DataNode::Pointer m_UncertaintyLabelNode; mitk::DataNode::Pointer m_DistanceLabelNode; vtkSmartPointer m_positiveFibersData; vtkSmartPointer m_newfibersFibersData; vtkSmartPointer m_picker1; mitk::StreamlineInteractor::Pointer m_StreamlineInteractor; mitk::StreamlineInteractorBrush::Pointer m_StreamlineInteractorBrush; std::shared_ptr< mitk::StreamlineFeatureExtractor > classifier; std::shared_ptr< mitk::StreamlineFeatureExtractor > validater; std::vector> m_metrics; std::vector> m_index; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED