diff --git a/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.cpp b/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.cpp index 32f2de0..bcf7c4a 100644 --- a/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.cpp +++ b/Modules/FiberDissection/Interactor/mitkStreamlineInteractor.cpp @@ -1,344 +1,322 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkStreamlineInteractor.h" //#include "mitkStreamlineMapper2D.h" // MITK includes #include #include #include #include #include #include #include #include #include #include // VTK includes #include #include #include #include #include #include #include #include #include #include mitk::StreamlineInteractor::StreamlineInteractor() { m_ColorForHighlight[0] = 1.0; m_ColorForHighlight[1] = 0.5; m_ColorForHighlight[2] = 0.0; m_ColorForHighlight[3] = 1.0; // TODO if we want to get this configurable, the this is the recipe: // - make the 2D mapper add corresponding properties to control "enabled" and "color" // - make the interactor evaluate those properties // - in an ideal world, modify the state machine on the fly and skip mouse move handling } mitk::StreamlineInteractor::~StreamlineInteractor() { } void mitk::StreamlineInteractor::ConnectActionsAndFunctions() { // CONNECT_CONDITION("isoverstreamline", HasPickedHandle); CONNECT_FUNCTION("addnegstreamline", AddStreamlineNegBundle); CONNECT_FUNCTION("addposstreamline", AddStreamlinePosBundle); // CONNECT_FUNCTION("FeedUndoStack", FeedUndoStack); } void mitk::StreamlineInteractor::SetNegativeNode(DataNode *node) { - DataInteractor::SetDataNode(node); - - m_NegStreamline= dynamic_cast(node->GetData()); - MITK_INFO << "Negative Node added"; + DataInteractor::SetDataNode(node); + m_NegStreamline= dynamic_cast(node->GetData()); + MITK_INFO << "Negative Node added"; } void mitk::StreamlineInteractor::SetToLabelNode(DataNode *node) { DataInteractor::SetDataNode(node); - - if (node && node->GetData()) - { m_manStreamline = dynamic_cast(node->GetData()); MITK_INFO << "Label node added"; - } + } void mitk::StreamlineInteractor::SetPositiveNode(DataNode *node) { DataInteractor::SetDataNode(node); m_PosStreamline= dynamic_cast(node->GetData()); - - MITK_INFO << "Positive Node added"; } void mitk::StreamlineInteractor::AddStreamlinePosBundle(StateMachineAction *, InteractionEvent *interactionEvent) { MITK_INFO << "PositiveBundle clicked"; -// auto positionEvent = dynamic_cast(interactionEvent); -// if (positionEvent == nullptr) -// { -// return; -// } -// return true; + auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) { MITK_INFO << "no position"; } if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D) { // m_PickedHandle = PickFrom2D(positionEvent); MITK_INFO << "2D"; } else { BaseRenderer *renderer = positionEvent->GetSender(); auto &picker = m_Picker[renderer]; - if (picker == nullptr) - { +// if (picker == nullptr) +// { + picker = vtkSmartPointer::New(); picker->SetTolerance(0.01); auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D); auto vtk_mapper = dynamic_cast(mapper); if (vtk_mapper) { // doing this each time is bizarre picker->AddPickList(vtk_mapper->GetVtkProp(renderer)); picker->PickFromListOn(); } - } +// } auto displayPosition = positionEvent->GetPointerPositionOnScreen(); -// MITK_INFO << displayPosition; picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer()); vtkIdType pickedCellID = picker->GetCellId(); - MITK_INFO << picker->GetCellId(); - MITK_INFO << "Number of Cells"; -// MITK_INFO << m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); - if (picker->GetCellId()==-1) { MITK_INFO << "Nothing picked"; } else { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); - MITK_INFO << vNewPolyData->GetNumberOfLines (); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); unsigned int counter = 0; for ( int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = m_PosStreamline->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++; } vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID); + 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); } vNewLines->InsertNextCell(container); vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // m_PosStreamline = mitk::FiberBundle::New(vNewPolyData); m_PosStreamline->GetFiberPolyData()->SetPoints(vNewPoints); m_PosStreamline->GetFiberPolyData()->SetLines(vNewLines); m_PosStreamline->SetFiberColors(0, 255, 0); m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID); m_manStreamline->GetFiberPolyData()->RemoveDeletedCells(); - - MITK_INFO << m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); - MITK_INFO << m_PosStreamline->GetFiberPolyData()->GetNumberOfCells(); } } } void mitk::StreamlineInteractor::AddStreamlineNegBundle(StateMachineAction *, InteractionEvent *interactionEvent) { MITK_INFO << "NegativeBundle clicked"; // auto positionEvent = dynamic_cast(interactionEvent); // if (positionEvent == nullptr) // { // return; // } // return true; auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) { MITK_INFO << "no position"; } if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D) { // m_PickedHandle = PickFrom2D(positionEvent); MITK_INFO << "2D"; } else { BaseRenderer *renderer = positionEvent->GetSender(); auto &picker = m_Picker[renderer]; - if (picker == nullptr) - { +// if (picker == nullptr) +// { picker = vtkSmartPointer::New(); picker->SetTolerance(0.01); auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D); auto vtk_mapper = dynamic_cast(mapper); if (vtk_mapper) { // doing this each time is bizarre picker->AddPickList(vtk_mapper->GetVtkProp(renderer)); picker->PickFromListOn(); } - } +// } auto displayPosition = positionEvent->GetPointerPositionOnScreen(); -// MITK_INFO << displayPosition; + picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer()); vtkIdType pickedCellID = picker->GetCellId(); - MITK_INFO << picker->GetCellId(); if (picker->GetCellId()==-1) { MITK_INFO << "Nothing picked"; } else { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); - MITK_INFO << vNewPolyData->GetNumberOfLines (); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); unsigned int counter = 0; for ( int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = m_NegStreamline->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++; } vtkCell* cell = m_manStreamline->GetFiberPolyData()->GetCell(pickedCellID); 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); } vNewLines->InsertNextCell(container); vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // m_NegStreamline = mitk::FiberBundle::New(vNewPolyData); m_NegStreamline->GetFiberPolyData()->SetPoints(vNewPoints); m_NegStreamline->GetFiberPolyData()->SetLines(vNewLines); m_NegStreamline->SetFiberColors(255, 0, 0); m_manStreamline->GetFiberPolyData()->DeleteCell(pickedCellID); m_manStreamline->GetFiberPolyData()->RemoveDeletedCells(); - MITK_INFO << m_manStreamline->GetFiberPolyData()->GetNumberOfCells(); - MITK_INFO << m_NegStreamline->GetFiberPolyData()->GetNumberOfCells(); } } } diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp index 22d0da8..a94d058 100644 --- a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp +++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp @@ -1,279 +1,281 @@ /*=================================================================== 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. ===================================================================*/ #include "mitkStreamlineFeatureExtractor.h" #define _USE_MATH_DEFINES #include #include #include #include namespace mitk{ StreamlineFeatureExtractor::StreamlineFeatureExtractor() : m_NumPoints(20) { } StreamlineFeatureExtractor::~StreamlineFeatureExtractor() { } -void StreamlineFeatureExtractor::SetTractogram(const mitk::FiberBundle::Pointer &Tractogram) +void StreamlineFeatureExtractor::SetTractogramPlus(const mitk::FiberBundle::Pointer &TractogramPlus) { - m_Tractogram = Tractogram; + m_TractogramPlus = TractogramPlus; +} + + +void StreamlineFeatureExtractor::SetTractogramMinus(const mitk::FiberBundle::Pointer &TractogramMinus) +{ + m_TractogramMinus = TractogramMinus; +} + +void StreamlineFeatureExtractor::SetTractogramTest(const mitk::FiberBundle::Pointer &TractogramTest) +{ + m_TractogramTest = TractogramTest; } std::vector > StreamlineFeatureExtractor::ResampleFibers(mitk::FiberBundle::Pointer tractogram) { mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy(); temp_fib->ResampleToNumPoints(m_NumPoints); std::vector< vnl_matrix > out_fib; 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, m_NumPoints); 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); } return out_fib; } std::vector > StreamlineFeatureExtractor::CalculateDmdf(std::vector > tractogram, std::vector > prototypes) { std::vector< vnl_matrix > dist_vec; - MITK_INFO << tractogram.size(); - MITK_INFO << prototypes.size(); - MITK_INFO << tractogram.at(0).cols(); for (unsigned int i=0; i distances; distances.set_size(1, prototypes.size()); distances.fill(0.0); for (unsigned int j=0; j single_distances; single_distances.set_size(1, tractogram.at(0).cols()); single_distances.fill(0.0); vnl_matrix single_distances_flip; single_distances_flip.set_size(1, tractogram.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); } -// MITK_INFO << dist_vec; + return dist_vec; } +void StreamlineFeatureExtractor::GetData() +{ + MITK_INFO << "Start Function Ged Data"; + int labels_arr [m_DistancesPlus.size()+m_DistancesMinus.size()]; + float data_arr [m_DistancesPlus.size()+m_DistancesMinus.size()][m_DistancesPlus.at(0).size()]; + + + int size_plus = 0; + for ( unsigned int i=0; i m_traindata = cv::ml::TrainData::create(data, cv::ml::ROW_SAMPLE, labels); + + cv::Ptr m_rtrees; + m_rtrees = cv::ml::RTrees::create(); + m_rtrees->setMaxDepth(3000); + m_rtrees->setMinSampleCount(1); + m_rtrees->setUse1SERule(false); + m_rtrees->setUseSurrogates(false); + m_rtrees->setPriors(cv::Mat()); + m_rtrees->setCVFolds(1); + + MITK_INFO << "Start Training"; + m_rtrees->train(m_traindata); + + MITK_INFO << "Predicting"; +// std::vector> test_arr(m_DistancesTest.size(), std::vector (m_DistancesPlus.at(0).size(), 0)); +// MITK_INFO << "test_arr"; +// for ( unsigned int i=m_DistancesTest.size(); ipredict(testingMat.row(i), predictLabels); +// val = std::lround(m_rtrees->predict(dataTest.row(i))); +// MITK_INFO << val; +// } + + + + + +} + +//void StreamlineFeatureExtractor::CreateClassifier() +//{ +// MITK_INFO << m_traindata->getResponses(); + + +//} + void StreamlineFeatureExtractor::GenerateData() { MITK_INFO << "Update"; mitk::FiberBundle::Pointer inputPrototypes = mitk::IOUtil::Load("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/prototypes_599671.trk"); T_Prototypes = ResampleFibers(inputPrototypes); - T_Tractogram = ResampleFibers(m_Tractogram); - - m_distances = CalculateDmdf(T_Tractogram, T_Prototypes); - - MITK_INFO << m_distances.at(0); - -// if (m_Metrics.empty()) -// { -// mitkThrow() << "No metric selected!"; -// return; -// } - -// T = ResampleFibers(m_Tractogram); -// if (T.empty()) -// { -// MITK_INFO << "No fibers in tractogram!"; -// return; -// } - -// std::vector< unsigned int > f_indices; -// for (unsigned int i=0; i clusters; -// if (m_InCentroids.IsNull()) -// { -// MITK_INFO << "Clustering fibers"; -// clusters = ClusterStep(f_indices, m_Distances); -// MITK_INFO << "Number of clusters: " << clusters.size(); -// clusters = MergeDuplicateClusters2(clusters); -// std::sort(clusters.begin(),clusters.end()); -// } -// else -// { -// std::vector > centroids = ResampleFibers(m_InCentroids); -// if (centroids.empty()) -// { -// MITK_INFO << "No fibers in centroid tractogram!"; -// return; -// } -// MITK_INFO << "Clustering with input centroids"; -// clusters = AddToKnownClusters(f_indices, centroids); -// no_match = clusters.back(); -// clusters.pop_back(); -// MITK_INFO << "Number of clusters: " << clusters.size(); -// clusters = MergeDuplicateClusters2(clusters); -// } - -// MITK_INFO << "Clustering finished"; -// int max = clusters.size()-1; -// if (m_MaxClusters>0 && clusters.size()-1>m_MaxClusters) -// max = m_MaxClusters; -// m_DiscardedClusters = 0; -// for (int i=clusters.size()-1; i>=0; --i) -// { -// Cluster c = clusters.at(i); -// if ( c.n>=(int)m_MinClusterSize && !(m_MaxClusters>0 && clusters.size()-i>m_MaxClusters) ) -// { -// m_OutClusters.push_back(c); - -// vtkSmartPointer weights = vtkSmartPointer::New(); -// vtkSmartPointer pTmp = m_Tractogram->GeneratePolyDataByIds(c.I, weights); -// mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp); -// if (max>0) -// fib->SetFiberWeights((float)i/max); -// m_OutTractograms.push_back(fib); -// m_OutFiberIndices.push_back(c.I); - -// // create centroid -// vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); -// vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); -// vtkSmartPointer polyData = vtkSmartPointer::New(); -// vtkSmartPointer container = vtkSmartPointer::New(); -// vnl_matrix centroid_points = c.h / c.n; -// for (unsigned int j=0; jInsertNextPoint(p); -// container->GetPointIds()->InsertNextId(id); -// } -// vtkNewCells->InsertNextCell(container); -// polyData->SetPoints(vtkNewPoints); -// polyData->SetLines(vtkNewCells); -// mitk::FiberBundle::Pointer centroid = mitk::FiberBundle::New(polyData); -// centroid->SetFiberColors(255, 255, 255); -// m_OutCentroids.push_back(centroid); -// } -// else -// { -// m_DiscardedClusters++; -// } -// } -// MITK_INFO << "Final number of clusters: " << m_OutTractograms.size() << " (discarded " << m_DiscardedClusters << " clusters)"; + T_TractogramMinus= ResampleFibers(m_TractogramMinus); + T_TractogramPlus= ResampleFibers(m_TractogramPlus); + T_TractogramTest= ResampleFibers(m_TractogramTest); + + MITK_INFO << "Calculate Features..."; + m_DistancesPlus = CalculateDmdf(T_TractogramPlus, T_Prototypes); + m_DistancesMinus = CalculateDmdf(T_TractogramMinus, T_Prototypes); + m_DistancesTest= CalculateDmdf(T_TractogramTest, T_Prototypes); + + MITK_INFO << "Sizes of Plus and Minus"; + MITK_INFO << m_DistancesPlus.size() + m_DistancesMinus.size(); + MITK_INFO << "Size of Test Data"; + MITK_INFO << m_DistancesTest.size(); + MITK_INFO << "Done with Datacreation"; -// int w = 0; -// for (auto fib : m_OutTractograms) -// { -// if (m_OutTractograms.size()>1) -// { -// fib->SetFiberWeights((float)w/(m_OutTractograms.size()-1)); -// m_OutCentroids.at(w)->SetFiberWeights((float)w/(m_OutTractograms.size()-1)); -// } -// else -// { -// fib->SetFiberWeights(1); -// m_OutCentroids.at(w)->SetFiberWeights(1); -// } -// fib->ColorFibersByFiberWeights(false, mitk::LookupTable::JET); -// ++w; -// } - -// if (no_match.n>0) -// { -// vtkSmartPointer weights = vtkSmartPointer::New(); -// vtkSmartPointer pTmp = m_Tractogram->GeneratePolyDataByIds(no_match.I, weights); -// mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp); -// fib->SetFiberColors(0, 0, 0); -// m_OutFiberIndices.push_back(no_match.I); -// m_OutTractograms.push_back(fib); -// } } + +void StreamlineFeatureExtractor::StartAlgorithm() +{ + MITK_INFO << "Printing"; + +// MITK_INFO << dataset->getResponses(); +} + + + } diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h index da20707..8ec9816 100644 --- a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h +++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h @@ -1,75 +1,95 @@ /*=================================================================== 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 StreamlineFeatureExtractor_h #define StreamlineFeatureExtractor_h #include "MitkFiberDissectionExports.h" // MITK #include #include // ITK #include // VTK #include #include #include #include #include +// OpenCV +#include +#include +#include + namespace mitk{ /** * \brief */ class MITKFIBERDISSECTION_EXPORT StreamlineFeatureExtractor { public: StreamlineFeatureExtractor(); ~StreamlineFeatureExtractor(); typedef itk::Image< float, 3 > FloatImageType; typedef itk::Image< unsigned char, 3 > UcharImageType; void Update(){ this->GenerateData(); } - void SetTractogram(const mitk::FiberBundle::Pointer &Tractogram); + void SetTractogramPlus(const mitk::FiberBundle::Pointer &Tractogram); + void SetTractogramMinus(const mitk::FiberBundle::Pointer &Tractogram); + + void SetTractogramTest(const mitk::FiberBundle::Pointer &Tractogram); + void CreateClassifier(); + void GetData(); +// void GetData(); +// cv::Ptr GetData(); + void StartAlgorithm(); protected: void GenerateData(); std::vector< vnl_matrix > ResampleFibers(FiberBundle::Pointer tractogram); std::vector > CalculateDmdf(std::vector > tractogram, std::vector > prototypes); unsigned int m_NumPoints; - mitk::FiberBundle::Pointer m_Tractogram; + mitk::FiberBundle::Pointer m_TractogramPlus; + mitk::FiberBundle::Pointer m_TractogramMinus; + mitk::FiberBundle::Pointer m_TractogramTest; std::vector > T_Prototypes; - std::vector > T_Tractogram; - std::vector > m_distances; + std::vector > T_TractogramPlus; + std::vector > T_TractogramMinus; + std::vector > T_TractogramTest; + std::vector > m_DistancesPlus; + std::vector > m_DistancesMinus; + std::vector > m_DistancesTest; + cv::Ptr m_traindata; }; } #endif 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 abf8884..e6648cf 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 @@ -1,593 +1,621 @@ /*=================================================================== 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 "usModuleRegistry.h" //#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_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 connect(m_Controls->m_ErazorButton, SIGNAL(toggled(bool)), this, SLOT( RemovefromBundle(bool) ) ); //need 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_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 } void QmitkInteractiveFiberDissectionView::UpdateGui() { m_Controls->m_FibLabel->setText("mandatory"); 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_addPointSetPushButton->setEnabled(false); m_Controls->m_StreamlineCreation->setEnabled(false); 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_addPointSetPushButton->setEnabled(false); m_Controls->m_AddRandomFibers->setEnabled(false); m_Controls->m_AddUncertainFibers->setEnabled(false); bool fibSelected = !m_SelectedFB.empty(); bool multipleFibsSelected = (m_SelectedFB.size()>1); bool sthSelected = m_SelectedImageNode.IsNotNull(); bool psSelected = m_SelectedPS.IsNotNull(); // bool nfibSelected = !m_newfibersSelectedBundles.empty(); // bool posSelected = !m_positivSelectedBundles.empty(); bool nfibSelected = m_newfibersSelectedBundles.IsNotNull(); // bool posSelected = !m_positivSelectedBundles.IsNotNull(); // bool negSelected = !m_negativeSelectedBundles.IsNotNull(); bool posSelected = this->GetDataStorage()->Exists(m_positivSelectedBundles); bool negSelected = this->GetDataStorage()->Exists(m_negativeSelectedBundles); // toggle visibility of elements according to selected method // are fiber bundles selected? if ( fibSelected ) { m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str())); m_Controls->m_addPointSetPushButton->setEnabled(true); m_Controls->m_AddRandomFibers->setEnabled(true); // more than two bundles needed to join/subtract if (multipleFibsSelected) { m_Controls->m_FibLabel->setText("multiple bundles selected"); } } // is image selected if (sthSelected) { m_Controls->m_addPointSetPushButton->setEnabled(true); } if (psSelected) { m_Controls->m_StreamlineCreation->setEnabled(true); } - if (nfibSelected) + if (nfibSelected && posSelected) { m_Controls->m_ErazorButton->setEnabled(true); } if (posSelected && negSelected) { - MITK_INFO << "Enable Algortihm"; m_Controls->m_TrainClassifier->setEnabled(true); } } void QmitkInteractiveFiberDissectionView::OnEndInteraction() { } 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); this->GetDataStorage()->Add(pointSetNode, m_SelectedImageNode); 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(); 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_positivSelectedBundles.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 ); m_positivSelectedBundles = node; this->GetDataStorage()->Add(m_positivSelectedBundles); MITK_INFO << "Create Bundle"; } if (!m_positivSelectedBundles.IsNull()) { this->GetDataStorage()->Remove(m_positivSelectedBundles); MITK_INFO << "Adding fibers"; } mitk::PointSet::Pointer pointSet = dynamic_cast(m_SelectedPS->GetData()); vnl_matrix streamline; streamline.set_size(3, pointSet->GetSize()); streamline.fill(0.0); mitk::PointSet::PointsIterator begin = pointSet->Begin(); mitk::PointSet::PointsIterator end = pointSet->End(); unsigned int i; mitk::PointSet::PointsContainer::Iterator it; 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); } vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); unsigned int counter = 0; for (unsigned int i=0; iGetNumberOfCells(); ++i) { 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); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); counter++; } // build Fiber vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned int j=0; jInsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } 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->SetTrackVisHeader(dynamic_cast(m_SelectedImageNode->GetData())->GetGeometry()); m_positiveBundle->SetFiberColors(0, 255, 0); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_positiveBundle); node->SetName("+Bundle"); m_positivSelectedBundles= node; MITK_INFO << "The + Bundle has Streamlines:"; auto m_NegStreamline= dynamic_cast(m_positivSelectedBundles->GetData()); MITK_INFO << m_NegStreamline->GetFiberPolyData()->GetNumberOfCells(); this->GetDataStorage()->Add(m_positivSelectedBundles); UpdateGui(); } void QmitkInteractiveFiberDissectionView::ExtractRandomFibersFromTractogram() { + m_Controls->m_ErazorButton->setChecked(false); + + MITK_INFO << "Number of Fibers to extract from Tractogram: "; MITK_INFO << m_Controls->m_NumRandomFibers->value(); - if (m_newfibersSelectedBundles.IsNull()) + if (this->GetDataStorage()->Exists(m_newfibersSelectedBundles)) { + MITK_INFO << "To Label Bundle Exists"; + mitk::FiberBundle::Pointer Stack = dynamic_cast(m_newfibersSelectedBundles->GetData()); + this->GetDataStorage()->Remove(m_newfibersSelectedBundles); + mitk::DataNode::Pointer node = mitk::DataNode::New(); m_newfibersFibersData = vtkSmartPointer::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer::New()); - m_newfibersFibersData->SetLines(vtkSmartPointer::New()); m_newfibersBundle = mitk::FiberBundle:: New(m_newfibersFibersData); + m_newfibersFibersData->SetLines(vtkSmartPointer::New()); - node->SetData( m_newfibersBundle ); - m_newfibersSelectedBundles = node ; +// node->SetData( m_newfibersBundle ); +// m_newfibersSelectedBundles = node ; MITK_INFO << "Create Bundle"; } mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.at(0)->GetData()); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); unsigned int counter = 0; - for ( int i=0; im_NumRandomFibers->value(); i++) + for ( int i=m_Controls->m_NumRandomFibers->value()*m_RandomExtractionCounter; im_NumRandomFibers->value()*(m_RandomExtractionCounter+1); 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++; - MITK_INFO << counter; - MITK_INFO << vNewLines; } 