diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp index b0c1fdd..e629050 100644 --- a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp +++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp @@ -1,515 +1,587 @@ /*=================================================================== 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 <math.h> #include <boost/progress.hpp> #include <vnl/vnl_sparse_matrix.h> #include <mitkIOUtil.h> namespace mitk{ StreamlineFeatureExtractor::StreamlineFeatureExtractor() : m_NumPoints(20) { } 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::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; m_DistancesTestName= path.append("_distances.csv"); } std::vector<vnl_matrix<float> > StreamlineFeatureExtractor::ResampleFibers(mitk::FiberBundle::Pointer tractogram) { mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy(); temp_fib->ResampleToNumPoints(m_NumPoints); std::vector< vnl_matrix<float> > out_fib; for (int i=0; i<temp_fib->GetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vnl_matrix<float> streamline; streamline.set_size(3, m_NumPoints); streamline.fill(0.0); for (int j=0; j<numPoints; j++) { double cand[3]; points->GetPoint(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<vnl_matrix<float> > StreamlineFeatureExtractor::CalculateDmdf(std::vector<vnl_matrix<float> > tractogram, std::vector<vnl_matrix<float> > prototypes) { std::vector< vnl_matrix<float> > dist_vec; for (unsigned int i=0; i<tractogram.size(); i++) { vnl_matrix<float> distances; distances.set_size(1, prototypes.size()); distances.fill(0.0); for (unsigned int j=0; j<prototypes.size(); j++) { vnl_matrix<float> single_distances; single_distances.set_size(1, tractogram.at(0).cols()); single_distances.fill(0.0); vnl_matrix<float> 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<tractogram.at(0).cols(); ik++) { double cur_dist; double cur_dist_flip; cur_dist = sqrt(pow(tractogram.at(i).get(0,ik) - prototypes.at(j).get(0,ik), 2.0) + pow(tractogram.at(i).get(1,ik) - prototypes.at(j).get(1,ik), 2.0) + pow(tractogram.at(i).get(2,ik) - prototypes.at(j).get(2,ik), 2.0)); cur_dist_flip = sqrt(pow(tractogram.at(i).get(0,ik) - prototypes.at(j).get(0,prototypes.at(0).cols()-(ik+1)), 2.0) + pow(tractogram.at(i).get(1,ik) - prototypes.at(j).get(1,prototypes.at(0).cols()-(ik+1)), 2.0) + pow(tractogram.at(i).get(2,ik) - prototypes.at(j).get(2,prototypes.at(0).cols()-(ik+1)), 2.0)); single_distances.put(0,ik, cur_dist); single_distances_flip.put(0,ik, cur_dist_flip); } if (single_distances_flip.mean()> single_distances.mean()) { distances.put(0,j, single_distances.mean()); } else { distances.put(0,j, single_distances_flip.mean()); } } dist_vec.push_back(distances); } return dist_vec; } -std::vector<unsigned int> StreamlineFeatureExtractor::GetData() +std::vector<std::vector<unsigned int>> StreamlineFeatureExtractor::GetData() { - MITK_INFO << "Start Function Ged Data"; -// int labels_arr [m_DistancesPlus.size()+m_DistancesMinus.size()]; + MITK_INFO << "Start Function Get Data"; + std::vector<std::vector<unsigned int>> index_vec; float labels_arr [m_DistancesPlus.size()+m_DistancesMinus.size()]; cv::Mat data; cv::Mat labels_arr_vec; int size_plus = 0; for ( unsigned int i=0; i<m_DistancesPlus.size(); i++) { float data_arr [m_DistancesPlus.at(0).size()]; labels_arr[i]=1; labels_arr_vec.push_back(1); for ( unsigned int j=0; j<m_DistancesPlus.at(0).cols(); j++) { data_arr[j] = m_DistancesPlus.at(i).get(0,j); } cv::Mat curdata(1, m_DistancesPlus.at(0).size(), CV_32F, data_arr); data.push_back(curdata); size_plus++; } for ( unsigned int i=m_DistancesPlus.size(); i<m_DistancesPlus.size()+m_DistancesMinus.size(); i++) { int it = i - size_plus; float data_arr [m_DistancesMinus.at(0).size()]; labels_arr[i]=0; labels_arr_vec.push_back(0); for ( unsigned int j=0; j<m_DistancesMinus.at(0).cols(); j++) { data_arr[j] = m_DistancesMinus.at(it).get(0,j); } cv::Mat curdata(1, m_DistancesPlus.at(0).size(), CV_32F, data_arr); data.push_back(curdata); size_plus++; } cv::Mat weights; int zerosgt = labels_arr_vec.rows - cv::countNonZero(labels_arr_vec); int onesgt = cv::countNonZero(labels_arr_vec); float plusval = labels_arr_vec.rows / (2.0 * onesgt ); float minusval = labels_arr_vec.rows / (2.0 * zerosgt ); // Create sample weights - for (int i=0; i<labels_arr_vec.rows; i++ ) - { - if (i<onesgt) - { - weights.push_back(plusval); - } - else { - weights.push_back(minusval); - } - } - +// for (int i=0; i<labels_arr_vec.rows; i++ ) +// { +// if (i<onesgt) +// { +// weights.push_back(plusval); +// } +// else { +// weights.push_back(minusval); +// } +// } + weights.push_back(minusval); + weights.push_back(plusval); MITK_INFO << "Weights"; - MITK_INFO << plusval; - MITK_INFO << minusval; - cv::Mat newweight; - newweight.push_back(zerosgt); - newweight.push_back(onesgt); + cv::Mat newweight; + newweight.push_back(minusval); + newweight.push_back(plusval); + MITK_INFO << "Weights"; + MITK_INFO << newweight; // cv::Mat labels(m_DistancesPlus.size()+m_DistancesMinus.size(), 1, CV_32S, labels_arr); cv::Mat labels(m_DistancesPlus.size()+m_DistancesMinus.size(), 1, CV_32F, labels_arr); // } // MITK_INFO << "data"; // MITK_INFO << data; // MITK_INFO << "labels"; // MITK_INFO << labels; cv::Ptr<cv::ml::TrainData> m_traindata = cv::ml::TrainData::create(data, cv::ml::ROW_SAMPLE, labels); // m_traindata->setTrainTestSplitRatio(1, true); m_traindata->shuffleTrainTest(); MITK_INFO << "Start Training"; auto statistic_model = cv::ml::RTrees::create(); //// auto criteria = cv::TermCriteria(); //// criteria.type = cv::TermCriteria::EPS + cv::TermCriteria::MAX_ITER; //// criteria.epsilon = 1e-8; //// criteria.maxCount = 5000; - statistic_model->setMaxCategories(2); - statistic_model->setMaxDepth(3); - statistic_model->setMinSampleCount(1); + statistic_model->setMaxCategories(80); + statistic_model->setMaxDepth(50); + statistic_model->setMinSampleCount(3); statistic_model->setTruncatePrunedTree(true); statistic_model->setUse1SERule(true); statistic_model->setUseSurrogates(false); - statistic_model->setTermCriteria(cv::TermCriteria(cv::TermCriteria::EPS + cv::TermCriteria::MAX_ITER, 800, 1e-6)); + statistic_model->setTermCriteria(cv::TermCriteria(1500, 1000, 1e-8)); statistic_model->setCVFolds(1); statistic_model->setPriors(newweight); statistic_model->train(m_traindata); // auto logistic_regression = cv::ml::LogisticRegression::create(); // statistic_model->setLearningRate(0.001); // statistic_model->setIterations(100); // statistic_model->setRegularization(cv::ml::LogisticRegression::REG_L2); // statistic_model->setTrainMethod(cv::ml::LogisticRegression::MINI_BATCH); // statistic_model->setMiniBatchSize(100); // statistic_model->train(m_traindata); MITK_INFO << "Predicting"; cv::Mat dataTest; for ( unsigned int i=0; i<m_DistancesTest.size(); i++) { float data_arr [m_DistancesTest.at(0).size()]; for ( unsigned int j=0; j<m_DistancesTest.at(0).cols(); j++) { data_arr[j] = m_DistancesTest.at(i).get(0,j); } cv::Mat curdata(1, m_DistancesTest.at(0).size(), CV_32F, data_arr); dataTest.push_back(curdata); } // MITK_INFO << "DataTest"; // MITK_INFO << dataTest.cols; // MITK_INFO << dataTest.rows; // MITK_INFO << dataTest; -// MITK_INFO << "________"; + MITK_INFO << "________"; - cv::Mat vote; - cv::Mat pred; -// int val; -// std::vector<int> pred; - std::vector<unsigned int> index; -// for (unsigned int i = 0; i < m_DistancesTest.size(); i++) -// { -//// MITK_INFO << dataTest.row(i); -// val = statistic_model->predict(dataTest.row(i)); -// pred.push_back(val); + int val; + std::vector<int> pred(m_DistancesTest.size()); + std::vector<unsigned int> index(m_DistancesTest.size()); + float one_prob; + float zero_prob; + int ones; + int zeros; + + + + std::vector<float> e(m_DistancesTest.size()) ; + -// if (val==1) -// { -// index.push_back(i); -// } -// } - statistic_model->getTermCriteria(); - statistic_model->getVotes(dataTest, vote, 0); - statistic_model->predict(dataTest, pred); - MITK_INFO << pred; + + cv::parallel_for_(cv::Range(0, m_DistancesTest.size()), [&](const cv::Range &range) + { + for (int i = range.start; i < range.end; i++) + { + + + cv::Mat vote; + val = statistic_model->predict(dataTest.row(i)); + statistic_model->getVotes(dataTest.row(i), vote, 0); + + ones = cv::countNonZero(vote); + zeros = vote.cols - cv::countNonZero(vote); + + one_prob = ones/ (vote.cols * 1.0); + zero_prob = zeros / (vote.cols * 1.0); + + e.at(i) = ( -one_prob * log2(one_prob) - zero_prob * log2(zero_prob)); + + + + pred.at(i) = val; + + + if (val==1) + { + index.at(i) = i; + } + + } + }); + index.erase( + std::remove(index.begin(), index.end(), 0), + index.end()); + index.shrink_to_fit(); + + + MITK_INFO << "--------------"; + e.erase( + std::remove(e.begin(), e.end(), 0), + e.end()); + e.shrink_to_fit(); + 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::cout << min_idx << ", " << max_idx << std::endl; // 1, 5 + + MITK_INFO << "--------------"; + + MITK_INFO << "Start the ordering"; + std::vector<unsigned int> indextolabel; + std::priority_queue<std::pair<float, int>> q; + for (unsigned int i = 0; i < e.size(); ++i) { + q.push(std::pair<float, int>(e[i], i)); + } + int k = m_DistancesTest.size(); // number of indices we need +// int k = 500; // number of indices we need + for (int i = 0; i < k; ++i) { + int ki = q.top().second; +// std::cout << "index[" << i << "] = " << ki << std::endl;x + indextolabel.push_back(ki); + q.pop(); + } + MITK_INFO << "Done"; + +// MITK_INFO << statistic_model->getTermCriteria().maxCount; +// MITK_INFO << statistic_model->getTermCriteria().type; +// MITK_INFO << statistic_model->getTermCriteria().epsilon; +// statistic_model->getVotes(dataTest.row(0), vote, 0); +// statistic_model->predict(dataTest, pred); +// cv::Mat vote; +// statistic_model->getVotes(dataTest, vote, 0); +// MITK_INFO << "vote"; +// MITK_INFO << vote.rows; +// MITK_INFO << vote.cols; +// MITK_INFO << pred; // mitke_INFO << vote; //// MITK_INFO << vote;s - MITK_INFO << vote.cols; - MITK_INFO << vote.rows; +// MITK_INFO << vote; MITK_INFO << "_______"; - int one = cv::countNonZero(vote); - MITK_INFO << one; - int zerorows = vote.rows - cv::countNonZero(vote); - MITK_INFO << zerorows; - index.push_back(1); - return index; + MITK_INFO << statistic_model->getPriors(); +// MITK_INFO << statistic_model->getNodes(); + +// index.push_back(1); + index_vec.push_back(index); + index_vec.push_back(indextolabel); + + return index_vec; } -void StreamlineFeatureExtractor::CreatePrediction(std::vector<unsigned int> &index) +mitk::FiberBundle::Pointer StreamlineFeatureExtractor::CreatePrediction(std::vector<unsigned int> &index) { - + mitk::FiberBundle::Pointer Prediction; MITK_INFO << "Create Bundle"; vtkSmartPointer<vtkPolyData> FibersData; FibersData = vtkSmartPointer<vtkPolyData>::New(); FibersData->SetPoints(vtkSmartPointer<vtkPoints>::New()); FibersData->SetLines(vtkSmartPointer<vtkCellArray>::New()); vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New(); vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New(); vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New(); unsigned int indexSize = index.size(); unsigned int counter = 0; MITK_INFO << "Start Loop"; for (unsigned int i=0; i<indexSize; i++) { vtkCell* cell = m_TractogramTest->GetFiberPolyData()->GetCell(index[i]); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New(); for (unsigned int j=0; j<numPoints; j++) { double p[3]; points->GetPoint(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<vtkPolyData>::New(); FibersData->SetPoints(vtkSmartPointer<vtkPoints>::New()); FibersData->SetLines(vtkSmartPointer<vtkCellArray>::New()); FibersData->SetPoints(vNewPoints); FibersData->SetLines(vNewLines); - m_Prediction = mitk::FiberBundle::New(vNewPolyData); + Prediction = mitk::FiberBundle::New(vNewPolyData); // Bundle->SetFiberColors(255, 255, 255); MITK_INFO << "Cells Prediciton"; - MITK_INFO << m_Prediction->GetFiberPolyData()->GetNumberOfCells(); + MITK_INFO << Prediction->GetFiberPolyData()->GetNumberOfCells(); MITK_INFO << "Cells Tractorgram"; MITK_INFO << m_TractogramTest->GetFiberPolyData()->GetNumberOfCells(); + + return Prediction; } -void StreamlineFeatureExtractor::GenerateData() +void StreamlineFeatureExtractor::GenerateData() { MITK_INFO << "Update"; mitk::FiberBundle::Pointer inputPrototypes = mitk::IOUtil::Load<mitk::FiberBundle>("/home/r948e/E132-Projekte/Projects/2022_Peretzke_Interactive_Fiber_Dissection/mitk_diff/prototypes_599671.trk"); T_Prototypes = ResampleFibers(inputPrototypes); T_TractogramMinus= ResampleFibers(m_TractogramMinus); T_TractogramPlus= ResampleFibers(m_TractogramPlus); m_DistancesMinus = CalculateDmdf(T_TractogramMinus, T_Prototypes); m_DistancesPlus = CalculateDmdf(T_TractogramPlus, T_Prototypes); std::ifstream f(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<float> 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; T_TractogramTest= ResampleFibers(m_TractogramTest); m_DistancesTest= CalculateDmdf(T_TractogramTest, T_Prototypes); 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"; - std::vector<unsigned int> index =GetData(); -// CreatePrediction (index); + m_index =GetData(); } //cv::Mat StreamlineFeatureExtractor::StartAlgorithm() //{ // MITK_INFO << "Printing"; // float data_arr [10] = {1, 2.4 ,4 ,4.5 ,6 ,7, 120.5, 100, 120, 100}; // cv::Mat curdata(1, 10, CV_32F, data_arr); // float data_arr2 [10] = {10, 20.4 ,40 ,40.5 ,60 ,70, 1200.5, 1000, 1200, 1000}; // cv::Mat curdata2(1, 10, CV_32F, data_arr2); // cv::Mat data; //// cv::Mat data2; // // data.row(1) = curdata.clone(); // data.push_back(curdata); // data.push_back(curdata2); //// cv::add(curdata,data2,data2); // cout << curdata; // cout << data; //// cout << data2; // return curdata.clone(); //} } diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h index 3069f60..2f7f95a 100644 --- a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h +++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.h @@ -1,96 +1,100 @@ /*=================================================================== 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 <mitkPlanarEllipse.h> #include <mitkFiberBundle.h> // ITK #include <itkProcessObject.h> // VTK #include <vtkSmartPointer.h> #include <vtkPolyData.h> #include <vtkCellArray.h> #include <vtkPoints.h> #include <vtkPolyLine.h> // OpenCV #include <opencv2/ml.hpp> #include <opencv2/opencv.hpp> #include <opencv2/highgui/highgui.hpp> 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 CreateClassifier(); - std::vector<unsigned int> GetData(); + std::vector<std::vector<unsigned int>> GetData(); - void CreatePrediction(std::vector<unsigned int> &index); +// void CreatePrediction(std::vector<unsigned int> &index); + mitk::FiberBundle::Pointer CreatePrediction(std::vector<unsigned int> &index); mitk::FiberBundle::Pointer m_Prediction; + mitk::FiberBundle::Pointer m_ToLabel; + + std::vector<std::vector<unsigned int>> m_index; protected: void GenerateData(); std::vector< vnl_matrix<float> > ResampleFibers(FiberBundle::Pointer tractogram); std::vector<vnl_matrix<float> > CalculateDmdf(std::vector<vnl_matrix<float> > tractogram, std::vector<vnl_matrix<float> > prototypes); unsigned int m_NumPoints; mitk::FiberBundle::Pointer m_TractogramPlus; mitk::FiberBundle::Pointer m_TractogramMinus; mitk::FiberBundle::Pointer m_TractogramTest; std::string m_DistancesTestName; std::vector<vnl_matrix<float> > T_Prototypes; std::vector<vnl_matrix<float> > T_TractogramPlus; std::vector<vnl_matrix<float> > T_TractogramMinus; std::vector<vnl_matrix<float> > T_TractogramTest; std::vector<vnl_matrix<float> > m_DistancesPlus; std::vector<vnl_matrix<float> > m_DistancesMinus; std::vector<vnl_matrix<float> > m_DistancesTest; cv::Ptr<cv::ml::TrainData> 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 35da9b2..33c1bd6 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 @@ -1,638 +1,697 @@ /*=================================================================== 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 <berryISelectionService.h> #include <berryIWorkbenchPart.h> #include <berryIWorkbenchWindow.h> // Qmitk #include "QmitkInteractiveFiberDissectionView.h" #include <QmitkRenderWindow.h> //Pointset #include <QmitkPointListWidget.h> //Pointset #include <QMessageBox> #include <mitkNodePredicateProperty.h> #include <mitkImageCast.h> #include <mitkPointSet.h> #include <mitkImageAccessByItk.h> #include <mitkDataNodeObject.h> #include <mitkTensorImage.h> #include "mitkNodePredicateDataType.h" #include <mitkNodePredicateProperty.h> #include <mitkNodePredicateAnd.h> #include <mitkNodePredicateNot.h> #include <mitkNodePredicateOr.h> //#include <mitkStreamlineFeatureExtractor.h> #include <mitkInteractionConst.h> #include "usModuleRegistry.h" //#include <itkFiberCurvatureFilter.h> #include <itkResampleImageFilter.h> #include <itkGaussianInterpolateImageFunction.h> #include <itkImageRegionIteratorWithIndex.h> #include <itkTractsToFiberEndingsImageFilter.h> #include <itkTractDensityImageFilter.h> #include <itkImageRegion.h> #include <itkTractsToRgbaImageFilter.h> #include <itkFiberExtractionFilter.h> #include <mitkInteractionEventObserver.h> #include <vtkCellPicker.h> #include <boost/algorithm/string.hpp> #include <boost/lexical_cast.hpp> #include <vnl/vnl_sparse_matrix.h> 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<mitk::PointSet>::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_CreatePrediction, SIGNAL( clicked() ), this, SLOT( CreatePredictionNode( ))); + + connect(m_Controls->m_AddUncertainFibers, SIGNAL( clicked() ), this, SLOT( CreateUncertaintySampleNode( ))); 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("<font color='red'>mandatory</font>"); 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); + bool indexSelected = !m_index.empty(); +// bool uncertaintySelected = !m_UncertaintyLabel.empty(); // 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); + } + + + + } 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<mitk::DataNode::Pointer>& 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<mitk::Image*>(node->GetData())) m_SelectedImage = dynamic_cast<mitk::Image*>(node->GetData()); else if ( dynamic_cast<mitk::FiberBundle*>(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<vtkPolyData>::New(); m_positiveFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New()); m_positiveFibersData->SetLines(vtkSmartPointer<vtkCellArray>::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<mitk::PointSet *>(m_SelectedPS->GetData()); vnl_matrix<float> 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<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New(); vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New(); vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New(); unsigned int counter = 0; for (unsigned int i=0; i<m_positiveFibersData->GetNumberOfCells(); ++i) { vtkCell* cell = m_positiveFibersData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New(); for (unsigned int j=0; j<numPoints; ++j) { double p[3]; points->GetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); counter++; } // build Fiber vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New(); for (unsigned int j=0; j<streamline.cols(); j++) { double p[3]; p[0] = streamline.get(0,j); p[1] = streamline.get(1,j); p[2] = streamline.get(2,j); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); m_positiveFibersData = vtkSmartPointer<vtkPolyData>::New(); m_positiveFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New()); m_positiveFibersData->SetLines(vtkSmartPointer<vtkCellArray>::New()); m_positiveFibersData->SetPoints(vNewPoints); m_positiveFibersData->SetLines(vNewLines); m_positiveBundle = mitk::FiberBundle::New(vNewPolyData); // m_positiveBundle->SetTrackVisHeader(dynamic_cast<mitk::Image*>(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<mitk::FiberBundle *>(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 (this->GetDataStorage()->Exists(m_newfibersSelectedBundles)) { MITK_INFO << "To Label Bundle Exists"; mitk::FiberBundle::Pointer Stack = dynamic_cast<mitk::FiberBundle *>(m_newfibersSelectedBundles->GetData()); this->GetDataStorage()->Remove(m_newfibersSelectedBundles); mitk::DataNode::Pointer node = mitk::DataNode::New(); m_newfibersFibersData = vtkSmartPointer<vtkPolyData>::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New()); m_newfibersBundle = mitk::FiberBundle:: New(m_newfibersFibersData); m_newfibersFibersData->SetLines(vtkSmartPointer<vtkCellArray>::New()); // node->SetData( m_newfibersBundle ); // m_newfibersSelectedBundles = node ; MITK_INFO << "Create Bundle"; } mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData()); vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New(); vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New(); vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New(); unsigned int counter = 0; for ( int i=m_Controls->m_NumRandomFibers->value()*m_RandomExtractionCounter; i<m_Controls->m_NumRandomFibers->value()*(m_RandomExtractionCounter+1); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New(); for (unsigned int j=0; j<numPoints; j++) { double p[3]; points->GetPoint(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<vtkPolyData>::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer<vtkPoints>::New()); m_newfibersFibersData->SetLines(vtkSmartPointer<vtkCellArray>::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(); + clusterer.reset(); MITK_INFO << "Extract Features"; m_negativeBundle = dynamic_cast<mitk::FiberBundle*>(m_negativeSelectedBundles->GetData()); - std::shared_ptr< mitk::StreamlineFeatureExtractor > clusterer = std::make_shared<mitk::StreamlineFeatureExtractor>(); + clusterer = std::make_shared<mitk::StreamlineFeatureExtractor>(); clusterer->SetTractogramPlus(m_positiveBundle); clusterer->SetTractogramMinus(m_negativeBundle); clusterer->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName()); + // m_distances = clusterer->get clusterer->Update(); - m_Prediction = clusterer->m_Prediction; + m_index = clusterer->m_index; + 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_PredictionNode); +// this->GetDataStorage()->Add(m_UncertaintyLabelNode); +// this->GetDataStorage()->Add(m_PredictionNode); // clusterer->GetData(); // MITK_INFO << data.at(0); // MITK_INFO << data.at(1); // cv::Ptr<cv::ml::TrainData> 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"; +// clusterer->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName()); + 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); + UpdateGui(); +} + +void QmitkInteractiveFiberDissectionView::CreateUncertaintySampleNode() +{ + MITK_INFO << "Create Fibers to label"; + std::vector<unsigned int> myvec = m_index.at(1); + myvec.resize(m_Controls->m_Numtolabel->value()); + MITK_INFO << m_index.at(1).size(); + MITK_INFO << myvec.size(); + +// clusterer->SetTractogramTest(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData()), m_SelectedFB.at(0)->GetName())); + m_UncertaintyLabel = clusterer->CreatePrediction(myvec); + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(m_UncertaintyLabel); + node->SetName("UncertaintyLabel"); + m_UncertaintyLabelNode = node; + this->GetDataStorage()->Add(m_UncertaintyLabelNode); } 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 6224d88..a9f4b0f 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 @@ -1,145 +1,150 @@ /*=================================================================== 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 <QInputDialog> //Pointset #include <QmitkPointListWidget.h>//Pointset #include <QmitkAbstractView.h>//Pointset #include <QmitkSingleNodeSelectionWidget.h>//Pointset #include <mitkFiberBundle.h> #include <mitkDataInteractor.h> #include <mitkIRenderWindowPartListener.h> //Pointset #include <mitkStreamlineInteractor.h> #include <mitkStreamlineFeatureExtractor.h> #include <itkCastImageFilter.h> #include <itkVTKImageImport.h> #include <itkVTKImageExport.h> #include <itkRegionOfInterestImageFilter.h> #include <vtkLinearExtrusionFilter.h> #include <vtkPolyDataToImageStencil.h> #include <vtkSelectEnclosedPoints.h> #include <vtkImageImport.h> #include <vtkImageExport.h> #include <vtkImageStencil.h> #include <vtkSmartPointer.h> #include <vtkSelection.h> #include <vtkSelectionNode.h> #include <vtkExtractSelectedThresholds.h> #include <vtkFloatArray.h> #include <vtkCellPicker.h> /*! \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 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<mitk::DataNode::Pointer>& 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<mitk::DataNode::Pointer> 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::FiberBundle::Pointer m_Prediction; + mitk::FiberBundle::Pointer m_UncertaintyLabel; mitk::DataNode::Pointer m_positivSelectedBundles; mitk::DataNode::Pointer m_newfibersSelectedBundles; mitk::DataNode::Pointer m_negativeSelectedBundles; mitk::DataNode::Pointer m_PredictionNode; + mitk::DataNode::Pointer m_UncertaintyLabelNode; vtkSmartPointer<vtkPolyData> m_positiveFibersData; vtkSmartPointer<vtkPolyData> m_newfibersFibersData; vtkSmartPointer<vtkCellPicker> m_picker1; mitk::StreamlineInteractor::Pointer m_StreamlineInteractor; + std::shared_ptr< mitk::StreamlineFeatureExtractor > clusterer; + std::vector<std::vector<unsigned int>> 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 ac2bd7b..228e916 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 @@ -1,634 +1,641 @@ <?xml version="1.0" encoding="UTF-8"?> <ui version="4.0"> <class>QmitkInteractiveFiberDissectionViewControls</class> <widget class="QWidget" name="QmitkInteractiveFiberDissectionViewControls"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>417</width> <height>711</height> </rect> </property> <property name="windowTitle"> <string>Form</string> </property> <property name="styleSheet"> <string>QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; }</string> </property> <layout class="QGridLayout" name="gridLayout_3"> <property name="leftMargin"> <number>9</number> </property> <property name="topMargin"> <number>9</number> </property> <property name="rightMargin"> <number>9</number> </property> <property name="bottomMargin"> <number>9</number> </property> <item row="0" column="0"> <widget class="QGroupBox" name="m_InputData"> <property name="title"> <string>Please Select Input Data</string> </property> <layout class="QGridLayout" name="gridLayout_9"> <property name="leftMargin"> <number>6</number> </property> <property name="topMargin"> <number>6</number> </property> <property name="rightMargin"> <number>6</number> </property> <property name="bottomMargin"> <number>6</number> </property> <item row="0" column="0"> <widget class="QLabel" name="label_2"> <property name="toolTip"> <string>Input DTI</string> </property> <property name="text"> <string>Fiber Bundle:</string> </property> </widget> </item> <item row="0" column="1"> <widget class="QLabel" name="m_FibLabel"> <property name="text"> <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string> </property> <property name="wordWrap"> <bool>true</bool> </property> </widget> </item> </layout> </widget> </item> <item row="1" column="0"> <widget class="QToolBox" name="toolBoxx"> <property name="enabled"> <bool>true</bool> </property> <property name="font"> <font> <bold>true</bold> </font> </property> <property name="toolTip"> <string>Label Fibers</string> </property> <property name="frameShape"> <enum>QFrame::NoFrame</enum> </property> <property name="currentIndex"> - <number>1</number> + <number>2</number> </property> <property name="tabSpacing"> <number>6</number> </property> <widget class="QWidget" name="page_3"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>399</width> <height>492</height> </rect> </property> <attribute name="label"> <string>Fiber Creation</string> </attribute> <layout class="QGridLayout" name="gridLayout_7"> <item row="0" column="0"> <widget class="QFrame" name="frame"> <property name="frameShape"> <enum>QFrame::StyledPanel</enum> </property> <property name="frameShadow"> <enum>QFrame::Raised</enum> </property> <layout class="QGridLayout" name="gridLayout_11"> <item row="0" column="0"> <widget class="QLabel" name="m_selectedPointSetLabel"> <property name="text"> <string>Selected Streamline Pointset</string> </property> </widget> </item> <item row="2" column="1"> <spacer name="horizontalSpacer_14"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="4" column="0" colspan="2"> <widget class="QGroupBox" name="groupBox"> <property name="title"> <string>Streamline Points</string> </property> <layout class="QGridLayout" name="gridLayout_10"> <item row="0" column="0"> <widget class="QmitkPointListWidget" name="m_poinSetListWidget" native="true"/> </item> <item row="1" column="0"> <spacer name="verticalSpacer_7"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> </item> <item row="1" column="1"> <spacer name="horizontalSpacer_13"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="0" column="1"> <spacer name="horizontalSpacer_12"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="2" column="0"> <widget class="QPushButton" name="m_addPointSetPushButton"> <property name="text"> <string>Add new Streamline Pointset</string> </property> </widget> </item> <item row="1" column="0"> <widget class="QmitkSingleNodeSelectionWidget" name="m_selectedPointSetWidget" native="true"> <property name="sizePolicy"> <sizepolicy hsizetype="Preferred" vsizetype="Minimum"> <horstretch>0</horstretch> <verstretch>0</verstretch> </sizepolicy> </property> <property name="minimumSize"> <size> <width>0</width> <height>40</height> </size> </property> </widget> </item> <item row="6" column="0"> <spacer name="verticalSpacer_3"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> <item row="7" column="0"> <widget class="QPushButton" name="m_StreamlineCreation"> <property name="text"> <string>Create Streamline</string> </property> </widget> </item> </layout> </widget> </item> </layout> </widget> <widget class="QWidget" name="page_2"> <property name="enabled"> <bool>true</bool> </property> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>414</width> <height>478</height> </rect> </property> <property name="accessibleName"> <string/> </property> <attribute name="label"> <string>Fiber Labelling</string> </attribute> <attribute name="toolTip"> <string>Dissect/Eraze Fibers by Erasion and Highlighting</string> </attribute> <layout class="QGridLayout" name="gridLayout_13"> <item row="4" column="0"> <spacer name="verticalSpacer_4"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> <item row="1" column="0"> <widget class="QFrame" name="m_LabelFrame"> <property name="enabled"> <bool>true</bool> </property> <property name="cursor"> <cursorShape>ArrowCursor</cursorShape> </property> <property name="frameShape"> <enum>QFrame::NoFrame</enum> </property> <property name="frameShadow"> <enum>QFrame::Raised</enum> </property> <layout class="QGridLayout" name="gridLayout_4"> <item row="0" column="0"> <widget class="QLabel" name="label"> <property name="text"> <string>Label individual Streamlines</string> </property> </widget> </item> </layout> </widget> </item> <item row="2" column="0"> <widget class="QLabel" name="label_3"> <property name="text"> <string>Streamlines to be labeled</string> </property> </widget> </item> <item row="3" column="0"> <widget class="QFrame" name="m_ExtractionToolsFrame"> <property name="frameShape"> <enum>QFrame::StyledPanel</enum> </property> <property name="frameShadow"> <enum>QFrame::Raised</enum> </property> <layout class="QGridLayout" name="gridLayout_2"> <item row="5" column="2"> <widget class="QLabel" name="label_4"> <property name="text"> <string>Label Streamlines</string> </property> </widget> </item> <item row="5" column="3"> <widget class="QPushButton" name="m_ErazorButton"> <property name="maximumSize"> <size> <width>30</width> <height>30</height> </size> </property> <property name="text"> <string/> </property> <property name="icon"> <iconset> <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png</iconset> </property> <property name="iconSize"> <size> <width>32</width> <height>32</height> </size> </property> <property name="flat"> <bool>true</bool> </property> </widget> </item> <item row="6" column="2"> <widget class="QLabel" name="label_6"> <property name="text"> <string>Reject: Rightclick + shift</string> </property> </widget> </item> <item row="2" column="7" colspan="3"> <spacer name="horizontalSpacer_2"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="2" column="2" colspan="2"> <widget class="QLabel" name="label_7"> <property name="text"> <string>Random Streamlines</string> </property> </widget> </item> <item row="7" column="3" colspan="5"> <spacer name="horizontalSpacer_8"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="5" column="4" colspan="5"> <spacer name="horizontalSpacer"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="6" column="3" colspan="6"> <spacer name="horizontalSpacer_3"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="2" column="6"> <widget class="QPushButton" name="m_AddRandomFibers"> <property name="text"> <string>Add</string> </property> </widget> </item> <item row="7" column="2"> <widget class="QLabel" name="label_8"> <property name="text"> <string>Accept: Rightclick + alt</string> </property> </widget> </item> <item row="8" column="2"> <spacer name="verticalSpacer_2"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> <item row="2" column="4"> <widget class="QSpinBox" name="m_NumRandomFibers"> <property name="minimum"> <number>1</number> </property> <property name="maximum"> <number>2000</number> </property> </widget> </item> </layout> </widget> </item> </layout> </widget> <widget class="QWidget" name="page_4"> <property name="geometry"> <rect> <x>0</x> <y>0</y> <width>399</width> <height>492</height> </rect> </property> <attribute name="label"> <string>Active Learning</string> </attribute> <widget class="QFrame" name="frame_2"> <property name="geometry"> <rect> <x>9</x> <y>9</y> <width>341</width> <height>391</height> </rect> </property> <property name="frameShape"> <enum>QFrame::StyledPanel</enum> </property> <property name="frameShadow"> <enum>QFrame::Raised</enum> </property> <layout class="QGridLayout" name="gridLayout_6"> <item row="2" column="3"> <spacer name="horizontalSpacer_7"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="0" column="0" colspan="3"> <widget class="QPushButton" name="m_TrainClassifier"> <property name="text"> <string>Train Classifier</string> </property> </widget> </item> <item row="3" column="1"> <widget class="QSpinBox" name="m_Numtolabel"> <property name="minimum"> <number>5</number> </property> <property name="value"> <number>10</number> </property> </widget> </item> <item row="1" column="0" colspan="3"> <widget class="QPushButton" name="m_CreatePrediction"> <property name="text"> <string>Create Prediction</string> </property> </widget> </item> <item row="6" column="2"> <spacer name="verticalSpacer_6"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> <item row="1" column="3"> <spacer name="horizontalSpacer_5"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="2" column="0" colspan="3"> <widget class="QPushButton" name="m_CreateUncertantyMap"> <property name="text"> <string>Create Uncertanty Map</string> </property> </widget> </item> <item row="3" column="2"> <widget class="QPushButton" name="m_AddUncertainFibers"> <property name="text"> <string>Add </string> </property> </widget> </item> <item row="3" column="0"> <widget class="QLabel" name="label_5"> <property name="text"> <string>To be labeled</string> </property> </widget> </item> <item row="3" column="3"> <spacer name="horizontalSpacer_6"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>40</width> <height>20</height> </size> </property> </spacer> </item> <item row="0" column="3"> <spacer name="horizontalSpacer_4"> <property name="orientation"> <enum>Qt::Horizontal</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>84</width> <height>22</height> </size> </property> </spacer> </item> + <item row="4" column="0"> + <widget class="QPushButton" name="m_newlabeling"> + <property name="text"> + <string>PushButton</string> + </property> + </widget> + </item> </layout> </widget> </widget> </widget> </item> <item row="2" column="0" rowspan="2"> <spacer name="verticalSpacer"> <property name="orientation"> <enum>Qt::Vertical</enum> </property> <property name="sizeType"> <enum>QSizePolicy::Fixed</enum> </property> <property name="sizeHint" stdset="0"> <size> <width>20</width> <height>40</height> </size> </property> </spacer> </item> </layout> </widget> <customwidgets> <customwidget> <class>QmitkSingleNodeSelectionWidget</class> <extends>QWidget</extends> <header location="global">QmitkSingleNodeSelectionWidget.h</header> </customwidget> <customwidget> <class>QmitkPointListWidget</class> <extends>QWidget</extends> <header location="global">QmitkPointListWidget.h</header> </customwidget> </customwidgets> <resources/> <connections/> </ui>