diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp index b2804c6..96bffe4 100644 --- a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp +++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp @@ -1,716 +1,715 @@ /*=================================================================== 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(40) { } StreamlineFeatureExtractor::~StreamlineFeatureExtractor() { } void StreamlineFeatureExtractor::SetTractogramPlus(const mitk::FiberBundle::Pointer &TractogramPlus) { m_TractogramPlus = TractogramPlus; } void StreamlineFeatureExtractor::SetTractogramMinus(const mitk::FiberBundle::Pointer &TractogramMinus) { m_TractogramMinus = TractogramMinus; } void StreamlineFeatureExtractor::SetActiveCycle(int &activeCycle) { m_activeCycle= activeCycle; } +//void StreamlineFeatureExtractor::SetRandomThreshold(int &threshold) +//{ +// m_thresh = threshold; +// MITK_INFO << m_thresh; +//} + + + void StreamlineFeatureExtractor::SetTractogramTest(const mitk::FiberBundle::Pointer &TractogramTest, std::string TractogramTestName) { std::string path = "/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/storage/"; path.append(TractogramTestName); m_TractogramTest= TractogramTest; auto s = std::to_string(m_NumPoints); m_DistancesTestName= path.append("_distances" + s + ".csv"); } std::vector > StreamlineFeatureExtractor::ResampleFibers(mitk::FiberBundle::Pointer tractogram) { mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy(); temp_fib->ResampleToNumPoints(m_NumPoints); MITK_INFO << "Resampling Done"; std::vector< vnl_matrix > out_fib(temp_fib->GetFiberPolyData()->GetNumberOfCells()); // std::vector< vnl_matrix > out_fib(); // cv::parallel_for_(cv::Range(0, temp_fib->GetFiberPolyData()->GetNumberOfCells()), [&](const cv::Range &range) // { // for (int i = range.start; i < range.end; i++) // #pragma omp parallel for // #pragma omp parallel for num_threads(10) collapse(1) 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); out_fib.at(i)=streamline; } // }); return out_fib; } -std::vector > StreamlineFeatureExtractor::CalculateDmdf(std::vector > tractogram, std::vector > prototypes, +std::vector > StreamlineFeatureExtractor::CalculateDmdf(std::vector > tractogram, + std::vector > prototypes, std::vector > positive_local_prototypes, std::vector > negative_local_prototypes) { - unsigned int pos_locals; - unsigned int neg_locals; - if (positive_local_prototypes.size() >= 50) - { - pos_locals= 50; - } - else { - pos_locals= positive_local_prototypes.size(); - } - - if (pos_locals <= positive_local_prototypes.size()) - { - neg_locals = pos_locals; - } - else { - neg_locals= negative_local_prototypes.size(); - } - MITK_INFO << "Locals:"; - MITK_INFO << neg_locals + pos_locals; + std::vector< vnl_matrix > merged_prototypes; - std::vector > merged_prototypes; - - - for (unsigned int k=0; k > dist_vec(tractogram.size());// MITK_INFO << "Start Calculating Dmdf"; cv::parallel_for_(cv::Range(0, tractogram.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, merged_prototypes.size()); + 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); dist_vec.at(i) = distances; } }); MITK_INFO << "Done Calculation"; MITK_INFO << dist_vec.at(0).size(); return dist_vec; } std::vector> StreamlineFeatureExtractor::GetData() { MITK_INFO << "Start Function Get Data"; - MITK_INFO << m_DistancesPlus.at(0); /*Vector which saves Prediction and Fibers to label based on uncertainty*/ std::vector> index_vec; // int labels_arr [m_DistancesPlus.size()+m_DistancesMinus.size()]; cv::Mat data; cv::Mat labels_arr_vec; int size_plus = 0; /*Create Trainingdata: Go through positive and negative Bundle and save distances as cv::Mat and create vector with labels*/ for ( unsigned int i=0; i(1,1)=minusval; +// newweight.at(1,2)=plusval; MITK_INFO << "Weights"; + MITK_INFO << minusval; + MITK_INFO << plusval; MITK_INFO << newweight; /*Shuffle Data*/ std::vector seeds; for (int cont = 0; cont < labels_arr_vec.rows; cont++) { seeds.push_back(cont); } cv::randShuffle(seeds); cv::Mat