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); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_newfibersBundle); node->SetName("ToLabel"); m_newfibersSelectedBundles = node; +// MITK_INFO << "Number of Streamlines in first function"; +// MITK_INFO << m_newfibersSelectedBundles->GetData()->GetFiberPolyData()->GetNumberOfCells(); this->GetDataStorage()->Add(m_newfibersSelectedBundles); + m_RandomExtractionCounter++; + UpdateGui(); } void QmitkInteractiveFiberDissectionView::RemovefromBundle( bool checked ) { if (checked) { if (m_StreamlineInteractor.IsNull()) { this->CreateStreamlineInteractor(); // if (m_negativeSelectedBundles.IsNull()) // { mitk::FiberBundle::Pointer m_negativeBundle = mitk::FiberBundle::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetName("-Bundle"); node->SetData(m_negativeBundle); m_negativeSelectedBundles = node; this->GetDataStorage()->Add(m_negativeSelectedBundles); // } // if (m_positivSelectedBundles.IsNull()) // { // mitk::FiberBundle::Pointer m_positiveBundle = mitk::FiberBundle::New(); // mitk::DataNode::Pointer m_positiveSelectedBundles = mitk::DataNode::New(); // m_positiveSelectedBundles->SetName("+Bundle"); // m_positiveSelectedBundles->SetData(m_positiveBundle); // this->GetDataStorage()->Add(m_positiveSelectedBundles);) // } m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->SetNegativeNode(m_negativeSelectedBundles); m_StreamlineInteractor->SetPositiveNode(m_positivSelectedBundles); m_StreamlineInteractor->SetToLabelNode(m_newfibersSelectedBundles); } else { m_StreamlineInteractor->EnableInteraction(true); +// MITK_INFO << "Number of Streamlines"; +// MITK_INFO << m_newfibersSelectedBundles->GetData()->GetFiberPolyData()->GetNumberOfCells(); + m_StreamlineInteractor->SetToLabelNode(m_newfibersSelectedBundles); } } else { m_StreamlineInteractor->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::StartAlgorithm() { +// m_traindata.clear(); + MITK_INFO << "Extract Features"; + m_negativeBundle = dynamic_cast(m_negativeSelectedBundles->GetData()); std::shared_ptr< mitk::StreamlineFeatureExtractor > clusterer = std::make_shared(); - clusterer->SetTractogram(m_positiveBundle); + clusterer->SetTractogramPlus(m_positiveBundle); + clusterer->SetTractogramMinus(m_negativeBundle); + clusterer->SetTractogramTest(dynamic_cast(m_SelectedFB.at(0)->GetData())); clusterer->Update(); + clusterer->GetData(); +// MITK_INFO << data.at(0); +// MITK_INFO << data.at(1); +// cv::Ptr m_traindata = clusterer->GetData(); +// MITK_INFO << clusterer->m_labels; +// MITK_INFO << data.at(1); +// MITK_INFO << "Start Classification"; +// clusterer->CreateClassifier(); + clusterer->StartAlgorithm(); + + - MITK_INFO << "HI"; + MITK_INFO << "Algorithm run succesfully"; } 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 cb97dd7..0d56cc7 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 @@ -1,141 +1,143 @@ /*=================================================================== 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 /*! \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 ExtractRandomFibersFromTractogram(); void StartAlgorithm(); 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(); Ui::QmitkInteractiveFiberDissectionViewControls* m_Controls; int m_IterationCounter; ///< used for data node naming + int m_RandomExtractionCounter; ///< used for random extracton of different Streamlines std::vector m_SelectedFB; ///< selected fiber bundle nodes 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::DataNode::Pointer m_positivSelectedBundles; mitk::DataNode::Pointer m_newfibersSelectedBundles; mitk::DataNode::Pointer m_negativeSelectedBundles; vtkSmartPointer m_positiveFibersData; vtkSmartPointer m_newfibersFibersData; vtkSmartPointer m_picker1; mitk::StreamlineInteractor::Pointer m_StreamlineInteractor; + }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED