diff --git a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp index 24c1e05..4698cf4 100644 --- a/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp +++ b/Modules/FiberDissection/MachineLearning/mitkStreamlineFeatureExtractor.cpp @@ -1,754 +1,752 @@ /*=================================================================== 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::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 i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) + { + vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); - for (int j=0; jGetPoint(j, cand); + vnl_matrix streamline; + streamline.set_size(3, m_NumPoints); + streamline.fill(0.0); - vnl_vector_fixed< float, 3 > candV; - candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; - streamline.set_column(j, candV); - } + 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; - } + out_fib.at(i)=streamline; + } // }); return out_fib; } std::vector > StreamlineFeatureExtractor::CalculateDmdf(std::vector > tractogram, std::vector > prototypes) { std::vector< vnl_matrix > 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, 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::MergeTractogram(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 <= negative_local_prototypes.size()) { neg_locals = pos_locals; } else { neg_locals= negative_local_prototypes.size(); } std::vector< vnl_matrix > merged_prototypes; for (unsigned int k=0; k StreamlineFeatureExtractor::Sort(std::vector sortingVector, int lengths) { std::vector index; std::priority_queue> q; for (unsigned int i = 0; i < sortingVector.size(); ++i) { q.push(std::pair(sortingVector[i], i)); } for (int i = 0; i < lengths; ++i) { int ki = q.top().second; index.push_back(ki); q.pop(); } return index; } std::vector> StreamlineFeatureExtractor::GetData() { MITK_INFO << "Start Function Get Data"; /*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 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])); } /*Create Dataset and initialize Classifier*/ cv::Ptr m_traindata = cv::ml::TrainData::create(samples_shuffled, cv::ml::ROW_SAMPLE, labels_shuffled); 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*/ MITK_INFO << "Start Training"; 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) + MITK_INFO << "Predicting on all cores"; +#pragma omp parallel for for (unsigned int i=0; ipredict(dataTest.row(i)); + + #pragma omp critical 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; } } + MITK_INFO << "Done"; /*Save entropy values for analysis*/ - std::ofstream myfile3; - myfile3.open("/home/r948e/mycsv/entropydata" + std::to_string(m_activeCycle) + ".csv"); - for (unsigned int i = 0; i < e.size(); i++) - { - myfile3 << e.at(i) << ' '; - } - myfile3.close(); +// std::ofstream myfile3; +// myfile3.open("/home/r948e/mycsv/entropydata" + std::to_string(m_activeCycle) + ".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=500; // int lengths = std::count_if(e.begin(), e.end(),[&](auto const& val){ return val >= 0.9; }); std::vector indexUnc = Sort(e, lengths); MITK_INFO << indexUnc.size(); 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 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); - indexUncDist.push_back(indexUnc.at(myidx.at(0))); // MITK_INFO << distances_matrix.get_row(myidx.at(i)+ sum_matrix.get_row(0) // for (int i=0; i sum_matrix; + /*Matrix that stores distances of used samples */ +// vnl_matrix sum_matrix; // sum_matrix.set_size(lengths, lengths); // sum_matrix.set_size(lengths, lengths); - MITK_INFO < 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); + indexUncDist.push_back(indexUnc.at(myidx.at(0))); /*Vecotr that stores minvalues of current iteration*/ vnl_matrix cur_vec; cur_vec.set_size(1,lengths); cur_vec.fill(0.0); for (int i=0; i sum_matrix; sum_matrix.set_size(myidx.size(), lengths); sum_matrix.fill(0); for (unsigned int ii=0; ii 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(); +// vtkSmartPointer weights = vtkSmartPointer::New(); +// weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers()); + 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)); +// 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/data/Synt_tract_40_prototypes.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"); std::vector > T_Prototypes; std::vector > T_TractogramPlus; std::vector > T_TractogramMinus; std::vector > T_TractogramTest; std::vector > T_mergedPrototypes; T_Prototypes = ResampleFibers(inputPrototypes); T_TractogramMinus= ResampleFibers(m_TractogramMinus); T_TractogramPlus= ResampleFibers(m_TractogramPlus); /* Merge T_Prototypes, T_TractogramMinus and T_TractogramPlus for extra Features*/ T_mergedPrototypes = MergeTractogram(T_Prototypes, T_TractogramPlus, T_TractogramMinus); MITK_INFO << "Calculate Features"; m_DistancesMinus = CalculateDmdf(T_TractogramMinus, T_mergedPrototypes); m_DistancesPlus = CalculateDmdf(T_TractogramPlus, T_mergedPrototypes); 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_mergedPrototypes); } 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/resource/Interactions/Streamline3DConfig.xml b/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml index 84399f3..7ed1a7f 100644 --- a/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml +++ b/Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml @@ -1,18 +1,18 @@ addtolabelstreamline - 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This is because - the compilers do not have flags that can change the architecture, - but rather depend on which compiler is being used -*/ -#if defined(_WIN32) && defined(_MSC_VER) -# if defined(_M_IA64) -# define ARCHITECTURE_ID "IA64" - -# elif defined(_M_ARM64EC) -# define ARCHITECTURE_ID "ARM64EC" - -# elif defined(_M_X64) || defined(_M_AMD64) -# define ARCHITECTURE_ID "x64" - -# elif defined(_M_IX86) -# define ARCHITECTURE_ID "X86" - -# elif defined(_M_ARM64) -# define ARCHITECTURE_ID "ARM64" - -# elif defined(_M_ARM) -# if _M_ARM == 4 -# define ARCHITECTURE_ID "ARMV4I" -# elif _M_ARM == 5 -# define ARCHITECTURE_ID "ARMV5I" -# else -# define ARCHITECTURE_ID "ARMV" STRINGIFY(_M_ARM) -# endif - -# elif defined(_M_MIPS) -# define ARCHITECTURE_ID "MIPS" - -# elif defined(_M_SH) -# define ARCHITECTURE_ID "SHx" - -# else /* unknown architecture */ -# define ARCHITECTURE_ID "" -# endif - -#elif defined(__WATCOMC__) -# if defined(_M_I86) -# define ARCHITECTURE_ID "I86" - -# elif defined(_M_IX86) -# define ARCHITECTURE_ID "X86" - -# else /* unknown architecture */ -# define ARCHITECTURE_ID "" -# endif - -#elif defined(__IAR_SYSTEMS_ICC__) || defined(__IAR_SYSTEMS_ICC) -# if defined(__ICCARM__) -# define ARCHITECTURE_ID "ARM" - -# elif defined(__ICCRX__) -# define ARCHITECTURE_ID "RX" - -# elif defined(__ICCRH850__) -# define ARCHITECTURE_ID "RH850" - -# elif defined(__ICCRL78__) -# define ARCHITECTURE_ID "RL78" - -# elif defined(__ICCRISCV__) -# define ARCHITECTURE_ID "RISCV" - -# elif defined(__ICCAVR__) -# define ARCHITECTURE_ID "AVR" - -# elif defined(__ICC430__) -# define ARCHITECTURE_ID "MSP430" - -# elif defined(__ICCV850__) -# define ARCHITECTURE_ID "V850" - -# elif defined(__ICC8051__) -# define ARCHITECTURE_ID "8051" - -# elif defined(__ICCSTM8__) -# define ARCHITECTURE_ID "STM8" - -# else /* unknown architecture */ -# define ARCHITECTURE_ID "" -# endif - -#elif defined(__ghs__) -# if defined(__PPC64__) -# define ARCHITECTURE_ID "PPC64" - -# elif defined(__ppc__) -# define ARCHITECTURE_ID "PPC" - -# elif defined(__ARM__) -# define ARCHITECTURE_ID "ARM" - -# elif defined(__x86_64__) -# define ARCHITECTURE_ID "x64" - -# elif defined(__i386__) -# define ARCHITECTURE_ID "X86" - -# else /* unknown architecture */ -# define ARCHITECTURE_ID "" -# endif - -#elif defined(__TI_COMPILER_VERSION__) -# if defined(__TI_ARM__) -# define ARCHITECTURE_ID "ARM" - -# elif defined(__MSP430__) -# define ARCHITECTURE_ID "MSP430" - -# elif defined(__TMS320C28XX__) -# define ARCHITECTURE_ID "TMS320C28x" - -# elif defined(__TMS320C6X__) || defined(_TMS320C6X) -# define ARCHITECTURE_ID "TMS320C6x" - -# else /* unknown architecture */ -# define ARCHITECTURE_ID "" -# endif - -#else -# define ARCHITECTURE_ID -#endif - -/* Convert integer to decimal digit literals. */ -#define DEC(n) \ - ('0' + (((n) / 10000000)%10)), \ - ('0' + (((n) / 1000000)%10)), \ - ('0' + (((n) / 100000)%10)), \ - ('0' + (((n) / 10000)%10)), \ - ('0' + (((n) / 1000)%10)), \ - ('0' + (((n) / 100)%10)), \ - ('0' + (((n) / 10)%10)), \ - ('0' + ((n) % 10)) - -/* Convert integer to hex digit literals. */ -#define HEX(n) \ - ('0' + ((n)>>28 & 0xF)), \ - ('0' + ((n)>>24 & 0xF)), \ - ('0' + ((n)>>20 & 0xF)), \ - ('0' + ((n)>>16 & 0xF)), \ - ('0' + ((n)>>12 & 0xF)), \ - ('0' + ((n)>>8 & 0xF)), \ - ('0' + ((n)>>4 & 0xF)), \ - ('0' + ((n) & 0xF)) - -/* Construct a string literal encoding the version number. */ -#ifdef COMPILER_VERSION -char const* info_version = "INFO" ":" "compiler_version[" COMPILER_VERSION "]"; - -/* Construct a string literal encoding the version number components. */ -#elif defined(COMPILER_VERSION_MAJOR) -char const info_version[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', - COMPILER_VERSION_MAJOR, -# ifdef COMPILER_VERSION_MINOR - '.', COMPILER_VERSION_MINOR, -# ifdef COMPILER_VERSION_PATCH - '.', COMPILER_VERSION_PATCH, -# ifdef COMPILER_VERSION_TWEAK - '.', COMPILER_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; -#endif - -/* Construct a string literal encoding the internal version number. */ -#ifdef COMPILER_VERSION_INTERNAL -char const info_version_internal[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_', - 'i','n','t','e','r','n','a','l','[', - COMPILER_VERSION_INTERNAL,']','\0'}; -#elif defined(COMPILER_VERSION_INTERNAL_STR) -char const* info_version_internal = "INFO" ":" "compiler_version_internal[" COMPILER_VERSION_INTERNAL_STR "]"; -#endif - -/* Construct a string literal encoding the version number components. */ -#ifdef SIMULATE_VERSION_MAJOR -char const info_simulate_version[] = { - 'I', 'N', 'F', 'O', ':', - 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', - SIMULATE_VERSION_MAJOR, -# ifdef SIMULATE_VERSION_MINOR - '.', SIMULATE_VERSION_MINOR, -# ifdef SIMULATE_VERSION_PATCH - '.', SIMULATE_VERSION_PATCH, -# ifdef SIMULATE_VERSION_TWEAK - '.', SIMULATE_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; -#endif - -/* Construct the string literal in pieces to prevent the source from - getting matched. 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- -/* Construct a string literal encoding the version number components. */ -#elif defined(COMPILER_VERSION_MAJOR) -char const info_version[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', - COMPILER_VERSION_MAJOR, -# ifdef COMPILER_VERSION_MINOR - '.', COMPILER_VERSION_MINOR, -# ifdef COMPILER_VERSION_PATCH - '.', COMPILER_VERSION_PATCH, -# ifdef COMPILER_VERSION_TWEAK - '.', COMPILER_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; -#endif - -/* Construct a string literal encoding the internal version number. */ -#ifdef COMPILER_VERSION_INTERNAL -char const info_version_internal[] = { - 'I', 'N', 'F', 'O', ':', - 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','_', - 'i','n','t','e','r','n','a','l','[', - COMPILER_VERSION_INTERNAL,']','\0'}; -#elif defined(COMPILER_VERSION_INTERNAL_STR) -char const* info_version_internal = "INFO" ":" "compiler_version_internal[" COMPILER_VERSION_INTERNAL_STR "]"; -#endif - -/* Construct a string literal encoding the version number components. */ -#ifdef SIMULATE_VERSION_MAJOR -char const info_simulate_version[] = { - 'I', 'N', 'F', 'O', ':', - 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', - SIMULATE_VERSION_MAJOR, -# ifdef SIMULATE_VERSION_MINOR - '.', SIMULATE_VERSION_MINOR, -# ifdef SIMULATE_VERSION_PATCH - '.', SIMULATE_VERSION_PATCH, -# ifdef SIMULATE_VERSION_TWEAK - '.', SIMULATE_VERSION_TWEAK, -# endif -# endif -# endif - ']','\0'}; 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implicit fwks: [] - - diff --git a/Plugins/build-org.mitk.gui.qt.diffusionimaging.fiberprocessing-Qt_5_12_12_GCC_64bit_temporary-Release/CMakeFiles/cmake.check_cache b/Plugins/build-org.mitk.gui.qt.diffusionimaging.fiberprocessing-Qt_5_12_12_GCC_64bit_temporary-Release/CMakeFiles/cmake.check_cache deleted file mode 100644 index 3dccd73..0000000 --- a/Plugins/build-org.mitk.gui.qt.diffusionimaging.fiberprocessing-Qt_5_12_12_GCC_64bit_temporary-Release/CMakeFiles/cmake.check_cache +++ /dev/null @@ -1 +0,0 @@ -# This file is generated by cmake for dependency checking of the CMakeCache.txt file diff --git a/Plugins/build-org.mitk.gui.qt.diffusionimaging.fiberprocessing-Qt_5_12_12_GCC_64bit_temporary-Release/qtcsettings.cmake b/Plugins/build-org.mitk.gui.qt.diffusionimaging.fiberprocessing-Qt_5_12_12_GCC_64bit_temporary-Release/qtcsettings.cmake deleted file mode 100644 index 1649748..0000000 --- a/Plugins/build-org.mitk.gui.qt.diffusionimaging.fiberprocessing-Qt_5_12_12_GCC_64bit_temporary-Release/qtcsettings.cmake +++ /dev/null @@ -1,2 +0,0 @@ -# This file is managed by Qt Creator, do not edit! - 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 9fa3b1c..5627da3 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 @@ -1,863 +1,1189 @@ /*=================================================================== 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_BundleBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isBundle= mitk::TNodePredicateDataType::New(); m_Controls->m_BundleBox->SetPredicate( isBundle ); + m_Controls->m_PrototypeBox->SetDataStorage(this->GetDataStorage()); + mitk::TNodePredicateDataType::Pointer isPrototype = mitk::TNodePredicateDataType::New(); + m_Controls->m_PrototypeBox->SetPredicate( isPrototype ); + 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_ResampleButton, SIGNAL( clicked() ), this, SLOT( ResampleTractogram( ) ) ); + + connect(m_Controls->m_RandomPrototypesButton, SIGNAL( clicked() ), this, SLOT( RandomPrototypes( ) ) ); + + connect(m_Controls->m_SFFPrototypesButton, SIGNAL( clicked() ), this, SLOT( SFFPrototypes( ) ) ); connect(m_Controls->m_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 nfibSelected = !m_newfibersBundleNode.empty(); // bool posSelected = !m_positivBundlesNode.empty(); - bool nfibSelected = m_newfibersSelectedBundles.IsNotNull(); + bool nfibSelected = m_newfibersBundleNode.IsNotNull(); // bool posSelected = !m_positivBundlesNode.IsNotNull(); -// bool negSelected = !m_negativeSelectedBundles.IsNotNull(); +// bool negSelected = !m_negativeBundleNode.IsNotNull(); bool posSelected = this->GetDataStorage()->Exists(m_positivBundlesNode); - bool negSelected = this->GetDataStorage()->Exists(m_negativeSelectedBundles); + bool negSelected = this->GetDataStorage()->Exists(m_negativeBundleNode); bool indexSelected = !m_index.empty(); bool uncertaintySelected = this->GetDataStorage()->Exists(m_UncertaintyLabelNode); bool distanceSelected = this->GetDataStorage()->Exists(m_DistanceLabelNode); bool predictionSelected = this->GetDataStorage()->Exists(m_PredictionNode); // toggle visibility of elements according to selected method // are fiber bundles selected? if ( 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::ResampleTractogram() +{ + mitk::DataNode::Pointer node = m_Controls->m_BundleBox->GetSelectedNode(); + auto tractogram = dynamic_cast(node->GetData()); + mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy(); + temp_fib->ResampleToNumPoints(40); + MITK_INFO << "Resampling Done"; + + mitk::DataNode::Pointer newnode = mitk::DataNode::New(); + newnode->SetData( temp_fib ); + newnode->SetName( node->GetName() + "_" + std::to_string(40) ); + this->GetDataStorage()->Add(newnode); + UpdateGui(); +} + +void QmitkInteractiveFiberDissectionView::RandomPrototypes() +{ + + + MITK_INFO << "Number of Fibers to use as Prototypes: "; + MITK_INFO << m_Controls->m_NumPrototypes->value(); + + mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_BundleBox->GetSelectedNode()->GetData()); + + MITK_INFO << fib->GetNumFibers(); + std::vector myvec; + for (unsigned int k=0; kGetNumFibers(); k++) + { + myvec.push_back(k); + } +// auto rng = std::default_random_engine {}; + std::random_shuffle(std::begin(myvec), std::end(myvec)); + + vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); + vtkSmartPointer vNewLines = vtkSmartPointer::New(); + vtkSmartPointer vNewPoints = vtkSmartPointer::New(); + + vtkSmartPointer weights = vtkSmartPointer::New(); + + /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ + unsigned int counter = 0; + + for (int i=0; im_NumPrototypes->value(); i++) + { + vtkCell* cell = fib->GetFiberPolyData()->GetCell(myvec.at(i)); + auto numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + vtkSmartPointer container = vtkSmartPointer::New(); + for (unsigned int j=0; jGetPoint(j, p); + + vtkIdType id = vNewPoints->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + } + weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); + vNewLines->InsertNextCell(container); + counter++; + + } + + + + vNewPolyData->SetLines(vNewLines); + vNewPolyData->SetPoints(vNewPoints); + + mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData); + PrototypesBundle->SetFiberWeights(weights); + + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(PrototypesBundle); + node->SetName("Random_Prototypes"); + +// MITK_INFO << "Number of Streamlines in first function"; +// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); + this->GetDataStorage()->Add(node); + + +} + +void QmitkInteractiveFiberDissectionView::SFFPrototypes() +{ + + + MITK_INFO << "Number of Fibers to use as Prototypes: "; + MITK_INFO << m_Controls->m_NumPrototypes->value(); + MITK_INFO << "Start Creating Prototypes based on SFF"; + + mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_BundleBox->GetSelectedNode()->GetData()); + + /* Get Subset of Tractogram*/ + int size_subset = std::max(1.0, ceil(2.0 * m_Controls->m_NumPrototypes->value() * std::log(m_Controls->m_NumPrototypes->value()))); + + MITK_INFO << fib->GetNumFibers(); + std::vector myvec; + for (unsigned int k=0; kGetNumFibers(); k++) + { + myvec.push_back(k); + } + + std::random_shuffle(std::begin(myvec), std::end(myvec)); + + vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); + vtkSmartPointer vNewLines = vtkSmartPointer::New(); + vtkSmartPointer vNewPoints = vtkSmartPointer::New(); + + vtkSmartPointer weights = vtkSmartPointer::New(); + + + unsigned int counter = 0; + + for (int i=0; iGetFiberPolyData()->GetCell(myvec.at(i)); + auto numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + vtkSmartPointer container = vtkSmartPointer::New(); + for (unsigned int j=0; jGetPoint(j, p); + + vtkIdType id = vNewPoints->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + } + weights->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); + vNewLines->InsertNextCell(container); + counter++; + + } + + + vNewPolyData->SetLines(vNewLines); + vNewPolyData->SetPoints(vNewPoints); + + mitk::FiberBundle::Pointer temp_fib = mitk::FiberBundle::New(vNewPolyData); + temp_fib->SetFiberWeights(weights); + + MITK_INFO << temp_fib->GetFiberPolyData()->GetNumberOfCells(); + /* Create std::vector of the SubsetBundle*/ + std::vector< vnl_matrix > out_fib(temp_fib->GetFiberPolyData()->GetNumberOfCells()); + + for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) + { + vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + vnl_matrix streamline; + streamline.set_size(3, cell->GetNumberOfPoints()); + streamline.fill(0.0); + + for (int j=0; jGetPoint(j, cand); + + vnl_vector_fixed< float, 3 > candV; + candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; + streamline.set_column(j, candV); + } + + // out_fib.push_back(streamline); + out_fib.at(i)=streamline; + } + + + /* Calculate the distancematrix of Subset*/ + std::vector< vnl_matrix > dist_vec(out_fib.size());// + cv::parallel_for_(cv::Range(0, out_fib.size()), [&](const cv::Range &range) + { + for (int i = range.start; i < range.end; i++) + + // for (unsigned int i=0; i distances; + distances.set_size(1, out_fib.size()); + distances.fill(0.0); + + + for (unsigned int j=0; j single_distances; + single_distances.set_size(1, out_fib.at(0).cols()); + single_distances.fill(0.0); + vnl_matrix single_distances_flip; + single_distances_flip.set_size(1, out_fib.at(0).cols()); + single_distances_flip.fill(0.0); + for (unsigned int ik=0; ik single_distances.mean()) + { + distances.put(0,j, single_distances.mean()); + } + else { + distances.put(0,j, single_distances_flip.mean()); + } + + + + } + // dist_vec.push_back(distances); + dist_vec.at(i) = distances; + } + }); + + + /*Index to find values in distancematrix*/ + std::vector myidx; + /*Index to find actual streamlines using indexUnc*/ + std::vector indexUncDist; + /*Start with the Streamline of the highest entropy, which is in distance_matrix at idx 0*/ + myidx.push_back(0); + + /*Vecotr that stores minvalues of current iteration*/ + vnl_matrix cur_vec; + cur_vec.set_size(1, size_subset); + cur_vec.fill(0.0); + for (int i=0; im_NumPrototypes->value(); i++) + { + + // unsigned int cur_i = indexUnc.at(myidx.at(i)); + + /*Save mean distance of all used Samples*/ + + vnl_matrix sum_matrix; + sum_matrix.set_size(myidx.size(), size_subset); + sum_matrix.fill(0); + for (unsigned int ii=0; ii vNewPolyData2 = vtkSmartPointer::New(); + vtkSmartPointer vNewLines2 = vtkSmartPointer::New(); + vtkSmartPointer vNewPoints2 = vtkSmartPointer::New(); + + vtkSmartPointer weights2 = vtkSmartPointer::New(); + + /* Check wether all Streamlines of the bundles are labeled... If all are labeled Skip for Loop*/ + counter = 0; + + for (int i=0; im_NumPrototypes->value(); i++) + { + + vtkCell* cell = fib->GetFiberPolyData()->GetCell(myidx.at(i)); + auto numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + vtkSmartPointer container = vtkSmartPointer::New(); + for (unsigned int j=0; jGetPoint(j, p); + + vtkIdType id = vNewPoints2->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + } + weights2->InsertValue(counter, fib->GetFiberWeight(myvec.at(i))); + vNewLines2->InsertNextCell(container); + counter++; + + } + + vNewPolyData2->SetLines(vNewLines2); + vNewPolyData2->SetPoints(vNewPoints2); + + mitk::FiberBundle::Pointer PrototypesBundle = mitk::FiberBundle::New(vNewPolyData2); + PrototypesBundle->SetFiberWeights(weights2); + MITK_INFO << PrototypesBundle->GetFiberPolyData()->GetNumberOfCells(); + + + + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(PrototypesBundle); + node->SetName("SFF_Prototypes"); + +//// MITK_INFO << "Number of Streamlines in first function"; +//// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); + this->GetDataStorage()->Add(node); + + } 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(); + auto m_PosStreamline= dynamic_cast(m_positivBundlesNode->GetData()); + MITK_INFO << m_PosStreamline->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)) + if (this->GetDataStorage()->Exists(m_newfibersBundleNode)) { MITK_INFO << "To Label Bundle Exists"; - mitk::FiberBundle::Pointer Stack = dynamic_cast(m_newfibersSelectedBundles->GetData()); - this->GetDataStorage()->Remove(m_newfibersSelectedBundles); + mitk::FiberBundle::Pointer Stack = dynamic_cast(m_newfibersBundleNode->GetData()); + this->GetDataStorage()->Remove(m_newfibersBundleNode); mitk::DataNode::Pointer node = mitk::DataNode::New(); m_newfibersFibersData = vtkSmartPointer::New(); m_newfibersFibersData->SetPoints(vtkSmartPointer::New()); m_newfibersBundle = mitk::FiberBundle:: New(m_newfibersFibersData); m_newfibersFibersData->SetLines(vtkSmartPointer::New()); // node->SetData( m_newfibersBundle ); -// m_newfibersSelectedBundles = node ; +// m_newfibersBundleNode = 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(); + vtkSmartPointer weights = vtkSmartPointer::New(); +// weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers()); + /* 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)); + 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); + m_newfibersBundle->SetFiberWeights(weights); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_newfibersBundle); node->SetName("ToLabel"); - m_newfibersSelectedBundles = node; + m_newfibersBundleNode = node; // MITK_INFO << "Number of Streamlines in first function"; -// MITK_INFO << m_newfibersSelectedBundles->GetData()->GetFiberPolyData()->GetNumberOfCells(); - this->GetDataStorage()->Add(m_newfibersSelectedBundles); +// MITK_INFO << m_newfibersBundleNode->GetData()->GetFiberPolyData()->GetNumberOfCells(); + this->GetDataStorage()->Add(m_newfibersBundleNode); m_RandomExtractionCounter++; } + m_Controls->m_ErazorButton->setChecked(true); + + 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);) -// } + + mitk::FiberBundle::Pointer m_negativeBundle = mitk::FiberBundle::New(); + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetName("-Bundle"); + node->SetData(m_negativeBundle); + m_negativeBundleNode = node; + this->GetDataStorage()->Add(m_negativeBundleNode); + m_StreamlineInteractor->EnableInteraction(true); - m_StreamlineInteractor->SetNegativeNode(m_negativeSelectedBundles); + m_StreamlineInteractor->SetNegativeNode(m_negativeBundleNode); m_StreamlineInteractor->SetPositiveNode(m_positivBundlesNode); - m_StreamlineInteractor->SetToLabelNode(m_newfibersSelectedBundles); + m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); } 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); + m_StreamlineInteractor->SetToLabelNode(m_newfibersBundleNode); } } 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); +// vtkSmartPointer< vtkFloatArray > weights = m_positiveBundle->GetFiberWeights(); +// MITK_INFO << weights->GetNumberOfValues(); +// MITK_INFO << m_positiveBundle->GetNumFibers(); +// for (unsigned int k=0; kGetNumFibers(); k++) +// { +// m_positiveBundle->SetFiberWeight(k, 1.0); + +// } +// vtkSmartPointer< vtkFloatArray > newweights = m_positiveBundle->GetFiberWeights(); +// MITK_INFO << newweights->GetNumberOfValues(); 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()); + m_negativeBundle = dynamic_cast(m_negativeBundleNode->GetData()); clusterer = std::make_shared(); - clusterer->SetTractogramPlus(m_positiveBundle); clusterer->SetActiveCycle(m_activeCycleCounter); + clusterer->SetTractogramPlus(m_positiveBundle); 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(); +// MITK_INFO << m_newfibersBundleNode->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_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 3eb0f7c..1712ea2 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 @@ -1,158 +1,161 @@ /*=================================================================== 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 ResampleTractogram(); + void RandomPrototypes(); + void SFFPrototypes(); 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_newfibersBundleNode; + mitk::DataNode::Pointer m_negativeBundleNode; 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 8fa0de4..9302577 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 @@ -1,776 +1,791 @@ QmitkInteractiveFiberDissectionViewControls 0 0 417 711 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 9 9 9 9 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 true true Label Fibers QFrame::NoFrame 0 6 + + + 0 + 0 + 399 + 455 + + Generate Prototypes Extract from - + - + Random Extraction - + 10 200 100 Number of Prototypes - + SFF Extraction Use Standard Prototypes Choose Prototypes Qt::Vertical 20 40 - + Resample Bundle 0 0 399 455 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 + 438 441 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 - + + + + 1 + + + 2000 + + + 10 + + + + + + + Random Streamlines + + + + Qt::Vertical 20 40 - - - - 1 + + + + + 30 + 30 + - - 2000 + + - - 10 + + + :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/eraze.png + + + + 32 + 32 + + + + true + + + + + + + Label Streamlines + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + Reject: Rightclick + shift + + + + + + + Unlabel: Leftclick + shift/alt 0 0 399 455 Active Learning 9 9 341 391 QFrame::StyledPanel QFrame::Raised 1 500 0 10 Qt::Horizontal 40 20 Uncertainty_Label .. Qt::Horizontal 40 20 Add Pred_Label Qt::Horizontal 84 22 Dist: to label Create Prediction Qt::Vertical 20 40 Create Uncertanty Map Add Train Classifier Unc: to label 1 500 10 Qt::Horizontal 40 20 Unc_dis_Label QmitkSingleNodeSelectionWidget QWidget
QmitkSingleNodeSelectionWidget.h
 QmitkPointListWidget QWidget
QmitkPointListWidget.h
 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h