labels_shuffled; cv::Mat samples_shuffled; for (int cont = 0; cont < labels_arr_vec.rows; cont++) { labels_shuffled.push_back(labels_arr_vec.row(seeds[cont])); } for (int cont = 0; cont < labels_arr_vec.rows; cont++) { samples_shuffled.push_back(data.row(seeds[cont])); } // std::ofstream myfile1; // myfile1.open("/home/r948e/mycsv/labels.csv"); // myfile1<< cv::format(labels_shuffled, cv::Formatter::FMT_CSV) << std::endl; // myfile1.close(); // std::ofstream myfile2; // myfile2.open("/home/r948e/mycsv/features.csv"); // myfile2<< cv::format(data, cv::Formatter::FMT_CSV) << std::endl; // myfile2.close(); /*Create Dataset and initialize Classifier*/ cv::Ptr m_traindata = cv::ml::TrainData::create(samples_shuffled, cv::ml::ROW_SAMPLE, labels_shuffled); - MITK_INFO << m_traindata->getSamples(); +// MITK_INFO << m_traindata->getSamples(); // m_traindata->setTrainTestSplitRatio(0.95, true); - MITK_INFO << m_traindata->getResponses(); +// MITK_INFO << m_traindata->getResponses(); // m_traindata->shuffleTrainTest(); - MITK_INFO << m_traindata->getClassLabels(); +// MITK_INFO << m_traindata->getClassLabels(); MITK_INFO << "Start Training"; auto statistic_model = cv::ml::RTrees::create(); auto criteria = cv::TermCriteria(); criteria.type = cv::TermCriteria::MAX_ITER; // criteria.epsilon = 1e-8; criteria.maxCount = 800; statistic_model->setMaxDepth(50); //set to three // statistic_model->setMinSampleCount(m_traindata->getNTrainSamples()*0.01); statistic_model->setMinSampleCount(2); statistic_model->setTruncatePrunedTree(false); statistic_model->setUse1SERule(false); statistic_model->setUseSurrogates(false); statistic_model->setTermCriteria(criteria); statistic_model->setCVFolds(1); statistic_model->setPriors(newweight); /*Train Classifier*/ statistic_model->train(m_traindata); /*Predict on Test Data*/ MITK_INFO << "Predicting"; /*Create Dataset as cv::Mat*/ cv::Mat dataTest; for ( unsigned int i=0; i indexPrediction; std::vector e(m_DistancesTest.size()); /*For every Sample/Streamline get Prediction and entropy (=based on counts of Random Forest)*/ #pragma omp parallel for num_threads(18) for (unsigned int i=0; ipredict(dataTest.row(i)); if (val==1) { indexPrediction.push_back(i); } cv::Mat vote; statistic_model->getVotes(dataTest.row(i), vote, 0); e.at(i) = ( -(vote.at(1,0)*1.0)/ (vote.at(1,0)+vote.at(1,1)) * log2((vote.at(1,0)*1.0)/ (vote.at(1,0)+vote.at(1,1))) - (vote.at(1,1)*1.0)/ (vote.at(1,0)+vote.at(1,1))* log2((vote.at(1,1)*1.0)/ (vote.at(1,0)+vote.at(1,1)))); if (isnan(e.at(i))) { e.at(i)=0; } } /*Save entropy values for analysis*/ std::ofstream myfile3; auto s = std::to_string(m_activeCycle); myfile3.open("/home/r948e/mycsv/entropydata" + s + ".csv"); for (unsigned int i = 0; i < e.size(); i++) { myfile3 << e.at(i) << ' '; } myfile3.close(); MITK_INFO << "--------------"; MITK_INFO << "Prediction vector size:"; MITK_INFO << indexPrediction.size(); MITK_INFO << "Entropy vector size:"; MITK_INFO << e.size(); MITK_INFO << "--------------"; /*Get index of most unertain data (lengths defines how many data is saved)*/ - int lengths=1000; + int lengths=500; // auto it = std::minmax_element(e.begin(), e.end()); // int min_idx = std::distance(e.begin(), it.first); // int max_idx = std::distance(e.begin(), it.second); std::vector indexUnc; std::priority_queue> q; for (unsigned int i = 0; i < e.size(); ++i) { q.push(std::pair(e[i], i)); } // auto lengths = std::count_if(e.begin(), e.end(),[&](auto const& val){ return val >= 0.9; }); MITK_INFO << "Streamlines with uncertainty higher than 0.9"; MITK_INFO << lengths; for (int i = 0; i < lengths; ++i) { int ki = q.top().second; indexUnc.push_back(ki); q.pop(); } // std::ofstream myfile4; // myfile4.open("/home/r948e/mycsv/indexUnc.csv"); // for (unsigned int i = 0; i < indexUnc.size(); i++) // { // myfile4 << indexUnc.at(i) << ' '; // } // myfile4.close(); - // Sorted depent on entropy now sort the 1/5 + // Sorted depends on entropy now sort the 1/5 vnl_matrix distances_matrix; distances_matrix.set_size(lengths, lengths); distances_matrix.fill(0.0); MITK_INFO << "Dist_start"; std::vector distances_matrix_mean; for (int i=0; i diff = m_DistancesTest.at(indexUnc.at(i)) - m_DistancesTest.at(indexUnc.at(k)); + /*Into the eucledean difference matrix, put the distance in Feature Space between every sample pair*/ distances_matrix.put(i,k,diff.absolute_value_sum()/m_DistancesTest.at(0).size()); } + /*For every Sample/Streamline get the mean eucledean distance to all other Samples => one value for every Sample*/ distances_matrix_mean.push_back(distances_matrix.get_row(i).mean()); // MITK_INFO << meanval.at(i); } vnl_vector sum_matrix; sum_matrix.set_size(lengths); sum_matrix.fill(0.0); - /*Index to find values is distancematrix*/ + /*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); // MITK_INFO << distances_matrix.get_row(myidx.at(i)+ sum_matrix.get_row(0) for (int i=0; i indexUncdist; std::priority_queue> qq; for (unsigned int i = 0; i < distances_matrix_mean.size(); ++i) { qq.push(std::pair(distances_matrix_mean[i], i)); } // int k = m_DistancesTest.size(); // number of indices we need // int k = lengths; // number of indices we need for (int i = 0; i < lengths; ++i) { int kki = qq.top().second; indexUncdist.push_back(indexUnc.at(kki)); qq.pop(); } MITK_INFO << "Dist_stop"; // std::ofstream myfile6; // myfile6.open("/home/r948e/mycsv/distances_matrix_mean.csv"); // for (unsigned int i = 0; i < distances_matrix_mean.size(); i++) // { // myfile6 << distances_matrix_mean.at(i) << ' '; // } // myfile6.close(); // std::ofstream myfile5; // myfile5.open("/home/r948e/mycsv/indexUncdist.csv"); // for (unsigned int i = 0; i < indexUncdist.size(); i++) // { // myfile5 << indexUncdist.at(i) << ' '; // } // myfile5.close(); // MITK_INFO << distances_matrix; // MITK_INFO << distances_matrix.max_value(); // MITK_INFO << distances_matrix.arg_max(); // vnl_matrix myx = m_DistancesTest.at(indexUnc.at(0)) - m_DistancesTest.at(indexUnc.at(1)); //// myx = (m_DistancesTest.at(indexUnc.at(0)) - m_DistancesTest.at(indexUnc.at(1))); // MITK_INFO << m_DistancesTest.at(indexUnc.at(0)); // MITK_INFO << m_DistancesTest.at(indexUnc.at(1)); // MITK_INFO << myx.get(0,0); // MITK_INFO << sqrt(pow(myx.get(0,0),2)); // MITK_INFO << myx.get(0,1); // MITK_INFO << myx.absolute_value_sum()/m_DistancesTest.at(0).size(); // MITK_INFO << "Done"; /*Save Prediction*/ index_vec.push_back(indexPrediction); /*Save index of uncertainty measures*/ index_vec.push_back(indexUnc); /*Save index of uncertainty measures influenced by distance*/ index_vec.push_back(indexUncDist); return index_vec; } mitk::FiberBundle::Pointer StreamlineFeatureExtractor::CreatePrediction(std::vector &index) { mitk::FiberBundle::Pointer Prediction; MITK_INFO << "Create Bundle"; vtkSmartPointer FibersData; FibersData = vtkSmartPointer::New(); FibersData->SetPoints(vtkSmartPointer::New()); FibersData->SetLines(vtkSmartPointer::New()); vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); unsigned int indexSize = index.size(); unsigned int counter = 0; MITK_INFO << "Start Loop"; for (unsigned int i=0; iGetFiberPolyData()->GetCell(index[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 << counter; vNewPolyData->SetLines(vNewLines); vNewPolyData->SetPoints(vNewPoints); FibersData = vtkSmartPointer::New(); FibersData->SetPoints(vtkSmartPointer::New()); FibersData->SetLines(vtkSmartPointer::New()); FibersData->SetPoints(vNewPoints); FibersData->SetLines(vNewLines); Prediction = mitk::FiberBundle::New(vNewPolyData); // Bundle->SetFiberColors(255, 255, 255); MITK_INFO << "Cells Prediciton"; MITK_INFO << Prediction->GetFiberPolyData()->GetNumberOfCells(); MITK_INFO << "Cells Tractorgram"; MITK_INFO << m_TractogramTest->GetFiberPolyData()->GetNumberOfCells(); return Prediction; } 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"); - +// mitk::FiberBundle::Pointer inputPrototypes = mitk::IOUtil::Load("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/prototypes_599671.trk"); + mitk::FiberBundle::Pointer inputPrototypes = mitk::IOUtil::Load("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/data/Synt_tract_40_prototypes.trk"); T_Prototypes = ResampleFibers(inputPrototypes); T_TractogramMinus= ResampleFibers(m_TractogramMinus); T_TractogramPlus= ResampleFibers(m_TractogramPlus); MITK_INFO << "Calculate Features"; m_DistancesMinus = CalculateDmdf(T_TractogramMinus, T_Prototypes, T_TractogramPlus, T_TractogramMinus); m_DistancesPlus = CalculateDmdf(T_TractogramPlus, T_Prototypes, T_TractogramPlus, T_TractogramMinus); std::ifstream f(m_DistancesTestName); MITK_INFO << m_DistancesTestName; if (f.good()) { MITK_INFO << "File exists"; m_DistancesTest.clear(); std::ifstream myFile(m_DistancesTestName); if(!myFile.is_open()) throw std::runtime_error("Could not open file"); std::string line; vnl_matrix curline; curline.set_size(1, m_DistancesPlus.at(0).cols()); curline.fill(0.0); float val; while(std::getline(myFile, line)) { // Create a stringstream of the current line std::stringstream ss(line); // MITK_INFO << ss; // Keep track of the current column index int colIdx = 0; // Extract each integer while(ss >> val){ // // Add the current integer to the 'colIdx' column's values vector curline.put(0,colIdx, val); // // If the next token is a comma, ignore it and move on // if(ss.peek() == ',') ss.ignore(); // // Increment the column index colIdx++; } m_DistancesTest.push_back(curline); } // Close file myFile.close(); } else { MITK_INFO << m_DistancesTestName; MITK_INFO << "Resample Test Data"; T_TractogramTest= ResampleFibers(m_TractogramTest); MITK_INFO << "Calculate Features of Test Data"; m_DistancesTest= CalculateDmdf(T_TractogramTest, T_Prototypes, T_TractogramPlus, T_TractogramMinus); // std::ofstream myFile(m_DistancesTestName); //// myFile << colname << "\n"; // for(long unsigned int i = 0; i < m_DistancesTest.size(); ++i) // { // myFile << m_DistancesTest.at(i); // } // myFile.close(); } MITK_INFO << m_DistancesTest.size(); 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"; m_index =GetData(); } } diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h index 7cde2ef..85f8e88 100644 --- a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h +++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h @@ -1,106 +1,108 @@ /*=================================================================== 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 SetTractogramPlus(const mitk::FiberBundle::Pointer &Tractogram); void SetTractogramMinus(const mitk::FiberBundle::Pointer &Tractogram); void SetTractogramTest(const mitk::FiberBundle::Pointer &Tractogram, std::string TractogramTestName); void SetActiveCycle(int &activeCycle); +// void SetRandomThreshold(int &threshold); void CreateClassifier(); std::vector> GetData(); // void CreatePrediction(std::vector &index); mitk::FiberBundle::Pointer CreatePrediction(std::vector &index); mitk::FiberBundle::Pointer m_Prediction; mitk::FiberBundle::Pointer m_ToLabel; std::vector> m_index; protected: void GenerateData(); std::vector< vnl_matrix > ResampleFibers(FiberBundle::Pointer tractogram); std::vector > CalculateDmdf(std::vector > tractogram, std::vector > prototypes, std::vector > positive_local_prototypes, std::vector > negative_local_prototypes); unsigned int m_NumPoints; int m_activeCycle; + int m_thresh; mitk::FiberBundle::Pointer m_TractogramPlus; mitk::FiberBundle::Pointer m_TractogramMinus; mitk::FiberBundle::Pointer m_TractogramTest; std::string m_DistancesTestName; std::vector > T_Prototypes; 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/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml b/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml index d852e6a..84399f3 100644 --- a/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml +++ b/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml @@ -1,18 +1,18 @@ addtolabelstreamline - - + + - - + + 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 09e1173..9dde4b2 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 @@ -1,869 +1,869 @@ /*=================================================================== 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_activeCycleCounter(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_trainbundleWidget->SetDataStorage(GetDataStorage());//testdata // m_Controls->m_trainbundleWidget->SetNodePredicate(mitk::NodePredicateAnd::New(//testdata // mitk::TNodePredicateDataType::New(),//testdata // mitk::NodePredicateNot::New(mitk::NodePredicateOr::New(//testdata // mitk::NodePredicateProperty::New("helper object"),//testdata // mitk::NodePredicateProperty::New("hidden object")))));//testdatat // m_Controls->m_trainbundleWidget->SetSelectionIsOptional(true);//testdata // m_Controls->m_trainbundleWidget->SetAutoSelectNewNodes(true);//testdat // m_Controls->m_trainbundleWidget->SetEmptyInfo(QString("Please select a tractogram"));//testdat // m_Controls->m_trainbundleWidget->SetPopUpTitel(QString("Select tractogram"));//testdat 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_CreatePrediction, SIGNAL( clicked() ), this, SLOT( CreatePredictionNode( ))); 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_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_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_unclabeling->setCheckable(true); m_Controls->m_unclabeling->setEnabled(false); m_Controls->m_predlabeling->setCheckable(true); m_Controls->m_predlabeling->setEnabled(false); m_Controls->m_distlabeling->setCheckable(true); m_Controls->m_distlabeling->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_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_unclabeling->setEnabled(false); m_Controls->m_predlabeling->setEnabled(false); m_Controls->m_distlabeling->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_positivBundlesNode.empty(); bool nfibSelected = m_newfibersSelectedBundles.IsNotNull(); // bool posSelected = !m_positivBundlesNode.IsNotNull(); // bool negSelected = !m_negativeSelectedBundles.IsNotNull(); bool posSelected = this->GetDataStorage()->Exists(m_positivBundlesNode); bool negSelected = this->GetDataStorage()->Exists(m_negativeSelectedBundles); 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 ( 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 && posSelected) { m_Controls->m_ErazorButton->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); } if (predictionSelected) { m_Controls->m_predlabeling->setEnabled(true); } if (distanceSelected) { m_Controls->m_distlabeling->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(); // 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_positivBundlesNode.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_positivBundlesNode = node; this->GetDataStorage()->Add(m_positivBundlesNode); MITK_INFO << "Create Bundle"; } if (!m_positivBundlesNode.IsNull()) { this->GetDataStorage()->Remove(m_positivBundlesNode); 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(); 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); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } 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::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); } // 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->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_positivBundlesNode= node; MITK_INFO << "The + Bundle has Streamlines:"; auto m_NegStreamline= dynamic_cast(m_positivBundlesNode->GetData()); MITK_INFO << m_NegStreamline->GetFiberPolyData()->GetNumberOfCells(); this->GetDataStorage()->Add(m_positivBundlesNode); // m_Controls->m_selectedPointSetWidget->m_ToggleAddPoint->setEnabled(false); UpdateGui(); } void QmitkInteractiveFiberDissectionView::ExtractRandomFibersFromTractogram() { m_SelectedFB.at(0)->SetVisibility(false); m_Controls->m_ErazorButton->setChecked(false); MITK_INFO << "Number of Fibers to extract from Tractogram: "; MITK_INFO << m_Controls->m_NumRandomFibers->value(); 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_newfibersBundle = mitk::FiberBundle:: New(m_newfibersFibersData); m_newfibersFibersData->SetLines(vtkSmartPointer::New()); // node->SetData( m_newfibersBundle ); // m_newfibersSelectedBundles = node ; MITK_INFO << "Create Bundle"; } 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(); /* 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()) { for ( int i=thresh1; iGetFiberPolyData()->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++; } 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_positivBundlesNode.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_positivBundlesNode); m_StreamlineInteractor->SetToLabelNode(m_newfibersSelectedBundles); } else { m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->SetPositiveNode(m_positivBundlesNode); // 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() { this->GetDataStorage()->Remove(m_UncertaintyLabelNode); this->GetDataStorage()->Remove(m_DistanceLabelNode); m_Controls->m_unclabeling->setChecked(false); m_Controls->m_distlabeling->setChecked(false); m_Controls->m_predlabeling->setChecked(false); clusterer.reset(); MITK_INFO << "Extract Features"; m_negativeBundle = dynamic_cast(m_negativeSelectedBundles->GetData()); clusterer = std::make_shared(); clusterer->SetTractogramPlus(m_positiveBundle); clusterer->SetActiveCycle(m_activeCycleCounter); clusterer->SetTractogramMinus(m_negativeBundle); clusterer->SetTractogramTest(dynamic_cast(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName()); // clusterer->SetTractogramTest(dynamic_cast(m_trainbundle->GetData()), m_trainbundle->GetName()); // m_distances = clusterer->get clusterer->Update(); m_index = clusterer->m_index; MITK_INFO << "Number of Cycles"; MITK_INFO << m_activeCycleCounter; m_activeCycleCounter += 1; // m_Prediction = clusterer->CreatePrediction(m_index.at(0)); // mitk::DataNode::Pointer node = mitk::DataNode::New(); // node->SetData(m_Prediction); // node->SetName("Prediction"); // m_PredictionNode = node; // this->GetDataStorage()->Add(m_PredictionNode); // m_UncertaintyLabel = clusterer->m_UncertaintyLabel; // mitk::DataNode::Pointer node2 = mitk::DataNode::New(); // node2->SetData(m_UncertaintyLabel); // node2->SetName("UncertaintyLabels"); // m_UncertaintyLabelNode = node2; // MITK_INFO << "Number of Streamlines in first function"; // MITK_INFO << m_newfibersSelectedBundles->GetData()->GetFiberPolyData()->GetNumberOfCells(); // this->GetDataStorage()->Add(m_UncertaintyLabelNode); // this->GetDataStorage()->Add(m_PredictionNode); // 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(); // cv::Mat curdata = clusterer->StartAlgorithm(); // MITK_INFO << curdata; MITK_INFO << "Algorithm run succesfully"; m_Controls->m_CreatePrediction->setEnabled(true); UpdateGui(); } void QmitkInteractiveFiberDissectionView::CreatePredictionNode() { MITK_INFO << "Create Prediction"; m_Prediction = clusterer->CreatePrediction(m_index.at(0)); 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::CreateUncertaintySampleNode() { MITK_INFO << "Create Fibers to label based on Uncertainty"; std::vector myvec = m_index.at(1); myvec.resize(m_Controls->m_Numtolabel->value()); MITK_INFO << m_index.at(1).size(); MITK_INFO << myvec.size(); m_UncertaintyLabel = clusterer->CreatePrediction(myvec); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_UncertaintyLabel); auto s = std::to_string(m_activeCycleCounter); node->SetName("UncertaintyLabel"+s); m_UncertaintyLabelNode = node; 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(); m_DistanceLabel = clusterer->CreatePrediction(myvec); 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_UncertaintyLabel->SetFiberColors(255, 255, 255); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->SetToLabelNode(m_UncertaintyLabelNode); } else { m_StreamlineInteractor->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->SetToLabelNode(m_DistanceLabelNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkInteractiveFiberDissectionView::RemovefromPrediction( bool checked ) { if (checked) { - m_Prediction->SetFiberColors(255, 255, 255); +// m_Prediction->SetFiberColors(255, 255, 255); m_StreamlineInteractor->EnableInteraction(true); m_StreamlineInteractor->SetToLabelNode(m_PredictionNode); } else { m_StreamlineInteractor->EnableInteraction(false); // m_StreamlineInteractor = nullptr; } } 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 e482df4..3eb0f7c 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 @@ -1,157 +1,158 @@ /*=================================================================== 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 CreatePredictionNode(); void CreateUncertaintySampleNode(); void CreateDistanceSampleNode(); void RemovefromUncertainty( bool checked ); void RemovefromDistance( bool checked ); void RemovefromPrediction( bool checked ); 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 int m_activeCycleCounter; +// int m_thresh2; std::vector m_SelectedFB; ///< selected fiber bundle nodes // 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_UncertaintyLabel; mitk::FiberBundle::Pointer m_DistanceLabel; mitk::DataNode::Pointer m_positivBundlesNode; mitk::DataNode::Pointer m_newfibersSelectedBundles; mitk::DataNode::Pointer m_negativeSelectedBundles; mitk::DataNode::Pointer m_PredictionNode; mitk::DataNode::Pointer m_UncertaintyLabelNode; mitk::DataNode::Pointer m_DistanceLabelNode; vtkSmartPointer m_positiveFibersData; vtkSmartPointer m_newfibersFibersData; vtkSmartPointer m_picker1; mitk::StreamlineInteractor::Pointer m_StreamlineInteractor; std::shared_ptr< mitk::StreamlineFeatureExtractor > clusterer; std::vector> m_index; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui index 4be3a22..5a210c4 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkInteractiveFiberDissectionViewControls.ui @@ -1,683 +1,739 @@ QmitkInteractiveFiberDissectionViewControls 0 0 417 711 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 9 9 9 9 true true Label Fibers QFrame::NoFrame - 2 + 0 6 + + + Generate Prototypes + + + + + + Extract from + + + + + + + SFF Extraction + + + + + + + PushButton + + + + + + + Random Extraction + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + 0 0 399 - 464 + 455 Fiber Creation QFrame::StyledPanel QFrame::Raised Selected Streamline Pointset Qt::Horizontal 40 20 Streamline Points Qt::Vertical 20 40 Qt::Horizontal 40 20 Qt::Horizontal 40 20 Add new Streamline Pointset 0 0 0 40 Qt::Vertical 20 40 Create Streamline true 0 0 414 - 450 + 441 Fiber Labelling Dissect/Eraze Fibers by Erasion and Highlighting Qt::Vertical 20 40 true ArrowCursor QFrame::NoFrame QFrame::Raised Label individual Streamlines Streamlines to be labeled QFrame::StyledPanel QFrame::Raised Label Streamlines 30 30 :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png 32 32 true Reject: Rightclick + shift Qt::Horizontal 40 20 Random Streamlines Qt::Horizontal 40 20 Qt::Horizontal 40 20 Qt::Horizontal 40 20 Add Accept: Rightclick + alt Qt::Vertical 20 40 1 2000 10 0 0 399 - 464 + 455 Active Learning 9 9 341 391 QFrame::StyledPanel QFrame::Raised - - - - Train Classifier + + + + 1 + + + 500 + + + 0 + + + 10 - - + + Qt::Horizontal 40 20 - - - - Pred_Label - - - Uncertainty_Label .. - - - - Create Prediction - - - - - + + Qt::Horizontal - 84 - 22 + 40 + 20 - - + + + + Add + + + + + + + Pred_Label + + + + + Qt::Horizontal - 40 - 20 + 84 + 22 - - + + - Unc_dis_Label + Dist: to label - - + + - Create Uncertanty Map + Create Prediction Qt::Vertical 20 40 + + + + Create Uncertanty Map + + + + + + + Add + + + + + + + Train Classifier + + + Unc: to label - - + + 1 500 - - 0 - 10 - - + + Qt::Horizontal 40 20 - - - - Add - - - - - - - Dist: to label - - - - - - - 1 - - - 500 - - - 10 - - - - - + + - Add + Unc_dis_Label Qt::Vertical QSizePolicy::Fixed 20 40 Please Select Input Data Input DTI Fiber Bundle: <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true QmitkSingleNodeSelectionWidget QWidget
QmitkSingleNodeSelectionWidget.h
 QmitkPointListWidget QWidget
QmitkPointListWidget.h
 + + QmitkDataStorageComboBox + QComboBox +
QmitkDataStorageComboBox.h
+